Citrus Sinensis ID: 043064

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190------
Protein Sequence
MANAEVDALDFEDDDLMDEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccccEEEEcccccccccccEEEEEEccHHHHHHHHHHcccccccccEEEEEEEEccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccEEEEEEcccccccHHHHHHHHHHHccEEEEEccEccccccEccEEEEEEccHHHHHHHHHHHcccEccccEcEEEEcEEcccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
manaevdaldfedddlmdedgtadvdasssprapqpklksaitggapkktkgrgfreeadserhsrladrnfeslgtdggpgpqrsiEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVdwafsngpstgpfkrknmrpgrthrsrsprrry
Flexible Loop (DISEMBL)
manaevdaldfedddlmdEDGTAdvdasssprapqpklksaitggapkktkgrgfreeadserhsrladrnfeslgtdggpgpqrSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFsngpstgpfkrknmrpgrthrsrsprrry
Low Complexity Region (SEG)
MANaevdaldfedddlmdedgtadVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMrpgrthrsrsprrrY
Disordered region (IsUnstruct)
**************************************************************************************IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS****************************
Disordered Region (DISOPRED)
****EVDALDFEDDDLMD************************************************************************IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV*********************************
Disordered Region (DISEMBL)
MANAEVDALDFEDDDLMDED*******************SAITGG********************RLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKR******************
Disordered Region (DISPRO)
**********************************************************************************PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG**************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MANAEVDALDFEDDDLMDEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY
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	196	2.2.26 [Sep-21-2011]
B5DGI7	175	RNA-binding protein 8A OS	N/A	no	0.755	0.845	0.461	1e-34
Q5D018	174	RNA-binding protein 8A OS	yes	no	0.596	0.672	0.553	8e-34
Q28BZ1	174	RNA-binding protein 8A OS	yes	no	0.612	0.689	0.556	1e-33
Q6PH90	174	RNA-binding protein 8A-B	N/A	no	0.612	0.689	0.556	1e-33
Q9V535	165	RNA-binding protein 8A OS	yes	no	0.612	0.727	0.531	1e-33
Q9DF42	174	RNA-binding protein 8A-A	N/A	no	0.612	0.689	0.556	2e-33
Q27W01	174	RNA-binding protein 8A OS	yes	no	0.576	0.649	0.555	1e-32
Q9Y5S9	174	RNA-binding protein 8A OS	yes	no	0.576	0.649	0.555	1e-32
Q3ZCE8	174	RNA-binding protein 8A OS	yes	no	0.576	0.649	0.555	1e-32
Q9CWZ3	174	RNA-binding protein 8A OS	yes	no	0.576	0.649	0.547	4e-32

>sp|B5DGI7|RBM8A_SALSA RNA-binding protein 8A OS=Salmo salar GN=rbm8a PE=2 SV=1

 Score =  145 bits (367), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 79/171 (46%), Positives = 107/171 (62%), Gaps = 23/171 (13%)

Query: 6   VDALDFED----DDLMDEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADS 61
            D LD  +    D  MDEDG   +           KLK        K+ KGRGF  E  +
Sbjct: 2   ADVLDLHEAGGEDFAMDEDGDDSI----------HKLKEK-----AKRRKGRGFGSEEGA 46

Query: 62  ERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH 120
               R    +++++  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F E+GEI+NLH
Sbjct: 47  RSRVR---EDYDTVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEFGEIKNLH 103

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           LNLDRRTG++KGYAL+EYE ++EAQ A+  +NG +++ Q ++VDW F  GP
Sbjct: 104 LNLDRRTGYLKGYALVEYETYKEAQAAMEGLNGQDMMGQPISVDWGFVRGP 154

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.
Salmo salar (taxid: 8030)

>sp|Q5D018|RBM8A_DANRE RNA-binding protein 8A OS=Danio rerio GN=rbm8a PE=2 SV=1

 Score =  143 bits (360), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 67/121 (55%), Positives = 90/121 (74%), Gaps = 4/121 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF  E  +    R    +++++  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFGSEEGARSRVR---EDYDTVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDVHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG 170
            E+GEI+NLHLNLDRRTG++KGYAL+EYE ++EAQ A+  +NG EL+ Q ++VDW F  G
Sbjct: 94  AEFGEIKNLHLNLDRRTGYLKGYALVEYETYKEAQAAMEGLNGQELMGQPISVDWCFVRG 153

Query: 171 P 171
           P
Sbjct: 154 P 154

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Danio rerio (taxid: 7955)

>sp|Q28BZ1|RBM8A_XENTR RNA-binding protein 8A OS=Xenopus tropicalis GN=rbm8a PE=2 SV=1

 Score =  142 bits (359), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 69/124 (55%), Positives = 94/124 (75%), Gaps = 4/124 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF   AD    +R+ + +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFG--ADEGTRARIRE-DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG 170
           GE+GEI+N+HLNLDRRTGF+KGYAL+EYE ++EA  A+  +NG +L+ Q ++VDW F  G
Sbjct: 94  GEFGEIKNIHLNLDRRTGFLKGYALVEYETYKEALAAMEGLNGQDLMGQPISVDWGFVRG 153

Query: 171 PSTG 174
           P  G
Sbjct: 154 PPKG 157

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Xenopus tropicalis (taxid: 8364)

>sp|Q6PH90|RB8AB_XENLA RNA-binding protein 8A-B OS=Xenopus laevis GN=rbm8a-b PE=2 SV=1

 Score =  142 bits (358), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 69/124 (55%), Positives = 94/124 (75%), Gaps = 4/124 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF   AD    +R+ + +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFG--ADEGTRTRIRE-DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG 170
           GE+GEI+N+HLNLDRRTGF+KGYAL+EYE ++EA  A+  +NG +L+ Q ++VDW F  G
Sbjct: 94  GEFGEIKNIHLNLDRRTGFLKGYALVEYETYKEALAAMEGLNGQDLMGQPVSVDWGFVRG 153

Query: 171 PSTG 174
           P  G
Sbjct: 154 PPKG 157

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Xenopus laevis (taxid: 8355)

>sp|Q9V535|RBM8A_DROME RNA-binding protein 8A OS=Drosophila melanogaster GN=tsu PE=1 SV=1

 Score =  142 bits (358), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 68/128 (53%), Positives = 90/128 (70%), Gaps = 8/128 (6%)

Query: 48  KKTKGRGFREEADSERHSRLADRNFESLGTDGG----PGPQRSIEGWIILVTGVHEEAQE 103
           K  KGRGF     S+ ++R A  ++E +  +      PGPQRS+EGWI+ VT +HEEAQE
Sbjct: 31  KHRKGRGF----GSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQE 86

Query: 104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           D++Q  F +YGEI+N+HLNLDRRTGF KGYAL+EYE  ++A  A  A+NG E++ QT+ V
Sbjct: 87  DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146

Query: 164 DWAFSNGP 171
           DW F  GP
Sbjct: 147 DWCFVKGP 154

Involved in mRNA quality control via the nonsense-mediated mRNA decay (NMD) pathway. Also involved in localization of osk (oskar) mRNA in the posterior pole of oocytes via its interaction with mago.

Drosophila melanogaster (taxid: 7227)

>sp|Q9DF42|RB8AA_XENLA RNA-binding protein 8A-A OS=Xenopus laevis GN=rbm8a-a PE=2 SV=1

 Score =  141 bits (356), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 69/124 (55%), Positives = 93/124 (75%), Gaps = 4/124 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF   AD    +R+ +  ++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFG--ADEGTKTRIREV-YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG 170
           GE+GEI+N+HLNLDRRTGF+KGYAL+EYE ++EA  A+  +NG +L+ Q ++VDW F  G
Sbjct: 94  GEFGEIKNIHLNLDRRTGFLKGYALVEYETYKEALAAMEGLNGQDLMGQPVSVDWGFVRG 153

Query: 171 PSTG 174
           P  G
Sbjct: 154 PPKG 157

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs.

Xenopus laevis (taxid: 8355)

>sp|Q27W01|RBM8A_RAT RNA-binding protein 8A OS=Rattus norvegicus GN=Rbm8a PE=2 SV=1

 Score =  139 bits (350), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/117 (55%), Positives = 87/117 (74%), Gaps = 4/117 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF 167
            EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F
Sbjct: 94  AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 150

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Rattus norvegicus (taxid: 10116)

>sp|Q9Y5S9|RBM8A_HUMAN RNA-binding protein 8A OS=Homo sapiens GN=RBM8A PE=1 SV=1

 Score =  139 bits (350), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/117 (55%), Positives = 87/117 (74%), Gaps = 4/117 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF 167
            EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F
Sbjct: 94  AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 150

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Homo sapiens (taxid: 9606)

>sp|Q3ZCE8|RBM8A_BOVIN RNA-binding protein 8A OS=Bos taurus GN=RBM8A PE=2 SV=2

 Score =  139 bits (350), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/117 (55%), Positives = 87/117 (74%), Gaps = 4/117 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF 167
            EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F
Sbjct: 94  AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 150

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Bos taurus (taxid: 9913)

>sp|Q9CWZ3|RBM8A_MOUSE RNA-binding protein 8A OS=Mus musculus GN=Rbm8a PE=1 SV=3

 Score =  137 bits (346), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 64/117 (54%), Positives = 87/117 (74%), Gaps = 4/117 (3%)

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           GRGF  +  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F
Sbjct: 37  GRGFGSKEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKF 93

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF 167
            EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F
Sbjct: 94  AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 150

Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). The heterodimer MAGOH-RBM8A interacts with PYM that function to enhance the translation of EJC-bearing spliced mRNAs by recruiting them to the ribosomal 48S preinitiation complex. Remains associated with mRNAs in the cytoplasm until the mRNAs engage the translation machinery. Its removal from cytoplasmic mRNAs requires translation initiation from EJC-bearing spliced mRNAs. Associates preferentially with mRNAs produced by splicing. Does not interact with pre-mRNAs, introns, or mRNAs produced from intronless cDNAs. Associates with both nuclear mRNAs and newly exported cytoplasmic mRNAs. Complex with MAGOH is a component of the nonsense mediated decay (NMD) pathway.

Mus musculus (taxid: 10090)

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	196
118488653	205	unknown [Populus trichocarpa]	1.0	0.956	0.775	3e-87
255544924	199	polyadenylate-binding protein, putative	0.969	0.954	0.770	1e-82
224106205	211	predicted protein [Populus trichocarpa]	0.954	0.886	0.744	1e-78
225431497	202	PREDICTED: RNA-binding protein 8A [Vitis	0.984	0.955	0.741	5e-78
224059250	205	predicted protein [Populus trichocarpa]	1.0	0.956	0.751	3e-74
116789657	205	unknown [Picea sitchensis] gi|224284327|	0.979	0.936	0.698	8e-72
297852880	201	hypothetical protein ARALYDRAFT_892123 [	0.918	0.895	0.724	3e-70
30524687	203	salt tolerance protein 4 [Beta vulgaris]	0.984	0.950	0.684	2e-69
76573355	195	unknown [Solanum tuberosum]	0.954	0.958	0.696	2e-68
449442559	197	PREDICTED: RNA-binding protein 8A-like [	0.897	0.893	0.720	1e-67

>gi|118488653|gb|ABK96138.1| unknown [Populus trichocarpa]

 Score =  326 bits (836), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 159/205 (77%), Positives = 174/205 (84%), Gaps = 9/205 (4%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGG-------APKKTK 51
           MAN E +A+DFE  DDDLMDEDG  DVDASSSPRAP PKLKSAITGG       APKKTK
Sbjct: 1   MANTEAEAVDFEPEDDDLMDEDGAVDVDASSSPRAPLPKLKSAITGGSASPSLSAPKKTK 60

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           GRGFREE D+ER SR + R F+SLG+DGGPGPQRS+EGWIILV+GVHEEAQ+D LQ  FG
Sbjct: 61  GRGFREEVDTERQSRFSGRGFDSLGSDGGPGPQRSVEGWIILVSGVHEEAQDDHLQEAFG 120

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           E+GEI+NLHLNLDRRTGFVKGYALIEYENFE+A+NAI +MNGG LL Q + VDWAFSNGP
Sbjct: 121 EFGEIKNLHLNLDRRTGFVKGYALIEYENFEQAENAIASMNGGTLLEQVINVDWAFSNGP 180

Query: 172 STGPFKRKNMRPGRTHRSRSPRRRY 196
           S    KRKNMRPGRTHRSRSPRRRY
Sbjct: 181 SNWALKRKNMRPGRTHRSRSPRRRY 205

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544924|ref|XP_002513523.1| polyadenylate-binding protein, putative [Ricinus communis] gi|223547431|gb|EEF48926.1| polyadenylate-binding protein, putative [Ricinus communis]

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 158/205 (77%), Positives = 175/205 (85%), Gaps = 15/205 (7%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGGA------PKKTKG 52
           MANA+ +A+DFE  +DDLMDEDG  D DAS  PRAP PKLKSAITGGA      P+KTKG
Sbjct: 1   MANADAEAVDFEPEEDDLMDEDGGVDADAS--PRAPLPKLKSAITGGAASSLSAPRKTKG 58

Query: 53  RGFREEADSERHSRLADR-NFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           RGFREEAD++R +RLA R +F+SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQN FG
Sbjct: 59  RGFREEADADRQTRLASRGDFDSLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNAFG 118

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           ++GEI+NLHLNLDRRTGFVKGYALIEYE FEEAQNAI ++NG ELLTQ + VDWAF NGP
Sbjct: 119 DFGEIKNLHLNLDRRTGFVKGYALIEYEKFEEAQNAIASLNGTELLTQIINVDWAFCNGP 178

Query: 172 STGPFKRKNMRPGRTHRSRSPRRRY 196
           +    KRKNMR GRTHRSRSPRRRY
Sbjct: 179 T----KRKNMRSGRTHRSRSPRRRY 199

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224106205|ref|XP_002314085.1| predicted protein [Populus trichocarpa] gi|222850493|gb|EEE88040.1| predicted protein [Populus trichocarpa]

 Score =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 146/196 (74%), Positives = 161/196 (82%), Gaps = 9/196 (4%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGG-------APKKTK 51
           MAN E +A+DFE  DDDLMDEDG  DVDASSSPRAP PKLKSAITGG       APKKTK
Sbjct: 1   MANTEAEAVDFEPEDDDLMDEDGAVDVDASSSPRAPLPKLKSAITGGSASPSLSAPKKTK 60

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           GRGFREE D+ER SR + R F+SLG+DGGPGPQRS+EGWIILV+GVHEEAQ+D LQ  FG
Sbjct: 61  GRGFREEVDTERQSRFSGRGFDSLGSDGGPGPQRSVEGWIILVSGVHEEAQDDHLQEAFG 120

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           E+GEI+NLHLNLDRRTGFVKGYALIEYENFE+A+NAI +MNGG LL Q + VDWAFSNGP
Sbjct: 121 EFGEIKNLHLNLDRRTGFVKGYALIEYENFEQAENAIASMNGGTLLEQVINVDWAFSNGP 180

Query: 172 STGPFKRKNMRPGRTH 187
           S    KRKNMR    H
Sbjct: 181 SNWALKRKNMRFVSMH 196

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431497|ref|XP_002281228.1| PREDICTED: RNA-binding protein 8A [Vitis vinifera] gi|296088561|emb|CBI37552.3| unnamed protein product [Vitis vinifera]

 Score =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 152/205 (74%), Positives = 172/205 (83%), Gaps = 12/205 (5%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGGAP-------KKTK 51
           MA+A+V+A+DFE  DDDLMDEDG  DVD +SSPRAP PKLKSAITGGAP       KKTK
Sbjct: 1   MASADVEAVDFEPEDDDLMDEDGAVDVD-NSSPRAPLPKLKSAITGGAPSSLAAAPKKTK 59

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           GRGFR++ D++R+SR A R+F+SL +DGGPGPQRSIEGWIILVTGVHEEAQEDDLQN FG
Sbjct: 60  GRGFRDDTDADRNSRFAARDFDSLDSDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNAFG 119

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           E+GE++NLHLNLDRRTGFVKGYALIEYEN EEAQ AI+AMNG ELLTQT++VDWAFSNGP
Sbjct: 120 EFGEVKNLHLNLDRRTGFVKGYALIEYENLEEAQAAISAMNGTELLTQTISVDWAFSNGP 179

Query: 172 STGPFKRKNMRPGRTHRSRSPRRRY 196
                 R+    G  HRSRSPRRRY
Sbjct: 180 FKRRNMRRRSPRG--HRSRSPRRRY 202

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224059250|ref|XP_002299789.1| predicted protein [Populus trichocarpa] gi|118484267|gb|ABK94013.1| unknown [Populus trichocarpa] gi|222847047|gb|EEE84594.1| predicted protein [Populus trichocarpa]

 Score =  283 bits (723), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 154/205 (75%), Positives = 173/205 (84%), Gaps = 9/205 (4%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGGA-------PKKTK 51
           MAN E +A+DFE  +DDLMDEDG AD DASSSPRAP PKLKSAITGG+       PKKTK
Sbjct: 1   MANTEAEAVDFEPEEDDLMDEDGAADADASSSPRAPLPKLKSAITGGSASSSLSAPKKTK 60

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           GRGFREE D+ER SRL+ R F+SLG+DGGPGPQRS+EGWIILV+GVHEEAQ+D LQ  FG
Sbjct: 61  GRGFREEVDAERQSRLSGRGFDSLGSDGGPGPQRSVEGWIILVSGVHEEAQDDHLQEAFG 120

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           E+GEI+NLHLNLDRRTGFVKGYALIEYE FE+A+NAI +MNGG LL Q + VDWAFSNGP
Sbjct: 121 EFGEIKNLHLNLDRRTGFVKGYALIEYEKFEQAENAIASMNGGTLLEQIIYVDWAFSNGP 180

Query: 172 STGPFKRKNMRPGRTHRSRSPRRRY 196
           S    +RKNMRP RT+RSRSPRRRY
Sbjct: 181 SNWASRRKNMRPERTNRSRSPRRRY 205

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116789657|gb|ABK25331.1| unknown [Picea sitchensis] gi|224284327|gb|ACN39899.1| unknown [Picea sitchensis]

 Score =  275 bits (703), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 146/209 (69%), Positives = 163/209 (77%), Gaps = 17/209 (8%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGGA-------PKKTK 51
           MA AEVDA+DFE  +DDLMD+D   D   + +   P PKLKS ITGG        PKKTK
Sbjct: 1   MAGAEVDAVDFEPEEDDLMDDDTAMDDGNADAVPTPAPKLKSTITGGTSQLGDGGPKKTK 60

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           GRGFREE D+ER+SR A R FESL +DGGPGPQRSIEGWIILVTGVHEEAQEDDL  +FG
Sbjct: 61  GRGFREETDAERNSRFAAREFESLDSDGGPGPQRSIEGWIILVTGVHEEAQEDDLHELFG 120

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           E+GEI+NLHLNLDRRTGFVKGYALIEYE F+EAQ AIT +NG ELLTQT++VDWAFSN  
Sbjct: 121 EFGEIKNLHLNLDRRTGFVKGYALIEYETFKEAQAAITNLNGAELLTQTISVDWAFSN-- 178

Query: 172 STGPFKRKNMR---PGRTHRSRSP-RRRY 196
             GPF+RK +R   P   HRSRSP RRRY
Sbjct: 179 --GPFRRKTVRRRSPRGGHRSRSPVRRRY 205

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297852880|ref|XP_002894321.1| hypothetical protein ARALYDRAFT_892123 [Arabidopsis lyrata subsp. lyrata] gi|297340163|gb|EFH70580.1| hypothetical protein ARALYDRAFT_892123 [Arabidopsis lyrata subsp. lyrata]

 Score =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 134/185 (72%), Positives = 153/185 (82%), Gaps = 5/185 (2%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGG---APKKTKGRGF 55
           MAN E +A+DFE  +DDLMDEDGTA   A  SPRA  P+LKSAI G    + KKTKGRGF
Sbjct: 1   MANIESEAVDFEPEEDDLMDEDGTAIDGADVSPRAGHPRLKSAIAGANGESAKKTKGRGF 60

Query: 56  REEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGE 115
           REE DS+R  RL+ R+FESLG+DGG GPQRSIEGWIILV+GVHEEAQEDDL N FG++GE
Sbjct: 61  REEKDSDRQRRLSSRDFESLGSDGGRGPQRSIEGWIILVSGVHEEAQEDDLTNAFGDFGE 120

Query: 116 IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGP 175
           I+NLHLNLDRRTGFVKGYALIEYE +EEAQ AI+AMNG ELLTQ ++VDWAFS GPS   
Sbjct: 121 IKNLHLNLDRRTGFVKGYALIEYEKYEEAQKAISAMNGAELLTQNVSVDWAFSRGPSAES 180

Query: 176 FKRKN 180
           ++RKN
Sbjct: 181 YRRKN 185

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30524687|emb|CAC85245.1| salt tolerance protein 4 [Beta vulgaris]

 Score =  267 bits (683), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 141/206 (68%), Positives = 162/206 (78%), Gaps = 13/206 (6%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITG-GAP-------KKT 50
           MA A+V+A+DFE  +DDLMDEDG A  +A  SPRAP PK+KSAITG GAP       KKT
Sbjct: 1   MAAADVEAVDFEPEEDDLMDEDGGA-AEADGSPRAPHPKIKSAITGAGAPSSGGFGAKKT 59

Query: 51  KGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           KGRGFRE+AD+ER+SR+  R F+SL +DGGPGP RSIEGWIILVTGVHEEAQE+DL NVF
Sbjct: 60  KGRGFREDADAERNSRMTAREFDSLDSDGGPGPARSIEGWIILVTGVHEEAQEEDLLNVF 119

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG 170
           GE+G+++NLHLNLDRRTGFVKGYALIEYE FEEAQ AI  MNG ++L Q + VDWAF NG
Sbjct: 120 GEFGQLKNLHLNLDRRTGFVKGYALIEYEKFEEAQAAIKEMNGAKMLEQPINVDWAFCNG 179

Query: 171 PSTGPFKRKNMRPGRTHRSRSPRRRY 196
           P      R+    G  HRSRSPRRRY
Sbjct: 180 PYRRRGNRRRSPRG--HRSRSPRRRY 203

Source: Beta vulgaris

Species: Beta vulgaris

Genus: Beta

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|76573355|gb|ABA46782.1| unknown [Solanum tuberosum]

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 142/204 (69%), Positives = 166/204 (81%), Gaps = 17/204 (8%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGG---APKKTKGRGF 55
           MANAEV+A+DFE  +DDLMDED    VDASSSPRA  PKLKSAITGG   APKKTKGRGF
Sbjct: 1   MANAEVEAVDFEPEEDDLMDED----VDASSSPRATIPKLKSAITGGSSSAPKKTKGRGF 56

Query: 56  REEA-DSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYG 114
           REEA +++R++R++ R F+SL ++GGPGP+RSIEGWI+LVTGV+EE QEDDL N FGE+G
Sbjct: 57  REEAAEADRNARMSAR-FDSLDSEGGPGPERSIEGWIVLVTGVNEETQEDDLHNDFGEFG 115

Query: 115 EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG 174
           EI+NLHLNLDRRTGFVKGYA IEYE+FEEAQ AI+  +G E LTQT+ V WAFS     G
Sbjct: 116 EIKNLHLNLDRRTGFVKGYAFIEYESFEEAQRAISEKDGAEFLTQTIHVAWAFSR----G 171

Query: 175 PFKRKNM--RPGRTHRSRSPRRRY 196
           PFKR+N   R    HRSRSPRRR+
Sbjct: 172 PFKRRNARRRSPHGHRSRSPRRRF 195

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449442559|ref|XP_004139049.1| PREDICTED: RNA-binding protein 8A-like [Cucumis sativus]

 Score =  261 bits (666), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 139/193 (72%), Positives = 160/193 (82%), Gaps = 17/193 (8%)

Query: 1   MANAEVDALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGGA-------PKKTK 51
           MA+A+V+A+DFE  +DDLMDEDG A+ DAS  PRAP PKLKSAITGGA       PKKTK
Sbjct: 1   MASADVEAVDFEPEEDDLMDEDGAAEADAS--PRAPFPKLKSAITGGASSSLSGGPKKTK 58

Query: 52  GRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG 111
           GRGFREE+D  R++RLA  +F+SL +  GPGPQRSIEGWIILVTGVHEEAQEDDLQN FG
Sbjct: 59  GRGFREESD--RNTRLAGSDFDSLKSADGPGPQRSIEGWIILVTGVHEEAQEDDLQNAFG 116

Query: 112 EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           E+GEI+NLHLNLDRRTGFVKGYALIEYE+FEEA+ AI+AM+G ELLTQ + VDWAFS+  
Sbjct: 117 EFGEIKNLHLNLDRRTGFVKGYALIEYESFEEAEKAISAMDGAELLTQIINVDWAFSH-- 174

Query: 172 STGPFKRKNMRPG 184
             GP +RKN RP 
Sbjct: 175 --GPIRRKNARPA 185

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	196
TAIR|locus:2033888	202	Y14 [Arabidopsis thaliana (tax	0.785	0.762	0.696	1.4e-55
UNIPROTKB|Q3ZCE8	174	RBM8A "RNA-binding protein 8A"	0.647	0.729	0.548	7.2e-36
UNIPROTKB|E2QV85	177	RBM8A "Uncharacterized protein	0.647	0.717	0.548	7.2e-36
UNIPROTKB|F6XAE9	174	RBM8A "Uncharacterized protein	0.647	0.729	0.548	7.2e-36
UNIPROTKB|Q9Y5S9	174	RBM8A "RNA-binding protein 8A"	0.647	0.729	0.548	7.2e-36
UNIPROTKB|I3LI59	177	RBM8A "Uncharacterized protein	0.647	0.717	0.548	7.2e-36
RGD|1310099	174	Rbm8a "RNA binding motif prote	0.647	0.729	0.548	7.2e-36
ZFIN|ZDB-GENE-050306-51	174	rbm8a "RNA binding motif prote	0.617	0.695	0.568	3.1e-35
FB|FBgn0033378	165	tsu "tsunagi" [Drosophila mela	0.622	0.739	0.539	2.3e-32
WB|WBGene00004387	142	rnp-4 [Caenorhabditis elegans	0.622	0.859	0.511	7.9e-30

TAIR|locus:2033888 Y14 [Arabidopsis thaliana (taxid:3702)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 110/158 (69%), Positives = 133/158 (84%)

Query:    27 ASSSPRAPQPKLKSAITGG---APKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP 83
             A  SPRA  P+LKSAI G    + KKTKGRGFREE DS+R  RL+ R+FESLG+DG PGP
Sbjct:    29 ADVSPRAGHPRLKSAIAGANGESAKKTKGRGFREEKDSDRQRRLSSRDFESLGSDGRPGP 88

Query:    84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEE 143
             QRS+EGWIILV+GVHEE QE+D+ N FG++GEI+NL+LNLDRR+G+VKGYALIEYE  EE
Sbjct:    89 QRSVEGWIILVSGVHEETQEEDITNAFGDFGEIKNLNLNLDRRSGYVKGYALIEYEKKEE 148

Query:   144 AQNAITAMNGGELLTQTLTVDWAFSNGPSTGP-FKRKN 180
             AQ+AI+AMNG ELLTQ ++VDWAFS+GPS G  ++RKN
Sbjct:   149 AQSAISAMNGAELLTQNVSVDWAFSSGPSGGESYRRKN 186

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0016604 "nuclear body" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

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

GO:0010628 "positive regulation of gene expression" evidence=IEP

UNIPROTKB|Q3ZCE8 RBM8A "RNA-binding protein 8A" [Bos taurus (taxid:9913)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 73/133 (54%), Positives = 96/133 (72%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    33 KKRKGRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDI 89

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW 
Sbjct:    90 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 149

Query:   167 FSNGPSTGPFKRK 179
             F  GP  G  KR+
Sbjct:   150 FVRGPPKG--KRR 160

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

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

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

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2QV85 RBM8A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 73/133 (54%), Positives = 96/133 (72%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    36 KKRKGRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDI 92

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW 
Sbjct:    93 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 152

Query:   167 FSNGPSTGPFKRK 179
             F  GP  G  KR+
Sbjct:   153 FVRGPPKG--KRR 163

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

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

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

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F6XAE9 RBM8A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 73/133 (54%), Positives = 96/133 (72%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    33 KKRKGRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDI 89

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW 
Sbjct:    90 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 149

Query:   167 FSNGPSTGPFKRK 179
             F  GP  G  KR+
Sbjct:   150 FVRGPPKG--KRR 160

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9Y5S9 RBM8A "RNA-binding protein 8A" [Homo sapiens (taxid:9606)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 73/133 (54%), Positives = 96/133 (72%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    33 KKRKGRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDI 89

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW 
Sbjct:    90 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 149

Query:   167 FSNGPSTGPFKRK 179
             F  GP  G  KR+
Sbjct:   150 FVRGPPKG--KRR 160

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0005737 "cytoplasm" evidence=NAS

GO:0003729 "mRNA binding" evidence=NAS

GO:0003723 "RNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

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

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

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

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

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

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

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|I3LI59 RBM8A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 73/133 (54%), Positives = 96/133 (72%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    36 KKRKGRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDI 92

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW 
Sbjct:    93 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 152

Query:   167 FSNGPSTGPFKRK 179
             F  GP  G  KR+
Sbjct:   153 FVRGPPKG--KRR 163

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

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

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

GO:0006396 "RNA processing" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|1310099 Rbm8a "RNA binding motif protein 8A" [Rattus norvegicus (taxid:10116)]

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 73/133 (54%), Positives = 96/133 (72%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  S    R    +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    33 KKRKGRGFGSEEGSRARMR---EDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDI 89

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW 
Sbjct:    90 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 149

Query:   167 FSNGPSTGPFKRK 179
             F  GP  G  KR+
Sbjct:   150 FVRGPPKG--KRR 160

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

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

GO:0051028 "mRNA transport" evidence=IEA

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

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-050306-51 rbm8a "RNA binding motif protein 8A" [Danio rerio (taxid:7955)]

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 71/125 (56%), Positives = 96/125 (76%)

Query:    48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDL 106
             KK KGRGF  E  +   SR+ + +++++  DG  PGPQRS+EGWI+ VTGVHEEA E+D+
Sbjct:    33 KKRKGRGFGSEEGAR--SRVRE-DYDTVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDV 89

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F E+GEI+NLHLNLDRRTG++KGYAL+EYE ++EAQ A+  +NG EL+ Q ++VDW 
Sbjct:    90 HDKFAEFGEIKNLHLNLDRRTGYLKGYALVEYETYKEAQAAMEGLNGQELMGQPISVDWC 149

Query:   167 FSNGP 171
             F  GP
Sbjct:   150 FVRGP 154

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0006417 "regulation of translation" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

FB|FBgn0033378 tsu "tsunagi" [Drosophila melanogaster (taxid:7227)]

 Score = 354 (129.7 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 68/126 (53%), Positives = 89/126 (70%)

Query:    48 KKTKGRGFREEADSER--HSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDD 105
             K  KGRGF  ++++    HS    RN +    +  PGPQRS+EGWI+ VT +HEEAQED+
Sbjct:    31 KHRKGRGFGSDSNTREAIHSYERVRNEDDDELE--PGPQRSVEGWILFVTSIHEEAQEDE 88

Query:   106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW 165
             +Q  F +YGEI+N+HLNLDRRTGF KGYAL+EYE  ++A  A  A+NG E++ QT+ VDW
Sbjct:    89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148

Query:   166 AFSNGP 171
              F  GP
Sbjct:   149 CFVKGP 154

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

GO:0007310 "oocyte dorsal/ventral axis specification" evidence=IMP

GO:0007314 "oocyte anterior/posterior axis specification" evidence=IMP

GO:0005737 "cytoplasm" evidence=IDA

GO:0000226 "microtubule cytoskeleton organization" evidence=IMP

GO:0007312 "oocyte nucleus migration involved in oocyte dorsal/ventral axis specification" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0007317 "regulation of pole plasm oskar mRNA localization" evidence=IMP;IPI

GO:0006406 "mRNA export from nucleus" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0045451 "pole plasm oskar mRNA localization" evidence=TAS

GO:0046595 "establishment of pole plasm mRNA localization" evidence=TAS

GO:0006396 "RNA processing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007294 "germarium-derived oocyte fate determination" evidence=IMP

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

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

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

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=IMP

WB|WBGene00004387 rnp-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 330 (121.2 bits), Expect = 7.9e-30, P = 7.9e-30
 Identities = 65/127 (51%), Positives = 86/127 (67%)

Query:    48 KKTKGRGFREEADSERHSR-LADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDL 106
             ++++GRG  +  + ER +  + D   ES  T G P  QRS+EGWI+ VT +HEEA EDD+
Sbjct:    16 ERSRGRGLAQSRNRERITYDVVDE--ESSATSGAP--QRSVEGWIVFVTNIHEEATEDDV 71

Query:   107 QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
              + F EYG+I+N+HLNLDRRTGF+KGYAL+EYE  +EA  AI   N  +LL Q + VDW 
Sbjct:    72 HDKFSEYGKIKNIHLNLDRRTGFLKGYALVEYETQKEANEAIDQSNDTDLLGQNVKVDWC 131

Query:   167 FSNGPST 173
             F  G  T
Sbjct:   132 FVKGKKT 138

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0006898 "receptor-mediated endocytosis" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0006915 "apoptotic process" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9V535	RBM8A_DROME	No assigned EC number	0.5312	0.6122	0.7272	yes	no
Q28BZ1	RBM8A_XENTR	No assigned EC number	0.5564	0.6122	0.6896	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	196
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-60
smart00360	73	smart00360, RRM, RNA recognition motif	1e-18
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	6e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-15
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-14
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-14
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-13
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	7e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	9e-13
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-12
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	7e-12
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-12
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-11
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-11
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-10
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	9e-10
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-09
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-09
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-09
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	5e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	7e-09
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-08
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-08
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	6e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	7e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	1e-07
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-07
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-07
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	4e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-07
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	5e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	6e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	8e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	8e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	8e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-06
cd12331	79	cd12331, RRM_NRD1_SEB1_like, RNA recognition motif	2e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-06
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	3e-06
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	4e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	4e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	5e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-06
cd12274	71	cd12274, RRM2_NEFsp, RNA recognition motif 2 in ve	6e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	6e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	8e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	1e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-05
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	2e-05
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-05
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-05
TIGR01649	481	TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus spl	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	4e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-05
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	5e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	7e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	9e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	9e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	1e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	1e-04
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	1e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-04
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-04
cd12424	71	cd12424, RRM3_hnRNPL_like, RNA recognition motif 1	2e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-04
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-04
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	2e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-04
cd12435	71	cd12435, RRM_GW182_like, RNA recognition motif in	3e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	3e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	3e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	3e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	4e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	4e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	5e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-04
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	5e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	6e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	7e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	7e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	7e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	7e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	7e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	7e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	9e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	9e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.001
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.001
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.001
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.001
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.001
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	0.001
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.001
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.001
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	0.001
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	0.002
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.002
cd12689	80	cd12689, RRM1_hnRNPL_like, RNA recognition motif 1	0.002
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.002
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.002
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.002
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.002
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.003
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.003
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.003
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.003
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.003
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.003
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.004
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.004
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	0.004
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.004
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.004

>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score =  182 bits (463), Expect = 4e-60
 Identities = 65/88 (73%), Positives = 75/88 (85%)

Query: 84  QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEE 143
           QRS+EGWII VTGVHEEAQE+D+ + F E+GEI+NLHLNLDRRTGFVKGYALIEYE  +E
Sbjct: 1   QRSVEGWIIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKE 60

Query: 144 AQNAITAMNGGELLTQTLTVDWAFSNGP 171
           AQ AI  +NG ELL QT++VDWAF  GP
Sbjct: 61  AQAAIEGLNGKELLGQTISVDWAFVKGP 88

This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). . Length = 88

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

 Score = 75.7 bits (187), Expect = 1e-18
 Identities = 24/72 (33%), Positives = 47/72 (65%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  E++L+ +F ++G++ ++ L  D+ TG  KG+A +E+E+ E+A+ A+ A+
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 152 NGGELLTQTLTV 163
           NG EL  + L V
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

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

 Score = 68.7 bits (169), Expect = 6e-16
 Identities = 23/61 (37%), Positives = 41/61 (67%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           +D L+ +F  YG ++++ L +DR     +GYA +E+E+ E+A+ AI  M+GG++  Q +T
Sbjct: 12  KDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVT 71

Query: 163 V 163
           V
Sbjct: 72  V 72

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

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

 Score = 68.1 bits (167), Expect = 1e-15
 Identities = 25/73 (34%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  E+DL+ +F ++GEI ++ +  D+  G  KG+A +E+E+ E+A+ A+ A+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 152 NGGELLTQTLTVD 164
           NG EL  + L V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 65.6 bits (161), Expect = 1e-14
 Identities = 28/76 (36%), Positives = 45/76 (59%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
            I VT + E+A EDDL+ +F  +G I  ++L  D+ TG  +G+A + +   E+A+ AI  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 151 MNGGELLTQTLTVDWA 166
           +NG       L+V+WA
Sbjct: 61  LNGFGYDNLILSVEWA 76

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

 Score = 70.0 bits (170), Expect = 2e-14
 Identities = 37/151 (24%), Positives = 60/151 (39%), Gaps = 3/151 (1%)

Query: 48  KKTKGRGFREEADSER--HSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDD 105
           K+   R   E+ D ER       +  F S         +   E   + V  +  +  E+D
Sbjct: 73  KEENEREMEEQNDGERGYTKEFEEELFRS-SESPKSRQKSKEENNTLFVGNLPYDVTEED 131

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW 165
           L+ +F ++G ++ + L  DR TG  +G+A +E+E+ E A+ AI  +NG EL  + L V  
Sbjct: 132 LRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQK 191

Query: 166 AFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
           A                      SR      
Sbjct: 192 AQPASQPRSELSNNLDASFAKKLSRGKALLL 222

Length = 306

>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 = 64.2 bits (157), Expect = 4e-14
 Identities = 27/67 (40%), Positives = 38/67 (56%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
           +A E+ L  +F E G + +  L  DR TG  KGY   E+E+ E A +AI  +NG E   +
Sbjct: 9   DATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGR 68

Query: 160 TLTVDWA 166
            L VD+A
Sbjct: 69  ALRVDFA 75

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

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

 Score = 63.4 bits (155), Expect = 7e-14
 Identities = 33/72 (45%), Positives = 45/72 (62%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  VH +  EDD+++VF  +G+I++  L  D  TG  KGY  IEYEN + AQ+AI +M
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 152 NGGELLTQTLTV 163
           N  +L  Q L 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 60.7 bits (148), Expect = 6e-13
 Identities = 24/71 (33%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  E+DL+++F ++G I ++ +  D  TG  KG+A +E+E+ E+A+ A+ A+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 152 NGGELLTQTLT 162
           NG EL  + L 
Sbjct: 60  NGKELGGRELR 70

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

>gnl|CDD|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 = 60.7 bits (148), Expect = 7e-13
 Identities = 23/72 (31%), Positives = 37/72 (51%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I + G+     ED ++ +   +G+++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 152 NGGELLTQTLTV 163
           NG +L  + LTV
Sbjct: 63  NGMQLGDKKLTV 74

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|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 60.4 bits (147), Expect = 9e-13
 Identities = 21/64 (32%), Positives = 37/64 (57%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           +++L+++F   G I +  +  DR TG   GY  ++Y +  +AQ AI  +NG E+  + L 
Sbjct: 14  QEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLK 73

Query: 163 VDWA 166
           V +A
Sbjct: 74  VSYA 77

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

 Score = 60.0 bits (146), Expect = 1e-12
 Identities = 25/63 (39%), Positives = 37/63 (58%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +H    EDDL+ +F  +GEI  + L  D  TG  KGY  I++ + E+A+ A+  +NG
Sbjct: 3   VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNG 62

Query: 154 GEL 156
            EL
Sbjct: 63  FEL 65

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|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 = 58.4 bits (142), Expect = 7e-12
 Identities = 22/75 (29%), Positives = 42/75 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+     E +L+ +F ++G +  + L  D  TG  +G+  + +E+ E+A  AI  +
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 152 NGGELLTQTLTVDWA 166
           NG EL  + + V+ A
Sbjct: 64  NGKELEGRVIKVEKA 78

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

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

 Score = 58.5 bits (142), Expect = 7e-12
 Identities = 20/75 (26%), Positives = 46/75 (61%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V +  + DDL+ +FG+YG I ++++ LD  T   +G+A +++E+  +A++A+  +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 152 NGGELLTQTLTVDWA 166
           +    L + + + +A
Sbjct: 63  DRTRFLGREIEIQFA 77

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

 Score = 58.1 bits (141), Expect = 9e-12
 Identities = 26/75 (34%), Positives = 39/75 (52%)

Query: 89  GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           GW I V  +  +A E  L  +F  +G + N+ +  D  T   KGY  +   N+EEA +AI
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 149 TAMNGGELLTQTLTV 163
            ++NG  L  + L V
Sbjct: 61  ASLNGYRLGGRVLQV 75

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

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

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 26/66 (39%), Positives = 42/66 (63%)

Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
             E+DL+++FG++GE+ +  +  DR TG  +G+  +E E  EEA  AI  +NG +   +T
Sbjct: 11  VTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRT 70

Query: 161 LTVDWA 166
           LTV+ A
Sbjct: 71  LTVNEA 76

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

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

 Score = 58.0 bits (141), Expect = 1e-11
 Identities = 25/62 (40%), Positives = 34/62 (54%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           E+ L+ VF  YG+IR L L  D  TGF KGYA +EYE+  +A  A    +   +    + 
Sbjct: 17  EETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEIF 76

Query: 163 VD 164
           VD
Sbjct: 77  VD 78

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

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

 Score = 57.6 bits (140), Expect = 1e-11
 Identities = 26/72 (36%), Positives = 41/72 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+ EE  E  L   F  +G+I+++ + LD  T   +G+A +E+E  E+A  AI  M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 152 NGGELLTQTLTV 163
           N  EL  +T+ V
Sbjct: 61  NESELFGRTIRV 72

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 28/73 (38%), Positives = 45/73 (61%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I + G+  E  E D+  VF +YGEI +++L  D++TG  KG+A + YE+      A+  +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 152 NGGELLTQTLTVD 164
           NG +LL +T+ VD
Sbjct: 72  NGIKLLGRTIRVD 84

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

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

 Score = 54.7 bits (132), Expect = 2e-10
 Identities = 25/65 (38%), Positives = 40/65 (61%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
           +A ED +   FGEYGEI ++ L  D  +G  KG+  +E+ + E AQ A+ A+ G +LL +
Sbjct: 9   DADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGR 68

Query: 160 TLTVD 164
            + +D
Sbjct: 69  PVRLD 73

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

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

 Score = 54.6 bits (132), Expect = 2e-10
 Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 3/67 (4%)

Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
             E DL+ +F  +G +    + + R   G  KG+A +++ +  +A+ AI  +NG ++  +
Sbjct: 11  CTEADLKKLFSPFGFV--WEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68

Query: 160 TLTVDWA 166
            + VDWA
Sbjct: 69  PVAVDWA 75

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 53.7 bits (130), Expect = 3e-10
 Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +     E+DL+  F  YG++  + L  ++     +G+A +E+ + E+A+ A+  +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRP--RGFAFVEFASPEDAEAALKKL 58

Query: 152 NG 153
           NG
Sbjct: 59  NG 60

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

>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 = 54.0 bits (130), Expect = 4e-10
 Identities = 26/80 (32%), Positives = 49/80 (61%), Gaps = 3/80 (3%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+     +++L+ +F ++G ++++ L +  R+G  KG A +EYEN   A  A+  M
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRL-VTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 152 NGGELLTQTLTVDWAFSNGP 171
           +G E+  +T++V  A SN P
Sbjct: 64  DGTEIKEKTISV--AISNPP 81

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|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 = 53.6 bits (129), Expect = 4e-10
 Identities = 29/75 (38%), Positives = 43/75 (57%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  EA E+ L+++F E G + +  L  DR TG  KGY   EY++ E A +A+  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 152 NGGELLTQTLTVDWA 166
           NG EL  + L VD A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 52.9 bits (128), Expect = 4e-10
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW 165
           L  +F  +G +  + L   +      G+A +E+   E A+ A+  +NG     + L VD+
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 166 A 166
           +
Sbjct: 56  S 56

(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|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 = 53.4 bits (129), Expect = 5e-10
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +     E++LQ  F  +G I  + +  D      KGYA + ++  E A  AI A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 152 NGGELLTQTLTVDW 165
           NG  +  QT+   W
Sbjct: 57  NGTSINGQTVKCSW 70

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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 53.6 bits (129), Expect = 5e-10
 Identities = 22/64 (34%), Positives = 38/64 (59%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           +D+++++F   GEI +  L  D+ TG   GY  + Y + E+A+ AI  +NG  L  +T+ 
Sbjct: 15  QDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIK 74

Query: 163 VDWA 166
           V +A
Sbjct: 75  VSYA 78

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 52.8 bits (127), Expect = 8e-10
 Identities = 17/53 (32%), Positives = 36/53 (67%)

Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
            +EDDL+ +F ++GE+  +H+ +D+++G  KG+A + + + E+A  A   ++G
Sbjct: 14  CKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDG 66

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

 Score = 52.8 bits (127), Expect = 9e-10
 Identities = 24/74 (32%), Positives = 39/74 (52%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  E   + L+  F  +GEI +  +  D +TG  KGY  + +   E+A+NAI +M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 152 NGGELLTQTLTVDW 165
           NG  L  + +  +W
Sbjct: 62  NGQWLGGRAIRTNW 75

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

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

 Score = 52.2 bits (125), Expect = 2e-09
 Identities = 24/60 (40%), Positives = 37/60 (61%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           VT +  +  ED+L+ +F  YG I   +L  D+ TG  +G A + Y+  EEAQ AI+++NG
Sbjct: 5   VTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNG 64

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 27/80 (33%), Positives = 41/80 (51%)

Query: 89  GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           GW I V  +  EA E  L  +FG +G + N+ +  D  T   KG+  +   N++EA  AI
Sbjct: 1   GWCIFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

Query: 149 TAMNGGELLTQTLTVDWAFS 168
            ++NG  L  + L V +  S
Sbjct: 61  ASLNGYRLGDRVLQVSFKTS 80

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC 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 AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. 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 = 85

>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 = 51.4 bits (124), Expect = 3e-09
 Identities = 22/54 (40%), Positives = 35/54 (64%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
            A E+D++ +F EYG I  + +  D+ TG  KG A +++ + EEAQ AI A++G
Sbjct: 10  TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63

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

 Score = 51.6 bits (124), Expect = 3e-09
 Identities = 22/61 (36%), Positives = 35/61 (57%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  + + A  + L+ VF +YG +  + L   + TG +KG+A IE+E  EEAQ A   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 152 N 152
           N
Sbjct: 62  N 62

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

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 21/65 (32%), Positives = 39/65 (60%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
            E DL+ VF  YG I  + +  D++TG  +G+  + +E+ E+A+ A   +NG E+  + +
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71

Query: 162 TVDWA 166
            VD++
Sbjct: 72  RVDYS 76

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

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 51.2 bits (122), Expect = 4e-09
 Identities = 25/77 (32%), Positives = 41/77 (53%)

Query: 89  GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           GW I +  + ++A E  L  +FG +G + N+ +  D  T   KG+  +   N+EEA  AI
Sbjct: 1   GWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

Query: 149 TAMNGGELLTQTLTVDW 165
            ++NG  L  + L V +
Sbjct: 61  ASLNGYRLGDKILQVSF 77

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), 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. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR 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 AU-rich RNA element (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 = 84

>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 = 50.8 bits (122), Expect = 4e-09
 Identities = 19/62 (30%), Positives = 34/62 (54%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +     E++L+ +F  +GEI  +HL LD+ T   KG+A + +   E A  A + +
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 152 NG 153
           +G
Sbjct: 62  DG 63

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

 Score = 55.1 bits (132), Expect = 4e-09
 Identities = 26/70 (37%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  VH +  E D+++VF  +GEI    L         KGY  IEY N +    AI +M
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 152 N----GGELL 157
           N    GG+ L
Sbjct: 267 NLFDLGGQYL 276

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 54.5 bits (131), Expect = 5e-09
 Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 7/103 (6%)

Query: 61  SERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH 120
           S+     A +       D  P   +      + V  +H    E +L+ +F  +G+I ++ 
Sbjct: 165 SQAEKNRAAKAATHQPGDI-PNFLK------LYVGNLHFNITEQELRQIFEPFGDIEDVQ 217

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           L+ D  TG  KG+  I++ + EEA+ A+  MNG EL  + + V
Sbjct: 218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 51.0 bits (123), Expect = 5e-09
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 9/71 (12%)

Query: 91  IILVTG--VHEEAQEDDLQNV----FGE--YGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           +++V G  V  E + + L+ V    F +   G+I  +++ +D  TG  KGYA +E+   E
Sbjct: 3   VVVVDGLPVVGEEKLEKLKKVLRKIFSKFGVGKIVGIYMPVDE-TGKTKGYAFVEFATPE 61

Query: 143 EAQNAITAMNG 153
           EA+ A+ A+NG
Sbjct: 62  EAKEAVKALNG 72

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), 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-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 50.4 bits (121), Expect = 7e-09
 Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 100 EAQEDDLQNVFGEYGEI-RNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
           E  E  L + F  +G I +   +  D  TG  KG+A I Y++FE +  AI AMNG  L  
Sbjct: 12  EVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCN 71

Query: 159 QTLTVDWAFSN 169
           + +TV +AF  
Sbjct: 72  RPITVSYAFKK 82

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

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 50.1 bits (119), Expect = 1e-08
 Identities = 25/80 (31%), Positives = 41/80 (51%)

Query: 89  GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           GW I V  +  +A E  L  +FG +G + N+ +  D  T   KG+  +   N++EA  AI
Sbjct: 3   GWCIFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 149 TAMNGGELLTQTLTVDWAFS 168
            ++NG  L  + L V +  +
Sbjct: 63  ASLNGYRLGDRVLQVSFKTN 82

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB 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 AU-rich RNA element (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 = 86

>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 = 49.6 bits (119), Expect = 1e-08
 Identities = 21/59 (35%), Positives = 34/59 (57%)

Query: 105 DLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           DL  +F  +G + +  + +D+ TG  K +  + Y+N E AQ AI AMNG ++  + L V
Sbjct: 14  DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKV 72

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

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKG----YALIEYENFEEAQNAITAMNGGELLT 158
           E  L  +F +YG+I+     L  ++G +KG    Y  + +E  EEA+ A+ ++NG   L 
Sbjct: 13  EFHLLKLFSKYGKIKKFDF-LFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALG 71

Query: 159 QTLTVDWA 166
           + L V WA
Sbjct: 72  KKLVVRWA 79

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 52.6 bits (126), Expect = 2e-08
 Identities = 25/85 (29%), Positives = 40/85 (47%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY 138
           G         G+ I V  +  +  E  L  +FG +G ++N+ +  D  T   KGY  +  
Sbjct: 259 GAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSM 318

Query: 139 ENFEEAQNAITAMNGGELLTQTLTV 163
            N++EA  AI ++NG  L  + L V
Sbjct: 319 TNYDEAAMAILSLNGYTLGNRVLQV 343

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 4/62 (6%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
              D++ +F   G +R + +           +A I +EN E AQ AI  +NG  +    +
Sbjct: 12  CLSDVKRLFETCGPVRKVTMLSRTVQP----HAFITFENLEAAQLAIETLNGASVDGNCI 67

Query: 162 TV 163
            V
Sbjct: 68  KV 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|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 24/77 (31%), Positives = 40/77 (51%)

Query: 89  GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           GW I V  +  ++ E  L  +FG +G + N+ +  D  T   KG+  +   N++EA  AI
Sbjct: 3   GWCIFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

Query: 149 TAMNGGELLTQTLTVDW 165
            ++NG  L  + L V +
Sbjct: 63  ASLNGYRLGDRVLQVSF 79

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD 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 = 86

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 48.8 bits (116), Expect = 3e-08
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V+G+ +   + +L+ +F +YG I    +  D+ TG  +G   I ++   EA+ AI  +NG
Sbjct: 5   VSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNG 64

Query: 154 GELL--TQTLTVDWA 166
            +    ++ +TV +A
Sbjct: 65  QKPEGASEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 48.4 bits (116), Expect = 4e-08
 Identities = 19/75 (25%), Positives = 34/75 (45%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E  ++  + +   +G +    L     TG  KGY  +EY +   A  A   +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 152 NGGELLTQTLTVDWA 166
           +G ++  + L VDWA
Sbjct: 62  DGKQIGGRKLQVDWA 76

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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 48.2 bits (114), Expect = 6e-08
 Identities = 24/75 (32%), Positives = 45/75 (60%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +++L+++FG  GEI +  L  D+ TG   GY  + Y + ++A+ AI  +
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 152 NGGELLTQTLTVDWA 166
           NG  L T+T+ V +A
Sbjct: 67  NGLRLQTKTIKVSYA 81

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB 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 AU-rich RNA element (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 = 83

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

 Score = 47.5 bits (113), Expect = 7e-08
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           E +L+  F ++G ++N+ +   ++TG  K Y  I++ N E A  A  +MN   L+ + L 
Sbjct: 13  EKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

Query: 163 V 163
           V
Sbjct: 73  V 73

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

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

 Score = 47.4 bits (113), Expect = 7e-08
 Identities = 22/62 (35%), Positives = 35/62 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E  ED ++  F  +G I+++ ++ D  T   KG+A +EYE  E AQ A+  M
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQM 62

Query: 152 NG 153
           NG
Sbjct: 63  NG 64

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 50.4 bits (120), Expect = 1e-07
 Identities = 42/133 (31%), Positives = 65/133 (48%), Gaps = 7/133 (5%)

Query: 55  FREEADSERHSRLAD----RNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           F  EADS+R  +  +    RN     +   PG + SI+   + VT +     +D L  +F
Sbjct: 156 FGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE-SIKDTNLYVTNLPRTITDDQLDTIF 214

Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLTVDWAFS 168
           G+YG+I   ++  D+ TG  +G A + +   EEAQ AI+A+N    E  +Q LTV  A  
Sbjct: 215 GKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEE 274

Query: 169 NGPSTGPFKRKNM 181
           +G +        M
Sbjct: 275 HGKAKAHHYMSQM 287

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). Length = 346

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

 Score = 46.8 bits (112), Expect = 1e-07
 Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 99  EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
           E+  ++ L+ +FG+YG+I +  +  D   G  KG+  + +EN E AQ A+  +NG E+  
Sbjct: 11  EDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNGKEVNG 69

Query: 159 QTLTV 163
           + L V
Sbjct: 70  KKLYV 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           EDDL+  F  +GEI+++ +  D++T   KG A +++     A  A+  MNG
Sbjct: 16  EDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNG 66

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

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 5/77 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHL--NLDRRTGFVKGYALIEYENFEEAQNAIT 149
           ILV  +  EA + D++ +F  YG+++++ +    D+     +G+A +E+   +EA NA+ 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAMN 59

Query: 150 AMNGGELLTQTLTVDWA 166
           A+    LL + L + +A
Sbjct: 60  ALKDTHLLGRRLVLQYA 76

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

>gnl|CDD|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 = 46.5 bits (111), Expect = 2e-07
 Identities = 21/75 (28%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  V  EA + +L+ +F  +G+++++ L   +  G  +G+A +E+   +EAQNA+ A+
Sbjct: 3   LIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEAL 61

Query: 152 NGGELLTQTLTVDWA 166
               L  + L +++A
Sbjct: 62  KSTHLYGRHLVLEYA 76

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

 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  ++ +  E  L+  F EYG I+ + L  D++TG  +GYA IE+E+  + + A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 152 NG 153
           +G
Sbjct: 64  DG 65

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 46.6 bits (110), Expect = 2e-07
 Identities = 23/75 (30%), Positives = 43/75 (57%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +++ +++FG  GEI +  L  D+ TG   GY  + Y +  +A  AI  +
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 152 NGGELLTQTLTVDWA 166
           NG +L T+T+ V +A
Sbjct: 66  NGLKLQTKTIKVSYA 80

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC 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 AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. 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 = 84

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

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  V      ++LQ  F   G I  + +  D+ TG  KG+A IE+ +    +NA+  +
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 152 NGGELLTQTLTV 163
           N  E   + + V
Sbjct: 61  NESEFRGRQIKV 72

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

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 46.3 bits (109), Expect = 3e-07
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +++ +++FG  GEI +  L  D+ TG   GY  + Y + ++A+ AI  +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 152 NGGELLTQTLTVDWA 166
           NG  L T+T+ V +A
Sbjct: 65  NGLRLQTKTIKVSYA 79

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD 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 = 83

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

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 17/79 (21%)

Query: 93  LVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN 152
           L  GV  E     L  VF +YG + +L +      G  K Y  + Y + E+A  A  A+N
Sbjct: 11  LGNGVSREE----LLRVFEKYGTVEDLVM----PPG--KPYCFVSYSSIEDAAAAYDALN 60

Query: 153 GGELLTQTLTVDWAFSNGP 171
           G EL       +    N P
Sbjct: 61  GKEL-------ELPQQNKP 72

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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 45.7 bits (108), Expect = 4e-07
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V G+     E DL+ VF  YG +  +++  D+RTG  +G+A + +E  ++++ A+   NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 154 GELLTQTLTVDWAFS 168
            EL  + + VD++ +
Sbjct: 64  MELDGRRIRVDYSIT 78

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 45.7 bits (109), Expect = 4e-07
 Identities = 16/52 (30%), Positives = 31/52 (59%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
            ++DL+ +F  +G+I++  +  D++TG    YA IE+E  E+ + A   M+ 
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDN 67

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+ +H +  E+DL+ +FG  GE++ + +N D R+G  +G A + +E  E+A+ AI   
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIKQF 61

Query: 152 NGGEL 156
           NG  L
Sbjct: 62  NGVLL 66

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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 45.5 bits (107), Expect = 5e-07
 Identities = 22/75 (29%), Positives = 43/75 (57%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +D+L+++F   GE+ +  L  D+  G   GY  + Y N ++A+ AI  +
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 152 NGGELLTQTLTVDWA 166
           NG  L ++T+ V +A
Sbjct: 64  NGLRLQSKTIKVSYA 78

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a 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. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR 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 AU-rich RNA element (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 = 81

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 45.4 bits (107), Expect = 6e-07
 Identities = 23/76 (30%), Positives = 42/76 (55%)

Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           EG  + +  + +E  + DL   F  +G + +  + +D++T   K +  + Y+N + AQ A
Sbjct: 3   EGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAA 62

Query: 148 ITAMNGGELLTQTLTV 163
           I AMNG ++ T+ L V
Sbjct: 63  IQAMNGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, 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 = 79

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

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 18/57 (31%), Positives = 31/57 (54%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           I V G+     +D L+  F ++GEI    +  DR+TG  +GY  + +++ E A+ A 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59

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

 Score = 45.2 bits (108), Expect = 6e-07
 Identities = 14/55 (25%), Positives = 27/55 (49%)

Query: 98  HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN 152
           H +  E  L  +F   G + ++ +  D  T    GYA + ++N  +A+ A+  +N
Sbjct: 8   HPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

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

 Score = 44.8 bits (106), Expect = 8e-07
 Identities = 18/74 (24%), Positives = 36/74 (48%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  E  +  L   F  +    +  +  D ++G  +GY  + + + ++A+NAI  M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 152 NGGELLTQTLTVDW 165
           NG  L ++ +  +W
Sbjct: 62  NGKWLGSRPIRCNW 75

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

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

 Score = 44.5 bits (106), Expect = 8e-07
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           E +L+  F ++G +  L L+  ++TG  KGYA +E+E+ E A+     MN 
Sbjct: 13  EPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNN 63

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

 Score = 44.9 bits (107), Expect = 8e-07
 Identities = 15/51 (29%), Positives = 30/51 (58%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           E  + + F E GE+ ++ +  +++TG   GY  +E+   E A+ A+ ++NG
Sbjct: 13  EAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           +++++++F   GEI +  L  D+ TG   GY  + Y   E+A+ A+ ++NG  L  +T+ 
Sbjct: 17  QEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIK 76

Query: 163 VDWAFSNGPSTGPFKRKNM 181
           V +A    PS+   K  N+
Sbjct: 77  VSYA---RPSSDSIKGANL 92

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 17/56 (30%), Positives = 34/56 (60%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE 155
           +A E++L+ +F ++GE++   +  D+ TG  KG A ++++  E AQ  + A +  E
Sbjct: 11  DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAE 66

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|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 = 44.5 bits (105), Expect = 1e-06
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  +  E  L+ VF +YG+I  + +  DR T   +G+  + +EN ++A++A+ AM
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 152 NGGELLTQTLTVDWA 166
           NG  +  + + VD A
Sbjct: 63  NGKSVDGRQIRVDQA 77

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

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

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 11/42 (26%), Positives = 26/42 (61%)

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           L+  F ++G++++ ++  D+ TG  KGY  + + + +  +NA
Sbjct: 16  LKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENA 57

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|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 44.1 bits (105), Expect = 1e-06
 Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 3/50 (6%)

Query: 104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           ++L ++FG+YG IR + +   + T   +G A + YE+  +A+NA   ++G
Sbjct: 17  EELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHLSG 63

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 20/64 (31%), Positives = 34/64 (53%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
            +DL  +F +YG++  + +  D+ T   KG A I + + E+A   + A+N  EL  +TL 
Sbjct: 15  NNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLK 74

Query: 163 VDWA 166
              A
Sbjct: 75  CSIA 78

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+     ED+L+++FG +GEI  + +   +  GFV+      + +   A+ AI  +
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQ------FVHRAAAEAAIQQL 57

Query: 152 NGGELLTQTLTVDW 165
            G  +    + + W
Sbjct: 58  QGTIIGGSRIRLSW 71

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

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           E+DL+ +F +YG +  +HL +D+ T   KG+A + Y   E A  A   ++G
Sbjct: 16  EEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDG 66

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

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           +   GV     E DL++ FG +GE+++  LN D+R  FVK Y      N  +A+NA  AM
Sbjct: 6   LFPGGVTFNMIEYDLRSGFGRFGEVQSCILNNDKRHAFVKMY------NRRDAENAREAM 59

Query: 152 NGGELLTQTLTVDWAFSNGP 171
              +     L   W    GP
Sbjct: 60  EQYKSGDMQLRTRWGVGFGP 79

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

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 23/71 (32%), Positives = 42/71 (59%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +      DDL+ VF +YGE+ ++++  DR T   +G+A + + +  +A++A+ AM+G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 154 GELLTQTLTVD 164
            EL  + 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  +  +++L   F  +G+I  L +NL +R      +A I++E  + A  A+ + 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKI--LEVNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 152 NGGELLTQTLTV 163
           N   L  +T+ V
Sbjct: 64  NHSMLKNKTMHV 75

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

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 99  EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
               E+ L+ +F EYGE+         R   +K YA + +E  ++A  A+  MNG EL  
Sbjct: 11  LSTTEEQLRELFSEYGEVE--------RVKKIKDYAFVHFEERDDAVKAMEEMNGKELEG 62

Query: 159 QTLTVDWA 166
             + V  A
Sbjct: 63  SPIEVSLA 70

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 8/60 (13%)

Query: 104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           +DL+ +F +YG+I  + L+        KGY  ++++N E+A+ A+   NG E+  Q L +
Sbjct: 16  EDLEEIFSKYGKILGISLH--------KGYGFVQFDNEEDARAAVAGENGREIAGQKLDI 67

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

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

 Score = 43.5 bits (102), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E   +D+++ F  +G+I +  +  D  TG  KGY  + + N  +A+NAI  M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 152 NGGELLTQTLTVDWA 166
            G  L  + +  +WA
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 25/87 (28%), Positives = 45/87 (51%)

Query: 86  SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           SI    + V+G+ +   + +L+ +F +YG I    + +D+ TG  +G   I ++   EA+
Sbjct: 2   SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 61

Query: 146 NAITAMNGGELLTQTLTVDWAFSNGPS 172
            AI  +NG +    T  +   F+N PS
Sbjct: 62  EAIKGLNGQKPPGATEPITVKFANNPS 88

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB 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 AU-rich RNA element (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 = 90

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

 Score = 42.9 bits (102), Expect = 4e-06
 Identities = 21/63 (33%), Positives = 37/63 (58%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           E+ +  +F   G+I+ + + LDR T    G+  +EY   E+A+NA+  +NG +L  + + 
Sbjct: 12  EEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIR 71

Query: 163 VDW 165
           VDW
Sbjct: 72  VDW 74

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

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

 Score = 42.6 bits (101), Expect = 4e-06
 Identities = 22/72 (30%), Positives = 39/72 (54%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  + E+  E+ L  +F + G + N+H+  DR T   +GY  +E+ + E+A  AI  M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 152 NGGELLTQTLTV 163
           N  +L  + + 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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 43.1 bits (101), Expect = 4e-06
 Identities = 19/62 (30%), Positives = 37/62 (59%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + ++G+     + D++++F  +G I N  + +D+ TG  +G A I ++   EA+ AIT+ 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 152 NG 153
           NG
Sbjct: 63  NG 64

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), 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. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR 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 AU-rich RNA element (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 = 84

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 20/68 (29%), Positives = 42/68 (61%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           +++ +++F   G ++N  +  D+RTG+  G+  ++Y++ E+AQ AI  +NG +L  + + 
Sbjct: 14  DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIK 73

Query: 163 VDWAFSNG 170
           V +A   G
Sbjct: 74  VAYARPGG 81

This subfamily corresponds to the RRM1 of 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 = 81

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 42.7 bits (101), Expect = 4e-06
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
           A+E D++  F  YG IR ++L          G+  +E+E+  +A +A+  +NG EL  + 
Sbjct: 11  ARERDVERFFKGYGRIREINLK--------NGFGFVEFEDPRDADDAVYELNGKELCGER 62

Query: 161 LTVDWA 166
           + V+ A
Sbjct: 63  VIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 42.7 bits (101), Expect = 5e-06
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V+G+ +   + +L+ +F  YG I    +  D  TG  +G   I ++   EA+ AI A+NG
Sbjct: 5   VSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNG 64

Query: 154 GEL--LTQTLTVDWA 166
                 T+ +TV +A
Sbjct: 65  TIPPGATEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

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

 Score = 42.4 bits (100), Expect = 5e-06
 Identities = 20/64 (31%), Positives = 40/64 (62%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           ++ L+  F ++G +    +  DR TG  +G+  +++E+ E+A+ AI AM+G EL  + + 
Sbjct: 13  DEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPIN 72

Query: 163 VDWA 166
           VD++
Sbjct: 73  VDFS 76

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

>gnl|CDD|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 = 42.3 bits (100), Expect = 5e-06
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 6/74 (8%)

Query: 97  VHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL 156
           + ++  E+DL+N+F EYGEI+++ +   R      G A +  E  ++A  A+  +   +L
Sbjct: 10  LSKKVTEEDLKNLFEEYGEIQSIDMIPPR------GCAYVCMETRQDAHRALQKLRNVKL 63

Query: 157 LTQTLTVDWAFSNG 170
             + + V WA + G
Sbjct: 64  AGKKIKVAWAPNKG 77

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

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

 Score = 45.4 bits (107), Expect = 6e-06
 Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E +ED ++  F  +G I++++++ D  TG  KG+A +EYE  E AQ A+  M
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 152 NGGELLTQTLTVDWAFSNGPSTGP 175
           NG  L  + + V    SN P   P
Sbjct: 170 NGQMLGGRNIKVGRP-SNMPQAQP 192

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

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

 Score = 42.2 bits (100), Expect = 6e-06
 Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 6/51 (11%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
             +L+  F  +G IR +    D   G  + YA IEYE+ E AQ A  A+ G
Sbjct: 12  LAELEREFDRFGAIRRI----DYDPG--RNYAYIEYESIEAAQAAKEALRG 56

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

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

 Score = 42.6 bits (101), Expect = 6e-06
 Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVK---GYALIEYENFEEAQNAI 148
           I V  +  +  EDDL+ +F ++GE+ ++ +   +     +   G+A + +++   A+NA+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 149 TAMNGGELLTQTLTV 163
             +NG EL  + ++V
Sbjct: 63  -QLNGTELGGRKISV 76

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

>gnl|CDD|240720 cd12274, RRM2_NEFsp, RNA recognition motif 2 in vertebrate putative RNA exonuclease NEF-sp

 Score = 42.2 bits (99), Expect = 6e-06
 Identities = 15/63 (23%), Positives = 29/63 (46%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V+G  +   E+ LQ  FG+  ++  + L  D  +G    Y  +++   + A  A+  +
Sbjct: 1   IYVSGFTKSLTEEFLQERFGQLSDLEAIFLPKDLLSGKPAKYCFLKFRQSQSATAALDHI 60

Query: 152 NGG 154
            G 
Sbjct: 61  TGE 63

This subfamily corresponds to the RRM2 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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 42.7 bits (100), Expect = 6e-06
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V G+     E DL+ VF +YG I ++ +  D+++   +G+A + +EN ++A+ A    NG
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 154 GELLTQTLTVDWAFS 168
            EL  + + VD++ +
Sbjct: 74  MELDGRRIRVDFSIT 88

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 44.9 bits (106), Expect = 8e-06
 Identities = 26/88 (29%), Positives = 46/88 (52%)

Query: 86  SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           SI+G  + V+G+ +   + +L+++F  +G+I    +  D  TG  KG   I ++  +EA 
Sbjct: 86  SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEAD 145

Query: 146 NAITAMNGGELLTQTLTVDWAFSNGPST 173
            AI  +NG      T  +   F+N PS+
Sbjct: 146 RAIKTLNGTTPSGCTEPITVKFANNPSS 173

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 42.3 bits (99), Expect = 8e-06
 Identities = 15/49 (30%), Positives = 31/49 (63%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN 140
           I V G+ E+ +E  L++ F +YG+I  + +  DR +G  +G+A + +++
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51

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

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

 Score = 41.8 bits (99), Expect = 8e-06
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
            +E DL   F + G++R++ +  DR +   KG A +E+ + E    A+  + G  LL Q 
Sbjct: 11  VRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTGQRLLGQP 69

Query: 161 LTV 163
           + V
Sbjct: 70  IMV 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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 41.9 bits (98), Expect = 1e-05
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V     E +++ +F E+G +  + +  D+RTG  +G   ++Y   +EA  AI A+
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 152 N 152
           +
Sbjct: 62  H 62

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

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score = 44.9 bits (106), Expect = 1e-05
 Identities = 24/92 (26%), Positives = 38/92 (41%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I +  +     ED ++ +   +G+++  +L  D  TG  KGYA  EY++      AI A+
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRP 183
           NG +     L V  A              M P
Sbjct: 358 NGKDTGDNKLHVQRACVGANQATIDTSNGMAP 389

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 17/60 (28%), Positives = 34/60 (56%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           + G+     ++DL+ +   +G+I +    LD++T   KGY  +++++ E A  AI  +NG
Sbjct: 5   IRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNG 64

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>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 = 41.3 bits (97), Expect = 1e-05
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 92  ILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           + V G      +E+D++ +F  +G +    +   R+T     +A +E+E+ E+A  A+ A
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI---RKT-----FAFVEFEDSEDATKALEA 53

Query: 151 MNGGELLTQTLTVDWA 166
           ++G  +    LTV++ 
Sbjct: 54  LHGSRIDGSVLTVEFV 69

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 91  IILVTGVHEEAQ--EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           ++LVT  +       D L  VF  YG +  +   +  +   V+  AL+++++ E A+NA 
Sbjct: 1   VLLVTISNLLYPVTVDVLHQVFSPYGAVEKI--LIFEKNTGVQ--ALVQFDSVESAENAK 56

Query: 149 TAMNGGELLTQTLTVDWAFSN 169
            A+NG  +     T+D  FS 
Sbjct: 57  KALNGRNIYDGCCTLDIQFSR 77

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  + +    ++L+ +F +YG +       D     VK Y  +  E  E+A++AI A+
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTV----TECDV----VKNYGFVHMEEEEDAEDAIKAL 53

Query: 152 NGGELLTQTLTV 163
           NG E + + + V
Sbjct: 54  NGYEFMGKRINV 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|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 17/75 (22%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +   A + +L++ F +YG +R++ +   R      G+A +E+E+  +A++A+ A+
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVA--RNP---PGFAFVEFEDPRDAEDAVRAL 56

Query: 152 NGGELLTQTLTVDWA 166
           +G  +    + V+ +
Sbjct: 57  DGRRICGNRVRVELS 71

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

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 23/75 (30%), Positives = 37/75 (49%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E   DD++  F  +G I +  +  D  TG  KGY  + + N  +A+NAI  M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 152 NGGELLTQTLTVDWA 166
            G  L  + +  +WA
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 8/75 (10%)

Query: 90  WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           W I V  V      D+L+ +F E+G +    +  D+    VK YA +  E  EEA  AI 
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRV----VECDK----VKDYAFVHMEREEEALAAIE 52

Query: 150 AMNGGELLTQTLTVD 164
           A+NG E+  + + V+
Sbjct: 53  ALNGKEVKGRRINVE 67

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

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 20/78 (25%), Positives = 41/78 (52%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+ +   + +++ +F +YG I    + +D+ TG  +G   I ++   EA+ AI  +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 152 NGGELLTQTLTVDWAFSN 169
           NG + L     +   F+N
Sbjct: 64  NGQKPLGAAEPITVKFAN 81

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC 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 AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. 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 = 81

>gnl|CDD|241083 cd12639, RRM3_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 = 40.6 bits (95), Expect = 3e-05
 Identities = 21/76 (27%), Positives = 40/76 (52%)

Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           EG  + +  + +E  + +L  +F  +G + +  + +DR T   K +  + ++N   AQ A
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 148 ITAMNGGELLTQTLTV 163
           I AMNG ++  + L V
Sbjct: 63  IQAMNGFQIGMKRLKV 78

This subgroup corresponds to the RRM3 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, 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 contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. 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 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 = 79

>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor family

 Score = 43.3 bits (102), Expect = 3e-05
 Identities = 39/143 (27%), Positives = 56/143 (39%), Gaps = 23/143 (16%)

Query: 25  VDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQ 84
            D  SS   P   L      G P             +   + LA          GGPG  
Sbjct: 222 HDGYSSHGGPLAPLAGGDRMGPP----HGPPSRYRPAYEAAPLAPAISSYGPAGGGPGS- 276

Query: 85  RSIEGWIILVTGVHEEAQE-DDLQNVFGEYGEIRNLHLNLDRRTGFV---KGYALIEYEN 140
                 +++V+G+H+E    D L N+F  YG +         R  F+   K  ALIE  +
Sbjct: 277 ------VLMVSGLHQEKVNCDRLFNLFCVYGNVE--------RVKFMKNKKETALIEMAD 322

Query: 141 FEEAQNAITAMNGGELLTQTLTV 163
             +AQ A+T +NG +L  + L V
Sbjct: 323 PYQAQLALTHLNGVKLFGKPLRV 345

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). Length = 481

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

 Score = 43.3 bits (102), Expect = 3e-05
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +     ED L+ +F ++GEI +  +  D  +G  +G+A + +E  E+A  A+  MNG
Sbjct: 183 VKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNG 241

Query: 154 GEL 156
            ++
Sbjct: 242 KKI 244

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

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
           A++DDL+  F E GE+ ++ +  D      KG+  +E+   E AQ A    +G ELL + 
Sbjct: 11  AEQDDLEEFFKECGEVVDVRIAQDDDGRS-KGFGHVEFATEEGAQKA-LEKSGEELLGRE 68

Query: 161 LTVDWA 166
           + VD A
Sbjct: 69  IRVDLA 74

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

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 22/76 (28%), Positives = 41/76 (53%)

Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           EG  + +  + +E  + DL  +F  +G + +  + +D++T   K +  + Y+N   AQ A
Sbjct: 6   EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 65

Query: 148 ITAMNGGELLTQTLTV 163
           I AMNG ++  + L V
Sbjct: 66  IQAMNGFQIGMKRLKV 81

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 40.2 bits (94), Expect = 4e-05
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQN 146
           I V G+  +  E+DL+  F +YG ++ + +  D R G  KGY  + +E  E+AQ 
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQK 58

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

 Score = 39.9 bits (94), Expect = 5e-05
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           +LV  +     + +L+++F ++GE++++     R     K    +E+ +   A+ A+ A+
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKDIRETPLRP--SQK---FVEFYDIRAAEAALDAL 58

Query: 152 NGGELLTQTLTVD 164
           NG   L   L V 
Sbjct: 59  NGRPFLGGRLKVK 71

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

>gnl|CDD|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 = 21/64 (32%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           ED L  +F + G I++  L  +        YA +EY +   A  A+  MNG  +L Q + 
Sbjct: 12  EDLLAELFSQIGPIKSCKLIREHGN---DPYAFVEYYDHRSAAAALQTMNGRLILGQEIK 68

Query: 163 VDWA 166
           V+WA
Sbjct: 69  VNWA 72

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

 Score = 39.3 bits (92), Expect = 7e-05
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 92  ILVTGVHEEAQEDDLQNV----FGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           I V G      EDD++      F   GEI  + +  DR TG  KG+A IE+++ +  + A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 148 ITAMNGGELLTQTLTVD 164
           +  ++G +L    L VD
Sbjct: 62  LE-LDGSDLGGGNLVVD 77

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 = 39.2 bits (92), Expect = 8e-05
 Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           + V+ +     ED+L+ +F + GEI ++ L  + + G  KGYA +E+EN E  Q A
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA 56

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

 Score = 39.4 bits (92), Expect = 9e-05
 Identities = 19/62 (30%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  ++++A E +++ VF  YG + ++++  D      +G A ++Y + E AQ AI A+
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKAL 60

Query: 152 NG 153
           NG
Sbjct: 61  NG 62

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

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 5/66 (7%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           +++V  +   A ED LQ VF +   IR     + +  G  KGYA +E+E+ E+A+ A+ +
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEKATSIR-----IPQNNGRPKGYAFVEFESAEDAKEALNS 57

Query: 151 MNGGEL 156
            N  E+
Sbjct: 58  CNNTEI 63

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

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 19/61 (31%), Positives = 38/61 (62%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V +  + +DL+  FG YG I ++++ LD  T   +G+A I++E+  +A++A+  +
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 152 N 152
           N
Sbjct: 63  N 63

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 9/73 (12%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEE 143
           I ++G+ ++  ED L  +FG  G I+         + +  D+ T   KG A + Y++   
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEP-KGEATVTYDDPSA 59

Query: 144 AQNAITAMNGGEL 156
           AQ AI   NG E 
Sbjct: 60  AQAAIEWFNGYEF 72

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|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           L++VF  +G + +++L   +  G+ K      Y + E A+ AIT ++G E+    L V
Sbjct: 16  LEDVFCRFGGLIDVYLVPGKNYGYAK------YADRESAERAITTLHGKEVNGVKLKV 67

This subfamily corresponds to the RRM4 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 = 68

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 18/73 (24%), Positives = 40/73 (54%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+    +  DL+N+FG+YG++ +  +  + R+   K Y ++   +  E    I+ +
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 152 NGGELLTQTLTVD 164
           +  EL  Q ++V+
Sbjct: 62  HRTELHGQQISVE 74

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains 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. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 14/57 (24%), Positives = 34/57 (59%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           + V G+ E+  E+DL+  F +YG + ++ +  D+ TG  +G+A + +++++     +
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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           ED L+ +F  +G I ++ L   +   F + +  + Y+  EEAQ A+   N   + T  +T
Sbjct: 14  EDKLRKLFEAFGTITDVQLKYTKDGKF-RKFGFVGYKTEEEAQKALKHFNNSFIDTSKIT 72

Query: 163 VD 164
           V+
Sbjct: 73  VE 74

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 38.5 bits (89), Expect = 1e-04
 Identities = 16/54 (29%), Positives = 30/54 (55%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           + V G+  +  E+ ++  FG +GEI N+ L +D +T   +G+  + Y + E  Q
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQ 55

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), 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 = 75

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 1/53 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEA 144
           I V G+  E  E+ ++  FG++G I  + L +D++T   +G+  I +++ EE 
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDS-EEP 53

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

>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+ +   + +L+ +F +YG I    + +D+ TG  +G   I ++   EA+ AI  +
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 152 NGGEL--LTQTLTVDWA 166
           NG +     + +TV +A
Sbjct: 65  NGQKPSGAAEPITVKFA 81

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD 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 = 81

>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 12/77 (15%)

Query: 91  IILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVK---GYALIEYENFEEAQN 146
           +++V G+ ++    D L N+F  YG   N+      R  F+K   G A+++  + + A+ 
Sbjct: 1   VLMVYGLDKDKMNCDKLFNLFCLYG---NVL-----RIKFLKSKPGTAMVQMGDPQAAER 52

Query: 147 AITAMNGGELLTQTLTV 163
           AI  +NG  L  Q L V
Sbjct: 53  AIEYLNGVVLFGQKLEV 69

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that 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. Like PTB, PTBPH3 contains four RRMs. Length = 71

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           I V G+  +  E++L++ F  +G ++++ +  DR  G  KGY  + +E  E+A+  +
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKIL 60

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 13/84 (15%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGE---IR--NLHLNLDRRTGFVKGYALIEYENFEEAQ 145
            + VT       + D++++F +YGE   IR  +L  N  RR      +  +++ + E A 
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR------FCYVQFTSPESAA 55

Query: 146 NAITAMNGGELLTQTLTVDWAFSN 169
            A+  +NG       L V    S+
Sbjct: 56  AAVALLNGKLGEGYKLVV--KISD 77

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

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+ E+  E+ L+  F   G I    +  DR TG  KG+  +++ + E+A+ A  AM
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSI-AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 152 NGGELLTQTLTVDWAFSNG 170
             GE+    +T+D+A   G
Sbjct: 60  EDGEIDGNKVTLDFAKPKG 78

This subfamily corresponds to the RRM4 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 = 78

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 19/68 (27%), Positives = 35/68 (51%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+H    + DL  +   YG+I +    LD+ T   KGY  +++++   AQ A+TA+
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

Query: 152 NGGELLTQ 159
               +  Q
Sbjct: 64  KASGVQAQ 71

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 17/78 (21%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
            + V  ++   ++++L+ +F ++G+IR L+     R     G+ ++ Y +   A+ A  A
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFGDIRTLYTACKHR-----GFIMVSYYDIRAARRAKRA 57

Query: 151 MNGGELLTQTLTVDWAFS 168
           + G EL  + L + ++  
Sbjct: 58  LQGTELGGRKLDIHFSIP 75

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|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family proteins

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 7/64 (10%)

Query: 90  WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           W++L   +  +     L+ +  ++G +   HLNL        G ALI Y + EEA  A +
Sbjct: 3   WLVL-RNLTPQIDGSTLRTLCMQHGPLLTFHLNLR------HGNALIRYSSKEEAAKAQS 55

Query: 150 AMNG 153
           A+N 
Sbjct: 56  ALNN 59

This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. . Length = 71

>gnl|CDD|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 6/63 (9%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I+ +  + EE  ++ L+ +F ++   + +      R    +G A +E+E  E+A  A+ A
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQFPGFKEV------RLVPRRGIAFVEFETEEQATVALQA 57

Query: 151 MNG 153
           + G
Sbjct: 58  LQG 60

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           V G  ++A  DD+Q  F ++G++ N+ +  D    F KG   +E++  E+A+  +  
Sbjct: 4   VKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKF-KGSVFVEFKTEEDAKKFLEK 59

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

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 16/57 (28%), Positives = 37/57 (64%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           + V  + ++ + +DL+  FG YG I ++++ LD  T   +G+A +++E+  +A++A+
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 22/65 (33%), Positives = 34/65 (52%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  +  ED+L  +F + G I +L L +D  TG  +GYA + +   E AQ A+   
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKLY 63

Query: 152 NGGEL 156
           N  E+
Sbjct: 64  NNHEI 68

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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 18/75 (24%), Positives = 42/75 (56%), Gaps = 8/75 (10%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + +  ++  A+E D++  F  YG IR++ L         +G+  +E+++  +A +A+  +
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAVYEL 53

Query: 152 NGGELLTQTLTVDWA 166
           +G EL  + +T++ A
Sbjct: 54  DGKELCNERVTIEHA 68

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 14/58 (24%), Positives = 33/58 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           ++V G+  +  E DL++ F  +GE+  + +  D +TG  KG+  + + ++E+    ++
Sbjct: 2   LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS 59

This subfamily corresponds to the RRM1 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 = 77

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

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 6/67 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+     EDDL+  F   GE+  + L  DR+      +A +E   F +A++A++A+
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQ--HSARFAFVE---FADAESALSAL 57

Query: 152 N-GGELL 157
           N  G LL
Sbjct: 58  NLSGTLL 64

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|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           +ILV  +     E++L+ +F ++G +  L L   R        AL+E+    +A+ A  +
Sbjct: 2   VILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRTI------ALVEFLEPSDARKAFKS 55

Query: 151 MNGGELLTQTLTVDWA 166
           +         L ++WA
Sbjct: 56  LAYKRFKHVPLYLEWA 71

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 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 homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 19/65 (29%), Positives = 35/65 (53%), Gaps = 8/65 (12%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
           +E D+Q  FG YG++  + L          GY  +E+E+  +A +A+  +NG +L  + +
Sbjct: 12  REKDIQRFFGGYGKLLEIDLK--------NGYGFVEFEDSRDADDAVYELNGKDLCGERV 63

Query: 162 TVDWA 166
            V+ A
Sbjct: 64  IVEHA 68

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>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 = 37.0 bits (86), Expect = 5e-04
 Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+  +  E++ +  F ++G++ +  L  D  TG  +G+  + +++ E A   + + 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDS-ESAVERVFSA 60

Query: 152 NGGEL 156
              EL
Sbjct: 61  GMLEL 65

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|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 = 37.0 bits (86), Expect = 5e-04
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 4/67 (5%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQ 159
           EDD++ +F  +G I    + L    G  KG A +++ +  EAQ AI A++G + +   + 
Sbjct: 15  EDDVRRLFEPFGTIEECTI-LRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASS 73

Query: 160 TLTVDWA 166
           +L V +A
Sbjct: 74  SLVVKFA 80

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 39.6 bits (92), Expect = 6e-04
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 80  GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE 139
           G  P R  E   + V  +  +  ED+L  +F + G I  L L +D  +G  +GYA + + 
Sbjct: 52  GVQPGRGCE---VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF-SGQNRGYAFVTFC 107

Query: 140 NFEEAQNAITAMNGGEL 156
             EEA+ A+  +N  E+
Sbjct: 108 GKEEAKEAVKLLNNYEI 124

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. Length = 578

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

 Score = 36.9 bits (86), Expect = 6e-04
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 8/68 (11%)

Query: 86  SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
             +G  + V G      E+ L+  F  +G I N+ +  ++  GFV       +E  E A 
Sbjct: 1   PRKGNTLYVHGY--GLTEEILKKAFSPFGNIINISMEKEKNCGFVT------FEKMESAD 52

Query: 146 NAITAMNG 153
            AI  +NG
Sbjct: 53  RAIAELNG 60

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

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  +      DDL  +FG YGEI+ +     R T   + +  IE+ +   A+ A+ A+
Sbjct: 4   LVVFNLDPSVSNDDLHQIFGAYGEIKEI-----RETPNKRHHKFIEFYDVRSAEAALKAL 58

Query: 152 NGGEL 156
           N  E+
Sbjct: 59  NRSEI 63

This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

>gnl|CDD|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 = 7e-04
 Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 3/50 (6%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY---ENFEEAQNAI 148
           +E DL+ +F ++G+I  L +  D+ TG  KG A + Y   E+  +AQ+A+
Sbjct: 18  EEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

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|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.0 bits (85), Expect = 7e-04
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 8/70 (11%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
           ++ D++ +F +YG +    ++        KGYA ++Y N   A+ A+   NG  L  QTL
Sbjct: 15  KKSDVETIFSKYGRVVGCSVH--------KGYAFVQYSNERHARGAVIGENGRVLAGQTL 66

Query: 162 TVDWAFSNGP 171
            ++ A    P
Sbjct: 67  DINMAGEPKP 76

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . 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 = 36.8 bits (85), Expect = 7e-04
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +     ED L+ +F   G ++N+ +  D+    V  Y  +EY    +A+ A+  +NG
Sbjct: 3   VGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVN-YGFVEYHQSHDAEIALQTLNG 61

Query: 154 GELLTQTLTVDWA 166
            ++    + V+WA
Sbjct: 62  RQIENNEIRVNWA 74

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 36.5 bits (85), Expect = 7e-04
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLH-LNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I ++ +    + +DL ++   YG ++N   +     T  V     + YE+ E+AQ A+  
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVN----VTYESPEQAQQAVNK 58

Query: 151 MNGGELLTQTLTVDW 165
           +NG E     L V +
Sbjct: 59  LNGHEYEGSKLKVSY 73

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 36.7 bits (85), Expect = 7e-04
 Identities = 18/49 (36%), Positives = 28/49 (57%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           E  ED+L+  FG  G IR + +     +G  KG+A +++E  E A NA+
Sbjct: 9   ETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           L+ +F + G+     L +    G  +G+A +EY   E+A+ A  A+NG
Sbjct: 20  LRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAEEAQQALNG 66

This subfamily corresponds to the RRM3 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 = 92

>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 = 36.4 bits (85), Expect = 9e-04
 Identities = 12/59 (20%), Positives = 28/59 (47%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           + + G+  +  E+ L+  F +YGE+ +  +  D  TG  +G+  + + +       + A
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

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|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 23/83 (27%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEE 143
           + V+ +     E DL   FG  G I+         + L  D+ TG  KG A + Y++   
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 144 AQNAITAMNGGELLTQTLTVDWA 166
           A  AI   N  + +  T+ V  A
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVSLA 83

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           I V G++ EA E+ ++  FGE+GEI  + L +D +T   +G+  I ++  +
Sbjct: 7   IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEED 57

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), 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 = 80

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 14/51 (27%), Positives = 32/51 (62%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           + V G+ E+ +E  L++ F EYG+I  + +  DR++G  +G+  + +++ +
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53

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

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           + V G+     E DL+  F  +G + ++ +   +  G  +G+A I+     EAQ
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR-TSEAQ 54

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 15/51 (29%), Positives = 33/51 (64%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           I V G+ E+ +E  L++ F +YG+I  + +  DR++G  +G+A + +++ +
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHD 53

This subgroup corresponds to the RRM2 of hnRNP A3, 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 = 80

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

 Score = 36.0 bits (84), Expect = 0.001
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL-LTQTL 161
           ED+L  +F + G I  L L +D  +G  +GYA + Y N E AQ A+  ++  E+   + L
Sbjct: 15  EDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQLHNYEIRPGKRL 73

Query: 162 TV 163
            V
Sbjct: 74  GV 75

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 7/64 (10%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           ED+L+ +F +YG++ ++ ++  +     KG A++E+ + + A+ A+    G  L +  L 
Sbjct: 18  EDELRKIFSKYGDVSDVVVSSKK-----KGSAIVEFASKKAAEAAVENECG--LPSNPLL 70

Query: 163 VDWA 166
           V W 
Sbjct: 71  VSWL 74

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 14/60 (23%), Positives = 31/60 (51%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+  +  E+ ++  FG +GE+ ++ L +D +T   +G+  I ++  E  +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, 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 = 75

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  ED+L  +F   G+I    L ++  +G  +GYA + Y   EEAQ AI  +
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIRIL 62

Query: 152 NGGEL 156
           N  E+
Sbjct: 63  NNYEI 67

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V     +  E  ++ +F  YG ++ + +        +  +A +E+E+ E A  A  +++G
Sbjct: 4   VRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDSVHG 55

Query: 154 GELLTQTLTV 163
             L    L V
Sbjct: 56  KVLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA--M 151
           VT +  +A E D+ + F   G+I  + +   +R+G     +   Y  F++ Q   TA  +
Sbjct: 3   VTNLSPKATERDIYDFFSFSGDIEYVEI---QRSGE---QSQTAYVTFKDPQAQETALLL 56

Query: 152 NGGELLTQTLTV 163
           +G  ++ Q++T+
Sbjct: 57  SGATIVDQSVTI 68

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 37.7 bits (87), Expect = 0.002
 Identities = 26/99 (26%), Positives = 49/99 (49%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           SLG+ G      +  G  ++V  + ++  + +L  +F   G I    +  D +TG+  GY
Sbjct: 92  SLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGY 151

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS 172
           A +++ +  ++Q AI  +NG  +  + L V +A   G S
Sbjct: 152 AFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGES 190

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). Length = 346

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 105 DLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           DL+++F E G +    +  D   G  KG+  + +E+ E+AQ AI   NG +L  + L V
Sbjct: 14  DLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 6/56 (10%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           V G+ +   E DL     E+G I  + +   +R       AL+E+E+  +A+  + 
Sbjct: 7   VRGLPDGVTEADLVEALSEFGPISYVTMMPKKRQ------ALVEFEDISDAKACVN 56

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

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

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 18/75 (24%), Positives = 40/75 (53%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +  L++ F  +G++ +  + +DR TG  +G+  + + +   A  AI+ M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 152 NGGELLTQTLTVDWA 166
           +G EL  + + V+ A
Sbjct: 97  DGKELNGRHIRVNPA 111

Length = 144

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 90  WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           W+    G+ E   E  L   F  YG +  +H+ +DR+    +G AL+ ++  E AQ A+ 
Sbjct: 11  WL---DGLDESVTEQYLTRHFSRYGPV--VHVVIDRQ----RGQALVFFDKVEAAQAAVN 61

Query: 150 AMNGGELLTQTLTVD 164
            M G +L  + L VD
Sbjct: 62  EMKGRKLGGRKLQVD 76

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW 165
           L+ +FG YG++R   +   R  G + G+A +  +  + A+ A+   NG E+  + + VDW
Sbjct: 18  LKKIFGRYGKVREATIPRKR-GGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76

Query: 166 AFS 168
           A  
Sbjct: 77  AVQ 79

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

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 105 DLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD 164
           DL  +F +   ++++ L  D+ T   KG+  +E+E+ E  + A+   +G     ++L VD
Sbjct: 17  DLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALE-YDGALFDDRSLRVD 74

Query: 165 WA 166
            A
Sbjct: 75  IA 76

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

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 35.1 bits (81), Expect = 0.003
 Identities = 13/56 (23%), Positives = 29/56 (51%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           I V G+     EDD++  F ++G++ +  L  D++T   +G+  + +E+ +     
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKV 57

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

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

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  +     L+ VF   G++    +  D+  G  +G  ++++E+  EA  AI+  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 152 NGGELLTQTLTV 163
           NG  L  + + V
Sbjct: 60  NGQMLFDRPMRV 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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 18/75 (24%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I+V  + +   ED L+  F   GE+ ++ + +  R G  + +  + +++ E+AQ A+   
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 152 NGGELLTQTLTVDWA 166
           N   + T  ++V+ A
Sbjct: 62  NKTFIDTSKISVELA 76

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

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
            + V  +  + +E +++++F +YG I ++ L L  R     GYA IE+E+  +A++AI  
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRP---PGYAFIEFEDARDAEDAIRG 57

Query: 151 MNGGELLTQTLTVD 164
            +G +   Q L V+
Sbjct: 58  RDGYDFDGQRLRVE 71

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

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

 Score = 34.8 bits (81), Expect = 0.003
 Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN 152
           + +E++L+  F + G++  + +  DR+TG  KG+    Y  F+   +   A+ 
Sbjct: 10  DIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFG---YVLFKTKDSVALALK 59

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

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 20/67 (29%), Positives = 34/67 (50%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  ED+L  +F + G I +L L +D  +G  +GYA I +   E AQ A+   
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKLC 63

Query: 152 NGGELLT 158
           +  E+  
Sbjct: 64  DNYEIRP 70

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

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 11/79 (13%)

Query: 106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW 165
           L + F ++G I +  +  D   G  +GY  + +E  E A+ AI  +NG  L  + + V  
Sbjct: 105 LFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYV-- 161

Query: 166 AFSNGPSTGPFKRKNMRPG 184
                   G F +K+ R  
Sbjct: 162 --------GRFIKKHEREA 172

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

 Score = 34.5 bits (79), Expect = 0.004
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           + V G+  +  E DL   F ++G +    +  D++TG  +G+  + ++N + A  A 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

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

>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           +I V+ +  +  E+D+ N   E+G I N+ +         K  AL+E+   E+A  A+
Sbjct: 9   MIHVSNLPSDVTEEDVINHLAEHGVIVNVKVFESNG----KKQALVEFATEEQATEAL 62

This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that 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. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           + V  + ++  E+ ++  F + GEIR + +            A+IE+E  +EA  A+T
Sbjct: 3   VKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGGLV----AVIEFETEDEALAALT 56

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

 Score = 34.5 bits (79), Expect = 0.004
 Identities = 12/49 (24%), Positives = 28/49 (57%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN 140
           + + G++ E  +D L+  FG++GE+ +  +  D  TG  +G+  + ++ 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	196
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.92
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.86
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.86
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.81
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.81
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.75
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.75
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.73
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.72
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.71
KOG0122	270	consensus Translation initiation factor 3, subunit	99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.7
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.7
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.69
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.69
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.68
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.68
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.67
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.66
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.65
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.64
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.63
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.62
PLN03120	260	nucleic acid binding protein; Provisional	99.6
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.59
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.59
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.58
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.57
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.56
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.56
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.56
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.55
PLN03213	759	repressor of silencing 3; Provisional	99.55
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.53
smart00362	72	RRM_2 RNA recognition motif.	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.51
PLN03121	243	nucleic acid binding protein; Provisional	99.51
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.51
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.5
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.49
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.49
smart00360	71	RRM RNA recognition motif.	99.49
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.47
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.47
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.46
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.46
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.46
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.46
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.45
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.43
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.4
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.36
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.36
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.35
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.33
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.33
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.31
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.31
smart00361	70	RRM_1 RNA recognition motif.	99.3
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.27
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.24
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.24
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.21
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.14
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.11
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.1
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.08
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.0
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.99
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.96
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.95
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.92
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.91
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.9
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.83
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.82
KOG0151	877	consensus Predicted splicing regulator, contains R	98.75
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.7
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.61
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.51
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.46
KOG0226	290	consensus RNA-binding proteins [General function p	98.45
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.45
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.43
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.43
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.37
KOG4210	285	consensus Nuclear localization sequence binding pr	98.36
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.36
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.33
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.14
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.14
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.14
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.13
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.08
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.96
KOG2314	698	consensus Translation initiation factor 3, subunit	97.82
KOG3152	278	consensus TBP-binding protein, activator of basal	97.8
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.79
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.69
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.66
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.62
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.55
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.51
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.5
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.5
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.44
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.33
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.33
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.24
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.16
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.14
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.98
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.81
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.78
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.67
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.48
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.4
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.33
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.31
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.25
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.22
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.18
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.04
KOG2135	526	consensus Proteins containing the RNA recognition	96.03
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.0
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.96
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.87
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.86
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.8
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	95.58
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.33
KOG4660	549	consensus Protein Mei2, essential for commitment t	94.48
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.96
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.76
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	93.76
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.75
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.68
KOG4210	285	consensus Nuclear localization sequence binding pr	93.2
COG0724	306	RNA-binding proteins (RRM domain) [General functio	92.97
KOG2591	684	consensus c-Mpl binding protein, contains La domai	92.2
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.33
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.0
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	90.5
KOG0122	270	consensus Translation initiation factor 3, subunit	86.77
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	85.58
KOG2318	650	consensus Uncharacterized conserved protein [Funct	85.56
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	84.41
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	81.85

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.92  E-value=6.5e-25  Score=153.84  Aligned_cols=136  Identities=60%  Similarity=1.034  Sum_probs=123.0

Q ss_pred             CcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccC
Q 043064           34 PQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEY  113 (196)
Q Consensus        34 ~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~  113 (196)
                      .+..++.     .++++||+||.+...+....+..-...........++|+.+..++.|||+++....|+++|.+.|..|
T Consensus        22 ~i~~~~e-----~Akk~kGRGf~~e~~sr~r~r~~yd~vee~~s~~~pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dy   96 (170)
T KOG0130|consen   22 AIAGLKE-----KAKKRKGRGFGSEKDSRRRRRLSYDDVEEDGSDMRPGPQRSVEGWIIFVTGVHEEATEEDIHDKFADY   96 (170)
T ss_pred             HHHHHHH-----HHHhhcCCCcccccchHHHhhhhhhhHhhcccccCCCCccceeeEEEEEeccCcchhHHHHHHHHhhc
Confidence            5677776     48899999999988777777766666666677778999999999999999999999999999999999


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCCCC
Q 043064          114 GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG  174 (196)
Q Consensus       114 G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~~~  174 (196)
                      |+|+.+.+..++.||..+|||+|+|.+...|+.|+..+||..|.|++|.|.|++.+.+..+
T Consensus        97 GeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~gp~~g  157 (170)
T KOG0130|consen   97 GEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKGPERG  157 (170)
T ss_pred             ccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecCCccC
Confidence            9999999999999999999999999999999999999999999999999999998887543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.86  E-value=4e-21  Score=159.04  Aligned_cols=139  Identities=27%  Similarity=0.337  Sum_probs=109.7

Q ss_pred             CCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC-------CCCCCCCCEEEEcCCCcc
Q 043064           28 SSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG-------PQRSIEGWIILVTGVHEE  100 (196)
Q Consensus        28 ~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~l~V~nLp~~  100 (196)
                      ...++..+..+++.    .+++++||+||+|. ...++..+...++...+...+.       .......++|||+|||+.
T Consensus       130 ~~G~V~~v~i~~d~----~tg~srGyaFVeF~-~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~~~~~~~lfV~nLp~~  204 (346)
T TIGR01659       130 TIGPINTCRIMRDY----KTGYSFGYAFVDFG-SEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRT  204 (346)
T ss_pred             hcCCEEEEEEEecC----CCCccCcEEEEEEc-cHHHHHHHHHHcCCCccCCceeeeecccccccccccceeEEeCCCCc
Confidence            34455556666665    45689999999998 4444544555566554443322       112345678999999999


Q ss_pred             CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEEEEcccCCC
Q 043064          101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTVDWAFSNGP  171 (196)
Q Consensus       101 ~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~~a~~~~~  171 (196)
                      +|+++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|.+  ++|+|.|+.....
T Consensus       205 vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       205 ITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             ccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            9999999999999999999999998899999999999999999999999999998865  7999999986544

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).

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

Probab=99.86  E-value=2.2e-20  Score=136.74  Aligned_cols=87  Identities=21%  Similarity=0.431  Sum_probs=81.6

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+++|.+||.|..|.|+.++.+++++|||||+|.+.++|+.||+.||+..|.|+.|+|.|
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            44567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.+++..
T Consensus       111 a~~~~~~  117 (144)
T PLN03134        111 ANDRPSA  117 (144)
T ss_pred             CCcCCCC
Confidence            9876653

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.82  E-value=1.5e-19  Score=140.26  Aligned_cols=133  Identities=22%  Similarity=0.302  Sum_probs=110.1

Q ss_pred             CCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC-----------------------CC
Q 043064           28 SSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG-----------------------PQ   84 (196)
Q Consensus        28 ~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------------~~   84 (196)
                      .-+.+...+.+|+.    .+.++||||||+|.....+ +-+...+++.++..+..                       -+
T Consensus        85 pFGevS~akvirD~----~T~KsKGYgFVSf~~k~dA-EnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQ  159 (321)
T KOG0148|consen   85 PFGEVSDAKVIRDM----NTGKSKGYGFVSFPNKEDA-ENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQ  159 (321)
T ss_pred             cccccccceEeecc----cCCcccceeEEeccchHHH-HHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhcc
Confidence            33445567778887    7789999999999954444 44556777766654321                       13


Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .+.+.++|||+||+..+|++.|+..|+.||.|.+|++.++      +||+||.|.+++.|..||..+||.+|.|+.+++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            4567899999999999999999999999999999999887      7999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |.+....
T Consensus       234 WGKe~~~  240 (321)
T KOG0148|consen  234 WGKEGDD  240 (321)
T ss_pred             ccccCCC
Confidence            9876553

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.81  E-value=4.7e-19  Score=147.44  Aligned_cols=82  Identities=28%  Similarity=0.488  Sum_probs=78.5

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      .+|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|..||..|||..|+|+.|+|.|+.++
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            46999999999999999999999999999999999889999999999999999999999999999999999999999877


Q ss_pred             CC
Q 043064          170 GP  171 (196)
Q Consensus       170 ~~  171 (196)
                      ..
T Consensus       350 ~~  351 (352)
T TIGR01661       350 AY  351 (352)
T ss_pred             CC
Confidence            53

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

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

Probab=99.81  E-value=2.2e-19  Score=156.60  Aligned_cols=139  Identities=27%  Similarity=0.282  Sum_probs=108.3

Q ss_pred             CCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC--------C----------CCCCCCC
Q 043064           29 SSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG--------P----------QRSIEGW   90 (196)
Q Consensus        29 ~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~----------~~~~~~~   90 (196)
                      .++...+..+++.    .+++++|||||+|.+ ...+..+...+++....+...        +          ......+
T Consensus       131 fG~I~sV~I~~D~----~TgkskGfAFVeF~s-~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~  205 (612)
T TIGR01645       131 FGPIKSINMSWDP----ATGKHKGFAFVEYEV-PEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN  205 (612)
T ss_pred             cCCEEEEEEeecC----CCCCcCCeEEEEeCc-HHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccc
Confidence            3455556666665    455899999999995 444444444444432222110        0          0112357


Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      +|||+|||+.+++++|+.+|+.||.|.+|.|..++.+++++|||||+|.+.++|..||..||+..|+|+.|+|.++.+.+
T Consensus       206 rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             eEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            89999999999999999999999999999999998889999999999999999999999999999999999999998755


Q ss_pred             CC
Q 043064          171 PS  172 (196)
Q Consensus       171 ~~  172 (196)
                      ..
T Consensus       286 ~~  287 (612)
T TIGR01645       286 DA  287 (612)
T ss_pred             cc
Confidence            43

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.75  E-value=1.8e-17  Score=142.52  Aligned_cols=129  Identities=26%  Similarity=0.410  Sum_probs=99.8

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCC-------------------CCCCCCCCCEEE
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGP-------------------GPQRSIEGWIIL   93 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~l~   93 (196)
                      ..+..+++.    .+++++|||||+|.+.+.+....  .+++....+.+                   .+......++||
T Consensus       117 ~~v~i~~d~----~~~~skg~afVeF~~~e~A~~Al--~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~  190 (457)
T TIGR01622       117 RDVQCIKDR----NSRRSKGVAYVEFYDVESVIKAL--ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLY  190 (457)
T ss_pred             eEEEEeecC----CCCCcceEEEEEECCHHHHHHHH--HhCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEE
Confidence            344445544    45678999999999655444432  22322211110                   001112258899


Q ss_pred             EcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           94 VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        94 V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      |+|||..+++++|+.+|++||.|..|.|+.+..+|+++|||||+|.+.++|..|+..|||..|.|+.|.|.|+.
T Consensus       191 v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       191 VGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             EcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            99999999999999999999999999999998889999999999999999999999999999999999999976

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.75  E-value=2e-18  Score=127.00  Aligned_cols=140  Identities=27%  Similarity=0.395  Sum_probs=118.7

Q ss_pred             CCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC--------CCCCCCCEEEEcCCCcc
Q 043064           29 SSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP--------QRSIEGWIILVTGVHEE  100 (196)
Q Consensus        29 ~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~l~V~nLp~~  100 (196)
                      ++|+..+...|+..+    ...+||||++|. ++.++.|+...++.+.+.+.+..        ....-+..|||+||.+.
T Consensus        33 agpVv~i~iPkDrv~----~~~qGygF~Ef~-~eedadYAikiln~VkLYgrpIrv~kas~~~~nl~vganlfvgNLd~~  107 (203)
T KOG0131|consen   33 AGPVVNLHIPKDRVT----QKHQGYGFAEFR-TEEDADYAIKILNMVKLYGRPIRVNKASAHQKNLDVGANLFVGNLDPE  107 (203)
T ss_pred             cCceeeeecchhhhc----ccccceeEEEEe-chhhhHHHHHHHHHHHhcCceeEEEecccccccccccccccccccCcc
Confidence            466777677777644    378999999999 88899999988887777765432        22334688999999999


Q ss_pred             CcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCCC
Q 043064          101 AQEDDLQNVFGEYGEIRN-LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPST  173 (196)
Q Consensus       101 ~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~~  173 (196)
                      +++..|.+.|+.||.|.. ..++++..||.++||+||.|.+.+.+.+|+..+||..+..++|+|.|++.+..++
T Consensus       108 vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  108 VDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             hhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            999999999999999876 4778888899999999999999999999999999999999999999999887654

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.73  E-value=1.5e-17  Score=124.73  Aligned_cols=89  Identities=27%  Similarity=0.431  Sum_probs=81.9

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      |+.......|-|-||...++.++|+.+|.+||.|-+|.|+.++.|..++|||||.|....+|+.|+..|+|.+|+|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            44555568899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043064          163 VDWAFSNGP  171 (196)
Q Consensus       163 v~~a~~~~~  171 (196)
                      |++|+-...
T Consensus        87 Vq~arygr~   95 (256)
T KOG4207|consen   87 VQMARYGRP   95 (256)
T ss_pred             ehhhhcCCC
Confidence            998875443

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=4.7e-17  Score=134.84  Aligned_cols=87  Identities=23%  Similarity=0.412  Sum_probs=81.4

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .......++|||+|||+++|+++|+++|+.||.|+.|.|+.++.+++++|||||+|.+.++|++||+.|++..|.+++|+
T Consensus       101 ~~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~  180 (346)
T TIGR01659       101 NDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLK  180 (346)
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceee
Confidence            34555689999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEcccC
Q 043064          163 VDWAFSN  169 (196)
Q Consensus       163 v~~a~~~  169 (196)
                      |.|+.+.
T Consensus       181 V~~a~p~  187 (346)
T TIGR01659       181 VSYARPG  187 (346)
T ss_pred             eeccccc
Confidence            9998764

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).

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

Probab=99.72  E-value=1.2e-16  Score=139.20  Aligned_cols=117  Identities=23%  Similarity=0.365  Sum_probs=89.2

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhccc--CCCCCC--------C----CCCCCCCCCEEEEcCCCccCcHHHHHHhhcc
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFES--LGTDGG--------P----GPQRSIEGWIILVTGVHEEAQEDDLQNVFGE  112 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~--~~~~~~--------~----~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~  112 (196)
                      ..+++||+||.|.+...+ ..+...+..  +...+.        +    ........++|||+||++.+++++|+++|++
T Consensus       178 kgKnRGFAFVeF~s~edA-a~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~  256 (578)
T TIGR01648       178 KKKNRGFAFVEYESHRAA-AMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSE  256 (578)
T ss_pred             cCccCceEEEEcCCHHHH-HHHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHh
Confidence            346899999999954444 333332221  111110        1    1111234578999999999999999999999


Q ss_pred             C--CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCC
Q 043064          113 Y--GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       113 ~--G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~  172 (196)
                      |  |.|+.|.++        ++||||+|.+.++|++|++.||+..|.|+.|+|.|++|....
T Consensus       257 f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       257 FKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             cCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcc
Confidence            9  999999775        469999999999999999999999999999999999886543

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.

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

Probab=99.72  E-value=8.1e-17  Score=140.20  Aligned_cols=83  Identities=27%  Similarity=0.398  Sum_probs=78.2

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||..+++++|+++|..||.|..+.|+.+..+|.++|||||+|.+.+.|..||..|||..|.|+.|.|.++.
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            35789999999999999999999999999999999998899999999999999999999999999999999999999986


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      ...
T Consensus       374 ~~~  376 (509)
T TIGR01642       374 VGA  376 (509)
T ss_pred             cCC
Confidence            543

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.71  E-value=1.1e-16  Score=133.25  Aligned_cols=138  Identities=22%  Similarity=0.346  Sum_probs=107.6

Q ss_pred             CCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC-------CCCCCCCCEEEEcCCCcc
Q 043064           28 SSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG-------PQRSIEGWIILVTGVHEE  100 (196)
Q Consensus        28 ~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~l~V~nLp~~  100 (196)
                      ..+++..+..++++    .+++++|||||.|.+. .++..+...++.....+...       ........+|||+|||..
T Consensus        26 ~~G~i~~v~i~~d~----~~g~s~g~afV~f~~~-~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~~~~~~l~v~~l~~~  100 (352)
T TIGR01661        26 SIGEIESCKLVRDK----VTGQSLGYGFVNYVRP-EDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKT  100 (352)
T ss_pred             ccCCEEEEEEEEcC----CCCccceEEEEEECcH-HHHHHHHhhcccEEECCeeEEEEeecccccccccceEEECCcccc
Confidence            44566667777776    3457999999999954 44444444555544433211       122345678999999999


Q ss_pred             CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEEEEcccCC
Q 043064          101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTVDWAFSNG  170 (196)
Q Consensus       101 ~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~~a~~~~  170 (196)
                      +++++|+.+|.+||.|..+.++.+..++.++|||||+|.+.++|+.||..|||..+.|  .+|.|.|+....
T Consensus       101 ~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       101 MTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             CCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            9999999999999999999999888788999999999999999999999999999877  578888886544

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

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.71  E-value=4.3e-17  Score=125.02  Aligned_cols=83  Identities=31%  Similarity=0.564  Sum_probs=80.1

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+..+|-|+||+.++++.+|.+||..||.|..|.|.+++.||.++|||||.|.+.++|.+||..|||+-+++-.|+|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            35788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 043064          167 FSN  169 (196)
Q Consensus       167 ~~~  169 (196)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            886

>PF00076 RRM_1: RNA recognition motif

Probab=99.70  E-value=1.3e-16  Score=102.08  Aligned_cols=70  Identities=26%  Similarity=0.601  Sum_probs=67.0

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      |||+|||+++|+.+|+++|++||.|..+.+..+ .++..+++|||+|.+.++|+.|+..|+|..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 6888999999999999999999999999999999885

(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 ....

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

Probab=99.70  E-value=1.8e-16  Score=139.75  Aligned_cols=122  Identities=24%  Similarity=0.396  Sum_probs=97.5

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCC----CCC-----C--------------------CCCCCCCCEEEEcCC
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTD----GGP-----G--------------------PQRSIEGWIILVTGV   97 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~----~~~-----~--------------------~~~~~~~~~l~V~nL   97 (196)
                      ..+++|||||.|.+.+.+.+ +...++.....    +..     .                    ......+.+|||+||
T Consensus       215 ~g~~~G~afV~F~~~e~A~~-Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl  293 (562)
T TIGR01628       215 SGRSRGFAFVNFEKHEDAAK-AVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNL  293 (562)
T ss_pred             CCCcccEEEEEECCHHHHHH-HHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCC
Confidence            45789999999995544433 33344433332    110     0                    001234678999999


Q ss_pred             CccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064           98 HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus        98 p~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      ++.+++++|+++|+.||.|.+|.++.+ .+|.++|||||+|.+.++|.+|+..||+..|+|++|.|.||..+.
T Consensus       294 ~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~  365 (562)
T TIGR01628       294 DDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKE  365 (562)
T ss_pred             CCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcH
Confidence            999999999999999999999999998 689999999999999999999999999999999999999988653

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

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

Probab=99.69  E-value=2.1e-16  Score=115.71  Aligned_cols=78  Identities=19%  Similarity=0.456  Sum_probs=72.6

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+||+..+++.+|+.+|..||+|..|+|-..+     .|||||+|.++.+|+.|+..|+|..|.|..|+|++..-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            6789999999999999999999999999999987655     89999999999999999999999999999999999876


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      .+.
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            554

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.69  E-value=9.8e-17  Score=132.13  Aligned_cols=117  Identities=24%  Similarity=0.378  Sum_probs=92.4

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCC----CC----------CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhcc
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGT----DG----------GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGE  112 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~----~~----------~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~  112 (196)
                      ..+++||+||+|. ....+.++...+-....    ..          .+........+.|||+||+.++|++.|+++|.+
T Consensus       204 k~KNRGFaFveYe-~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~  282 (506)
T KOG0117|consen  204 KTKNRGFAFVEYE-SHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNE  282 (506)
T ss_pred             cccccceEEEEee-cchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHh
Confidence            5588999999999 45555555544332211    11          111122334689999999999999999999999


Q ss_pred             CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCC
Q 043064          113 YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       113 ~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~  172 (196)
                      ||.|..|..++|        ||||+|.+.++|.+|++.+|++.|+|..|.|.+|+|....
T Consensus       283 ~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  283 FGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             ccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhh
Confidence            999999987744        9999999999999999999999999999999999886543

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=7.9e-17  Score=132.19  Aligned_cols=142  Identities=22%  Similarity=0.321  Sum_probs=110.3

Q ss_pred             CCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC-------C---CCCCCCEEEEcCCC
Q 043064           29 SSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP-------Q---RSIEGWIILVTGVH   98 (196)
Q Consensus        29 ~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~---~~~~~~~l~V~nLp   98 (196)
                      -.-+..+-.+|+++++    .++|++||.|.....+.+......+.....+...|       .   .....++|||+.|+
T Consensus        58 yg~V~einl~kDk~t~----~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFvg~ls  133 (510)
T KOG0144|consen   58 YGNVYEINLIKDKSTG----QSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERIVEERKLFVGMLS  133 (510)
T ss_pred             hCceeEEEeecccccC----cccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhccccchhhhhhhcc
Confidence            3446678889999665    79999999999555544433333333333332222       1   12236789999999


Q ss_pred             ccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCC--cEeEEEEcccCCCCCCC
Q 043064           99 EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE-LLT--QTLTVDWAFSNGPSTGP  175 (196)
Q Consensus        99 ~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-l~g--~~l~v~~a~~~~~~~~~  175 (196)
                      +.+||.+++++|++||.|++|.|+++ ..+.+||||||.|.+.+.|..||+.||+.. +.|  .+|.|.||.++.++...
T Consensus       134 K~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~  212 (510)
T KOG0144|consen  134 KQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGK  212 (510)
T ss_pred             ccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchHH
Confidence            99999999999999999999999998 488999999999999999999999999974 665  68999999998876443

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.68  E-value=1.2e-16  Score=123.80  Aligned_cols=135  Identities=22%  Similarity=0.376  Sum_probs=110.2

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-------CCCCCCCCCCEEEEcCCCccCcH
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGG-------PGPQRSIEGWIILVTGVHEEAQE  103 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~l~V~nLp~~~te  103 (196)
                      ...+.+.+|++++|    .+-|||||.|.+ ..++..+...++++.+...       ...........|||++||+.+|.
T Consensus        67 eiEScKLvRDKitG----qSLGYGFVNYv~-p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtq  141 (360)
T KOG0145|consen   67 EIESCKLVRDKITG----QSLGYGFVNYVR-PKDAEKAINTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQ  141 (360)
T ss_pred             ceeeeeeeeccccc----cccccceeeecC-hHHHHHHHhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchH
Confidence            34467778888765    688999999994 5555555667777655432       22334566788999999999999


Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEEEEcccCC
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTVDWAFSNG  170 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~~a~~~~  170 (196)
                      .+|+.+|++||.|..-+|+.+..+|.++|.+||.|....+|+.||+.|||..-.|  .+|.|.||....
T Consensus       142 kelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPs  210 (360)
T KOG0145|consen  142 KELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPS  210 (360)
T ss_pred             HHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcc
Confidence            9999999999999988999998999999999999999999999999999998655  589999986443

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.67  E-value=2.5e-16  Score=109.80  Aligned_cols=82  Identities=22%  Similarity=0.465  Sum_probs=77.5

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..+++|||+||+..++|++|.++|+++|+|..|.|-.++.+..+.|||||+|.+.++|+.|++-++++.|+.++|++.|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            45789999999999999999999999999999999999989999999999999999999999999999999999999986


Q ss_pred             cc
Q 043064          167 FS  168 (196)
Q Consensus       167 ~~  168 (196)
                      ..
T Consensus       114 ~G  115 (153)
T KOG0121|consen  114 AG  115 (153)
T ss_pred             cc
Confidence            43

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

Probab=99.66  E-value=6.3e-16  Score=136.27  Aligned_cols=136  Identities=21%  Similarity=0.309  Sum_probs=104.6

Q ss_pred             CCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC--------C-CCCCCCCEEEEcCCCc
Q 043064           29 SSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG--------P-QRSIEGWIILVTGVHE   99 (196)
Q Consensus        29 ~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~-~~~~~~~~l~V~nLp~   99 (196)
                      .+++..+..+++.    .+++++|||||.|.+...+.+ +...++.....+.+.        + .......+|||+|||.
T Consensus        24 ~G~v~~v~v~~d~----~t~~s~G~afV~F~~~~~A~~-Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~   98 (562)
T TIGR01628        24 FGPVLSVRVCRDS----VTRRSLGYGYVNFQNPADAER-ALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDK   98 (562)
T ss_pred             cCCEEEEEEEecC----CCCCcceEEEEEECCHHHHHH-HHHHhCCCEECCeeEEeecccccccccccCCCceEEcCCCc
Confidence            3455677777776    446899999999995444444 444444332222211        1 1122346799999999


Q ss_pred             cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064          100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       100 ~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      ++++++|+++|+.||.|..|.++.+ .+|+++|||||+|.+.++|..|+..|||..+.++.|.|....++.
T Consensus        99 ~~~~~~L~~~F~~~G~i~~~~i~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~  168 (562)
T TIGR01628        99 SVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKH  168 (562)
T ss_pred             cCCHHHHHHHHHhcCCcceeEeeec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccccc
Confidence            9999999999999999999999887 488899999999999999999999999999999999998765543

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

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=1.1e-15  Score=128.76  Aligned_cols=83  Identities=22%  Similarity=0.580  Sum_probs=76.7

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|.|.|||+.+...+|+.+|+.||.|..|.|+..+ .|+.+|||||+|....+|..||+.+|+..|+|++|-|.||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            36889999999999999999999999999999999664 56667999999999999999999999999999999999998


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      ++..
T Consensus       195 ~Kd~  198 (678)
T KOG0127|consen  195 DKDT  198 (678)
T ss_pred             cccc
Confidence            8764

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.64  E-value=4.5e-15  Score=116.93  Aligned_cols=89  Identities=26%  Similarity=0.351  Sum_probs=82.5

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+-+||||+.|+.+++|..|+..|..||+|+.|.|+.++.||+++|||||+|.+..+...|.+..+|..|+|+.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccCCCCCC
Q 043064          166 AFSNGPSTG  174 (196)
Q Consensus       166 a~~~~~~~~  174 (196)
                      -....-++|
T Consensus       178 ERgRTvkgW  186 (335)
T KOG0113|consen  178 ERGRTVKGW  186 (335)
T ss_pred             ccccccccc
Confidence            766555444

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.63  E-value=4.6e-15  Score=95.30  Aligned_cols=70  Identities=26%  Similarity=0.586  Sum_probs=64.6

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      |||+|||+++++++|.++|+.||.|..+.+..++. +..+++|||+|.+.++|..|+..+++..|+|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999875 89999999999999999999999999999999874

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 ....

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.62  E-value=2e-15  Score=115.41  Aligned_cols=83  Identities=23%  Similarity=0.305  Sum_probs=75.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ....-++|||++|+|.+..+.|+++|.+||+|.+..++.|+.+|+++||+||+|.+.++|++|++- .+..|+|++..|.
T Consensus         8 ~DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcn   86 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCN   86 (247)
T ss_pred             CCceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccc
Confidence            344568899999999999999999999999999999999999999999999999999999999963 6678999998887


Q ss_pred             Eccc
Q 043064          165 WAFS  168 (196)
Q Consensus       165 ~a~~  168 (196)
                      +|.-
T Consensus        87 lA~l   90 (247)
T KOG0149|consen   87 LASL   90 (247)
T ss_pred             hhhh
Confidence            7643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.60  E-value=8.5e-15  Score=115.12  Aligned_cols=77  Identities=19%  Similarity=0.324  Sum_probs=70.8

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+.+++.+|+++|+.||.|.+|.|+.+..   .+|||||+|.+.++|+.||. |+|..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            57899999999999999999999999999999987753   46899999999999999995 999999999999999864


Q ss_pred             C
Q 043064          169 N  169 (196)
Q Consensus       169 ~  169 (196)
                      -
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            3

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=4.7e-15  Score=122.31  Aligned_cols=151  Identities=16%  Similarity=0.227  Sum_probs=112.4

Q ss_pred             CcCCccCCCCCCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCC--CCCCCCCCCEEEEc
Q 043064           18 DEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGP--GPQRSIEGWIILVT   95 (196)
Q Consensus        18 ded~~~~~d~~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~V~   95 (196)
                      .||+....-+..++.-.++.+.++++|    .+|||+||.|.+.+. +..+...++...+..+.  +-.-+...++|||+
T Consensus        96 ~EdeLvplfEkiG~I~elRLMmD~~sG----~nRGYAFVtf~~Ke~-Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG  170 (506)
T KOG0117|consen   96 FEDELVPLFEKIGKIYELRLMMDPFSG----DNRGYAFVTFCTKEE-AQEAIKELNNYEIRPGKLLGVCVSVANCRLFIG  170 (506)
T ss_pred             cchhhHHHHHhccceeeEEEeecccCC----CCcceEEEEeecHHH-HHHHHHHhhCccccCCCEeEEEEeeecceeEec
Confidence            344445555566677778888888665    789999999995444 44455677776554322  22346678999999


Q ss_pred             CCCccCcHHHHHHhhccCCC-eeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCcEeEEEEcccCCC
Q 043064           96 GVHEEAQEDDLQNVFGEYGE-IRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLTVDWAFSNGP  171 (196)
Q Consensus        96 nLp~~~te~~L~~~F~~~G~-i~~v~i~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~--~~l~g~~l~v~~a~~~~~  171 (196)
                      |||++.++++|.+.|++.++ |..|.+.... ...+++|||||+|.++..|..|-..|-.  ..|-|..+.|.||.|...
T Consensus       171 ~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e  250 (506)
T KOG0117|consen  171 NIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEE  250 (506)
T ss_pred             cCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccC
Confidence            99999999999999999865 5566554443 3468999999999999999999877643  347899999999998775


Q ss_pred             CC
Q 043064          172 ST  173 (196)
Q Consensus       172 ~~  173 (196)
                      ..
T Consensus       251 ~d  252 (506)
T KOG0117|consen  251 PD  252 (506)
T ss_pred             CC
Confidence            43

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

Probab=99.59  E-value=6.2e-15  Score=128.97  Aligned_cols=81  Identities=31%  Similarity=0.449  Sum_probs=76.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+++++|+++|.+||.|.+|.|+.++.+++++|||||+|.+.++|++|++.|||..|.|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999998654


Q ss_pred             c
Q 043064          168 S  168 (196)
Q Consensus       168 ~  168 (196)
                      .
T Consensus       186 ~  186 (612)
T TIGR01645       186 N  186 (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.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.58  E-value=4.5e-14  Score=109.61  Aligned_cols=84  Identities=30%  Similarity=0.518  Sum_probs=79.4

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..++.|||-||.++..|..|+.+|+.||.|..|++++|..+.+.+||+||...+-++|..||..|||+.++++.|.|.|.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34789999999999999999999999999999999999988999999999999999999999999999999999999997


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      ..+.
T Consensus       356 tnk~  359 (360)
T KOG0145|consen  356 TNKA  359 (360)
T ss_pred             cCCC
Confidence            6654

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.57  E-value=1.6e-14  Score=106.96  Aligned_cols=80  Identities=23%  Similarity=0.382  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||.++.+.+|.++|.+||.|..|.|...   -....||||+|++..+|+.||..-+|+.++|+.|+|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4678999999999999999999999999999987532   2236799999999999999999999999999999999987


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      .-.
T Consensus        82 ggr   84 (241)
T KOG0105|consen   82 GGR   84 (241)
T ss_pred             CCC
Confidence            654

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.56  E-value=6.7e-16  Score=113.79  Aligned_cols=83  Identities=33%  Similarity=0.511  Sum_probs=77.9

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .-.++..|||+|||..+||.+|.-+|++||+|..|.+++++.||+++||||+.|.+..+-..|+..|||..|.|+.|+|.
T Consensus        31 ~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVD  110 (219)
T KOG0126|consen   31 EYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVD  110 (219)
T ss_pred             hcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEee
Confidence            44567889999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      ...
T Consensus       111 Hv~  113 (219)
T KOG0126|consen  111 HVS  113 (219)
T ss_pred             ecc
Confidence            644

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

Probab=99.56  E-value=1.4e-14  Score=126.44  Aligned_cols=139  Identities=16%  Similarity=0.258  Sum_probs=100.0

Q ss_pred             CCCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCC-C-CCCCCCCCCCEEEEcCCCccCcHH
Q 043064           27 ASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDG-G-PGPQRSIEGWIILVTGVHEEAQED  104 (196)
Q Consensus        27 ~~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~l~V~nLp~~~te~  104 (196)
                      ....++..+..+++     .+++++||+||.|. ..+++..+...++...... . .....+...++|||+|||+.++++
T Consensus        80 ~~~G~I~~vrl~~D-----~sG~sRGfaFV~F~-~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~~~rLFVgNLP~~~Tee  153 (578)
T TIGR01648        80 EKAGPIYELRLMMD-----FSGQNRGYAFVTFC-GKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKRE  153 (578)
T ss_pred             HhhCCEEEEEEEEC-----CCCCccceEEEEeC-CHHHHHHHHHHcCCCeecCCccccccccccCceeEeecCCcchhhH
Confidence            34455555655566     25589999999999 4555554555666544421 1 112234557899999999999999


Q ss_pred             HHHHhhccCCC-eeEEEE-eecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCcEeEEEEcccCCC
Q 043064          105 DLQNVFGEYGE-IRNLHL-NLDRRTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       105 ~L~~~F~~~G~-i~~v~i-~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~l~g~~l~v~~a~~~~~  171 (196)
                      +|.++|++++. +..+.+ ......++++|||||+|.++++|..|+..|+.  ..|.|+.|.|.|+.+...
T Consensus       154 eL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~  224 (578)
T TIGR01648       154 EILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEE  224 (578)
T ss_pred             HHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccc
Confidence            99999999864 344333 23334567899999999999999999988764  358899999999987653

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.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.56  E-value=4.7e-15  Score=112.46  Aligned_cols=92  Identities=27%  Similarity=0.465  Sum_probs=84.9

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .....++|||++|...+++.-|...|-.||.|..|.++.+..+++++||+||+|...++|..||..||...|-|+.|+|.
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcccCCCCCCCC
Q 043064          165 WAFSNGPSTGPF  176 (196)
Q Consensus       165 ~a~~~~~~~~~~  176 (196)
                      ||+|..-..+++
T Consensus        86 ~AkP~kikegsq   97 (298)
T KOG0111|consen   86 LAKPEKIKEGSQ   97 (298)
T ss_pred             ecCCccccCCCC
Confidence            999877654443

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.55  E-value=3.3e-14  Score=115.01  Aligned_cols=135  Identities=27%  Similarity=0.275  Sum_probs=110.2

Q ss_pred             CCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC---C---------------CCCCCC
Q 043064           29 SSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP---Q---------------RSIEGW   90 (196)
Q Consensus        29 ~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~---------------~~~~~~   90 (196)
                      .+|..++.-.=++    .+.++|||+||+|+ ....+.++...+++.-..++..+   +               ....-.
T Consensus       137 FGPIKSInMSWDp----~T~kHKgFAFVEYE-vPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fn  211 (544)
T KOG0124|consen  137 FGPIKSINMSWDP----ATGKHKGFAFVEYE-VPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN  211 (544)
T ss_pred             CCCcceeeccccc----ccccccceEEEEEe-CcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhh
Confidence            3444444444455    45699999999999 77777788888887665553221   1               122357


Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      +|||..+++++++.+|+..|..||+|..|.+-+.+..+.++||+||+|.+......|+..||-+.|+|+.|+|..+-.
T Consensus       212 RiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  212 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             eEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            899999999999999999999999999999999988889999999999999999999999999999999999976543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.55  E-value=2e-14  Score=120.15  Aligned_cols=78  Identities=22%  Similarity=0.373  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCH--HHHHHHHHHhCCceeCCcEeEEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF--EEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~--~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ...+|||+||++.+++++|..+|+.||.|..|.|+  +.+|  +|||||+|.+.  .++.+||..|||..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            45789999999999999999999999999999998  4577  89999999987  789999999999999999999998


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8664

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.53  E-value=7.4e-14  Score=116.58  Aligned_cols=135  Identities=21%  Similarity=0.299  Sum_probs=108.4

Q ss_pred             CCCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC--CCCCCCCEEEEcCCCccCcHH
Q 043064           27 ASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP--QRSIEGWIILVTGVHEEAQED  104 (196)
Q Consensus        27 ~~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~V~nLp~~~te~  104 (196)
                      ..++++++++.+|+. |      +-||||+.|.+...+.+ +...++-....+.+..  ....+...|||.||++.++..
T Consensus        20 ~~~~~v~s~rvc~d~-t------slgy~yvnf~~~~da~~-A~~~~n~~~~~~~~~rim~s~rd~~~~~i~nl~~~~~~~   91 (369)
T KOG0123|consen   20 SPAGPVLSIRVCRDA-T------SLGYAYVNFQQPADAER-ALDTMNFDVLKGKPIRIMWSQRDPSLVFIKNLDESIDNK   91 (369)
T ss_pred             cccCCceeEEEeecC-C------ccceEEEecCCHHHHHH-HHHHcCCcccCCcEEEeehhccCCceeeecCCCcccCcH
Confidence            356788999999996 3      88999999995555444 4456666555554321  112223339999999999999


Q ss_pred             HHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCC
Q 043064          105 DLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       105 ~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~  172 (196)
                      .|.++|+.||+|.+|.+..+. +| ++|| ||+|.+.+.|.+|+..+||..+.++.|.|.....+..+
T Consensus        92 ~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   92 SLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             HHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            999999999999999999884 66 7999 99999999999999999999999999999888776543

>smart00362 RRM_2 RNA recognition motif

Probab=99.53  E-value=8.5e-14  Score=88.40  Aligned_cols=72  Identities=33%  Similarity=0.640  Sum_probs=66.5

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      +|||+|||..++..+|+.+|.+||.|..+.+..+.  +.++++|||+|.+.+.|+.|+..+++..+.|+.|.|.
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            48999999999999999999999999999888764  6778999999999999999999999999999998873

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=4.5e-14  Score=112.62  Aligned_cols=81  Identities=17%  Similarity=0.304  Sum_probs=74.4

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|+|+|||+...+.||+.+|.+||.|.+|.|+.+- - -++||+||+|.+.++|++|-..|||..|.|++|.|..|..
T Consensus        96 pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE-R-GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATa  173 (376)
T KOG0125|consen   96 PKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE-R-GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATA  173 (376)
T ss_pred             CceeEeecCCccccCccHHHHHHhhCceeeEEEEecc-C-CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccch
Confidence            5789999999999999999999999999999999762 3 3589999999999999999999999999999999999887


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      +-.
T Consensus       174 rV~  176 (376)
T KOG0125|consen  174 RVH  176 (376)
T ss_pred             hhc
Confidence            654

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

Probab=99.51  E-value=1.1e-13  Score=119.13  Aligned_cols=83  Identities=24%  Similarity=0.392  Sum_probs=77.1

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||..+++.+|+++|++||.|..|.|+.++.+++++|||||+|.+.++|.+||. |+|..|.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            4457899999999999999999999999999999999999899999999999999999999995 899999999999998


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      +...
T Consensus       165 ~~~~  168 (457)
T TIGR01622       165 SQAE  168 (457)
T ss_pred             cchh
Confidence            7543

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.51  E-value=1.3e-13  Score=106.92  Aligned_cols=76  Identities=17%  Similarity=0.281  Sum_probs=68.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      .+++|||+||++.+|+.+|+++|+.||.|.+|.|+.+.   ...+||||+|.+.+.++.|+ .|+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            46899999999999999999999999999999999774   33579999999999999999 699999999999997643

>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=8.1e-14  Score=108.62  Aligned_cols=86  Identities=30%  Similarity=0.526  Sum_probs=81.4

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .......+||+-|.+.++-+.|++.|.+||+|.++++++|..|++++||+||.|.+.++|+.||..|||.-|+++.|+-.
T Consensus        58 t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTN  137 (321)
T KOG0148|consen   58 TSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTN  137 (321)
T ss_pred             ccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecc
Confidence            33446779999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      ||..++
T Consensus       138 WATRKp  143 (321)
T KOG0148|consen  138 WATRKP  143 (321)
T ss_pred             ccccCc
Confidence            998887

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.50  E-value=1.6e-13  Score=92.50  Aligned_cols=79  Identities=20%  Similarity=0.417  Sum_probs=71.9

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ...|||.|||..+|.+++.++|.+||.|..|+|-..+   ..+|-|||.|++..+|.+|+..|+|+-+.++.|.|.|..+
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            6789999999999999999999999999999986443   4489999999999999999999999999999999998766


Q ss_pred             CC
Q 043064          169 NG  170 (196)
Q Consensus       169 ~~  170 (196)
                      ..
T Consensus        95 ~~   96 (124)
T KOG0114|consen   95 ED   96 (124)
T ss_pred             HH
Confidence            43

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

Probab=99.49  E-value=1.4e-13  Score=119.29  Aligned_cols=80  Identities=23%  Similarity=0.378  Sum_probs=69.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCC--eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE-----
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGE--IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT-----  160 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~--i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~-----  160 (196)
                      ++.+|||+|||..+++++|+++|+.||.  |..+.+.... ++ .+++|||+|.+.++|..||..||++.|.++.     
T Consensus       393 ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~  470 (481)
T TIGR01649       393 PSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPY  470 (481)
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccc
Confidence            4578999999999999999999999998  7888775432 33 4789999999999999999999999999885     


Q ss_pred             -eEEEEcccC
Q 043064          161 -LTVDWAFSN  169 (196)
Q Consensus       161 -l~v~~a~~~  169 (196)
                       |+|.|++++
T Consensus       471 ~lkv~fs~~~  480 (481)
T TIGR01649       471 HLKVSFSTSR  480 (481)
T ss_pred             eEEEEeccCC
Confidence             999998664

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).

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.49  E-value=8.2e-14  Score=112.24  Aligned_cols=87  Identities=25%  Similarity=0.376  Sum_probs=81.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.+.|||-.|.+.+|.++|.-+|+.||.|.+|.+++++.||.+..||||+|.+.++++.|.-.|++..|+.+.|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            44556889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.+-..
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            9776543

>smart00360 RRM RNA recognition motif

Probab=99.49  E-value=2e-13  Score=86.29  Aligned_cols=71  Identities=35%  Similarity=0.649  Sum_probs=66.4

Q ss_pred             EcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           94 VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        94 V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      |+|||..+++++|+.+|.+||.|..+.+..++.++.++++|||+|.+.+.|..|+..+++..+.|+.|.|.
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            57999999999999999999999999998887778899999999999999999999999999999998873

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=4.4e-13  Score=113.23  Aligned_cols=84  Identities=29%  Similarity=0.442  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh-----CC-ceeCCcE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM-----NG-GELLTQT  160 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l-----~~-~~l~g~~  160 (196)
                      ..+.+|||.|||+++|++.|...|++||+|..+.|+.++.|+.++|.|||.|.+..+|..||...     .+ ..|.|+.
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            34689999999999999999999999999999999999999999999999999999999999875     23 5689999


Q ss_pred             eEEEEcccCC
Q 043064          161 LTVDWAFSNG  170 (196)
Q Consensus       161 l~v~~a~~~~  170 (196)
                      |+|..|.++.
T Consensus       370 Lkv~~Av~Rk  379 (678)
T KOG0127|consen  370 LKVTLAVTRK  379 (678)
T ss_pred             EeeeeccchH
Confidence            9999887664

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

Probab=99.47  E-value=2.9e-13  Score=107.20  Aligned_cols=80  Identities=33%  Similarity=0.555  Sum_probs=76.8

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ..+|||+|||..+++++|.++|..||.|..+.+..++.++..+|||||.|.+.+.|..|+..+++..|.|+.|.|.++.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58999999999999999999999999999999999988999999999999999999999999999999999999999754

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.47  E-value=9.6e-14  Score=102.45  Aligned_cols=81  Identities=28%  Similarity=0.365  Sum_probs=77.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ....+|||+||+..++++.|.++|-+.|+|..+.++.++.+...+|||||+|.+.++|+-|++.||...|.|++|+|..+
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            34678999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             c
Q 043064          167 F  167 (196)
Q Consensus       167 ~  167 (196)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            6

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

Probab=99.46  E-value=4.6e-13  Score=116.10  Aligned_cols=78  Identities=31%  Similarity=0.435  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      .++++|||+||++ .+|+++|+.+|+.||.|..|.|+.++     +|||||+|.+.++|..||..|||..|.|+.|+|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3678999999998 69999999999999999999998764     68999999999999999999999999999999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      ++..
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8654

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).

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.46  E-value=1.2e-13  Score=108.69  Aligned_cols=115  Identities=19%  Similarity=0.299  Sum_probs=92.2

Q ss_pred             cCcccccCCCcHHHHHHhhhhcccC-----CCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecC
Q 043064           51 KGRGFREEADSERHSRLADRNFESL-----GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDR  125 (196)
Q Consensus        51 kG~gf~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~  125 (196)
                      |.||||..+ ...+++-+...++..     .++....+.++...++|+|+||.+.++..+|+..|.+||++.+|.|+   
T Consensus        36 KNYgFVHiE-dktaaedairNLhgYtLhg~nInVeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv---  111 (346)
T KOG0109|consen   36 KNYGFVHIE-DKTAAEDAIRNLHGYTLHGVNINVEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV---  111 (346)
T ss_pred             cccceEEee-cccccHHHHhhcccceecceEEEEEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeee---
Confidence            579999887 333444333433333     33333344556678999999999999999999999999999999998   


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCCCC
Q 043064          126 RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG  174 (196)
Q Consensus       126 ~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~~~  174 (196)
                           ++|+||.|.-.++|..|++.|+|.++.|++++|+.+.++-....
T Consensus       112 -----kdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtap  155 (346)
T KOG0109|consen  112 -----KDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAP  155 (346)
T ss_pred             -----cceeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCC
Confidence                 55999999999999999999999999999999999887755433

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.46  E-value=1.5e-13  Score=116.13  Aligned_cols=82  Identities=30%  Similarity=0.468  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +...|||+||++++++..|+.+|..||.|..|.+.++..+|.++||+||+|.+.+.|.+|++.|||..|-|+.|+|....
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            33449999999999999999999999999999999998899999999999999999999999999999999999998655


Q ss_pred             cC
Q 043064          168 SN  169 (196)
Q Consensus       168 ~~  169 (196)
                      -+
T Consensus       357 ~r  358 (549)
T KOG0147|consen  357 ER  358 (549)
T ss_pred             ee
Confidence            43

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.46  E-value=2.3e-13  Score=114.94  Aligned_cols=83  Identities=29%  Similarity=0.478  Sum_probs=79.5

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ..|||+|||+++++++|..+|+..|.|.+++++.|+.+|+.+||+|++|.+.+.|..|+..|||..+.|++|+|.|+...
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            78999999999999999999999999999999999999999999999999999999999999999999999999999766


Q ss_pred             CCC
Q 043064          170 GPS  172 (196)
Q Consensus       170 ~~~  172 (196)
                      ...
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            543

>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=99.45  E-value=1.2e-12  Score=83.52  Aligned_cols=74  Identities=31%  Similarity=0.640  Sum_probs=67.9

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      +|+|+|||+.+++++|+.+|..+|.|..+.+..+..+ ..+++|||+|.+.+.|..|+..+++..+.|+.|.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999877533 6789999999999999999999999999999999875

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).

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

Probab=99.43  E-value=7.8e-13  Score=115.28  Aligned_cols=81  Identities=17%  Similarity=0.300  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCcc--C--------cHHHHHHhhccCCCeeEEEEeecC---CCCCcceEEEEEecCHHHHHHHHHHhCCc
Q 043064           88 EGWIILVTGVHEE--A--------QEDDLQNVFGEYGEIRNLHLNLDR---RTGFVKGYALIEYENFEEAQNAITAMNGG  154 (196)
Q Consensus        88 ~~~~l~V~nLp~~--~--------te~~L~~~F~~~G~i~~v~i~~~~---~~g~~~g~afv~f~~~~~a~~al~~l~~~  154 (196)
                      +..+|+|.||...  +        ..++|+.+|.+||.|..|.|+.+.   .++...|++||+|.+.++|++||..|||.
T Consensus       408 ~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr  487 (509)
T TIGR01642       408 PTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGR  487 (509)
T ss_pred             CceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCC
Confidence            5678999999642  1        236789999999999999998652   34566799999999999999999999999


Q ss_pred             eeCCcEeEEEEccc
Q 043064          155 ELLTQTLTVDWAFS  168 (196)
Q Consensus       155 ~l~g~~l~v~~a~~  168 (196)
                      .|+|+.|.|.|...
T Consensus       488 ~~~gr~v~~~~~~~  501 (509)
T TIGR01642       488 KFNDRVVVAAFYGE  501 (509)
T ss_pred             EECCeEEEEEEeCH
Confidence            99999999999754

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

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.40  E-value=5.6e-13  Score=115.48  Aligned_cols=120  Identities=25%  Similarity=0.436  Sum_probs=93.6

Q ss_pred             CcCcccccCCCcHHHHHHhhhhcccCCCCCC----------------CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccC
Q 043064           50 TKGRGFREEADSERHSRLADRNFESLGTDGG----------------PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEY  113 (196)
Q Consensus        50 ~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~  113 (196)
                      +.|||||+|.+.+.+.. +...+++..+.+.                ........+++|.|.|||+..+-.+++.+|..|
T Consensus       559 SmGfgFVEF~~~e~A~~-a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aF  637 (725)
T KOG0110|consen  559 SMGFGFVEFAKPESAQA-ALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAF  637 (725)
T ss_pred             ccceeEEEecCHHHHHH-HHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcc
Confidence            55999999995554433 2233332222211                111222236799999999999999999999999


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064          114 GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       114 G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      |.|..|+|+.....+.++|||||.|-++.+|.+|+..|.++-|.|+.|.++||....
T Consensus       638 GqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  638 GQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             cceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            999999998765567789999999999999999999999888999999999997654

>PF13893 RRM_5: RNA recognition motif

Probab=99.36  E-value=4.9e-12  Score=77.69  Aligned_cols=56  Identities=30%  Similarity=0.699  Sum_probs=50.6

Q ss_pred             HHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064          106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus       106 L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      |..+|++||.|..+.+....     +++|||+|.+.++|..|+..||+..+.|++|+|.||
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            67899999999999987553     589999999999999999999999999999999986

(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 ....

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.36  E-value=7.1e-13  Score=107.34  Aligned_cols=77  Identities=32%  Similarity=0.491  Sum_probs=74.7

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      -++|||+.|.+.+.|+.|+..|..||+|++|.+.+|+.|++++|||||+|.-++.|+.|++.|||..++|+.|+|..
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999974

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.35  E-value=3.5e-12  Score=103.57  Aligned_cols=134  Identities=15%  Similarity=0.307  Sum_probs=100.4

Q ss_pred             cccccccccCCCCCCCcCcccccCCCcHHHHH-Hhhh--hcccCCCCCCC--------CCCCCCCCCEEEEcCCCccCcH
Q 043064           35 QPKLKSAITGGAPKKTKGRGFREEADSERHSR-LADR--NFESLGTDGGP--------GPQRSIEGWIILVTGVHEEAQE  103 (196)
Q Consensus        35 ~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~-~~~~--~~~~~~~~~~~--------~~~~~~~~~~l~V~nLp~~~te  103 (196)
                      .-.+++.    .+++++||||+.|........ +...  .+.+.......        .........+|||++||.++++
T Consensus        36 ~~vm~d~----~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e  111 (311)
T KOG4205|consen   36 CVVMRDP----STGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTE  111 (311)
T ss_pred             EEEeccC----CCCCcccccceecCCCcchheeecccccccCCccccceeccCcccccccccccceeEEEecCcCCCCch
Confidence            3445555    567999999999984443332 2211  11221111111        1112223569999999999999


Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCCC
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPST  173 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~~  173 (196)
                      .+|+.+|.+||.|..+.++.+..+..++||+||.|.+.+.+.+++. ..-+.|.++.+.|..|.|+.-..
T Consensus       112 ~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  112 EDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             HHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhcc
Confidence            9999999999999999999999999999999999999999999985 47788999999999999987553

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.33  E-value=2.1e-12  Score=101.73  Aligned_cols=73  Identities=22%  Similarity=0.409  Sum_probs=68.6

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      .+|||+|||..+++.+|+.+|.+||+|.+|.|++        .|+||..++...++.||..||+++|+|..|+|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvK--------NYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVK--------NYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeec--------ccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            3599999999999999999999999999999995        48999999999999999999999999999999998877


Q ss_pred             C
Q 043064          170 G  170 (196)
Q Consensus       170 ~  170 (196)
                      .
T Consensus        75 s   75 (346)
T KOG0109|consen   75 S   75 (346)
T ss_pred             C
Confidence            4

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.33  E-value=6.2e-12  Score=95.97  Aligned_cols=83  Identities=19%  Similarity=0.406  Sum_probs=75.0

Q ss_pred             CCCCEEEEcCCCccCcHHHHHH----hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQN----VFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~----~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .+..+|||.||+..+..++|+.    +|++||.|..|...   .+.+.+|.|||.|.+.+.|-.|+..|+|..+.|++++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999988888    99999999998765   4778899999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |+||+.+.+.
T Consensus        84 iqyA~s~sdi   93 (221)
T KOG4206|consen   84 IQYAKSDSDI   93 (221)
T ss_pred             eecccCccch
Confidence            9999988765

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.31  E-value=1.4e-11  Score=99.25  Aligned_cols=83  Identities=24%  Similarity=0.415  Sum_probs=74.3

Q ss_pred             CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH-hCCceeCC
Q 043064           80 GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA-MNGGELLT  158 (196)
Q Consensus        80 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~-l~~~~l~g  158 (196)
                      ...|++.....+|||++|...+++.+|+++|.+||+|.++.+...      +++|||+|.+.++|+.|... ++...|+|
T Consensus       219 ~lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G  292 (377)
T KOG0153|consen  219 TLEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVING  292 (377)
T ss_pred             ccCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecc
Confidence            355777888899999999999999999999999999999988765      56899999999999999876 56667999


Q ss_pred             cEeEEEEccc
Q 043064          159 QTLTVDWAFS  168 (196)
Q Consensus       159 ~~l~v~~a~~  168 (196)
                      ++|+|.|+.+
T Consensus       293 ~Rl~i~Wg~~  302 (377)
T KOG0153|consen  293 FRLKIKWGRP  302 (377)
T ss_pred             eEEEEEeCCC
Confidence            9999999988

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=5e-12  Score=104.27  Aligned_cols=85  Identities=27%  Similarity=0.439  Sum_probs=76.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eC--CcEeEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE-LL--TQTLTV  163 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-l~--g~~l~v  163 (196)
                      .+.-++||+-||..++|.+|+.+|.+||.|.+|.|++|+.++.++|||||.|.+.++|.+|+..||+.. |-  ..+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            445679999999999999999999999999999999999999999999999999999999999999876 43  578999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .||.....
T Consensus       112 k~Ad~E~e  119 (510)
T KOG0144|consen  112 KYADGERE  119 (510)
T ss_pred             cccchhhh
Confidence            99876543

>smart00361 RRM_1 RNA recognition motif

Probab=99.30  E-value=1.6e-11  Score=78.97  Aligned_cols=61  Identities=25%  Similarity=0.488  Sum_probs=54.6

Q ss_pred             HHHHHHhhc----cCCCeeEEE-EeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064          103 EDDLQNVFG----EYGEIRNLH-LNLDRRT--GFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus       103 e~~L~~~F~----~~G~i~~v~-i~~~~~~--g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      +++|+++|+    +||.|.++. ++.++.+  +.++||+||.|.+.++|.+|+..|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            567888888    999999985 6666656  889999999999999999999999999999999986

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=7.3e-12  Score=97.77  Aligned_cols=88  Identities=25%  Similarity=0.369  Sum_probs=82.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      +..++|.|||..||......+|...|-.||.|.+.++..|+.|..+++|+||.|.++.+|+.||..|||+.|+=++|+|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      +.+|+...
T Consensus       361 LKRPkdan  368 (371)
T KOG0146|consen  361 LKRPKDAN  368 (371)
T ss_pred             hcCccccC
Confidence            99887654

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.24  E-value=3.7e-11  Score=90.51  Aligned_cols=87  Identities=25%  Similarity=0.358  Sum_probs=78.6

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEY-GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~-G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      ++.......+||..+|..+.+..|..+|.+| |.+..+++.+++.||.++|||||+|.+.+.|..|.+.||++.|.++.|
T Consensus        43 ~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL  122 (214)
T KOG4208|consen   43 KPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLL  122 (214)
T ss_pred             CCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhee
Confidence            3344456679999999999999999999998 788888888999999999999999999999999999999999999999


Q ss_pred             EEEEcccC
Q 043064          162 TVDWAFSN  169 (196)
Q Consensus       162 ~v~~a~~~  169 (196)
                      .|.+-.|.
T Consensus       123 ~c~vmppe  130 (214)
T KOG4208|consen  123 ECHVMPPE  130 (214)
T ss_pred             eeEEeCch
Confidence            99988665

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.24  E-value=3.8e-11  Score=99.36  Aligned_cols=79  Identities=24%  Similarity=0.398  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGE-YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..+.+||+|||.++.+.+|+++|.. .|+|+.|.++.| .+|+.+|+|.|+|++++.+++|++.||.+.+.|++|.|.-.
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            3456999999999999999999985 799999999999 59999999999999999999999999999999999999754


Q ss_pred             c
Q 043064          167 F  167 (196)
Q Consensus       167 ~  167 (196)
                      .
T Consensus       122 ~  122 (608)
T KOG4212|consen  122 H  122 (608)
T ss_pred             C
Confidence            3

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.21  E-value=5.5e-11  Score=99.42  Aligned_cols=136  Identities=23%  Similarity=0.348  Sum_probs=105.5

Q ss_pred             CCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-------------------------CC
Q 043064           28 SSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGG-------------------------PG   82 (196)
Q Consensus        28 ~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------~~   82 (196)
                      ..++..++..+++.     ..+++||||+.|.+ ...+..+...++.......                         ..
T Consensus       190 ~~g~i~s~~v~~~~-----~g~~~~~gfv~f~~-~e~a~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~  263 (369)
T KOG0123|consen  190 AYGSITSVAVMRDS-----IGKSKGFGFVNFEN-PEDAKKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAK  263 (369)
T ss_pred             ccCcceEEEEeecC-----CCCCCCccceeecC-hhHHHHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhh
Confidence            33445566666664     55699999999995 4444434444444333210                         01


Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      +........|||.||+..++...|..+|+.||.|..+.|+.+ ..++++||+||.|.+.++|..|+..+|+..+.+++|.
T Consensus       264 ~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~-~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~  342 (369)
T KOG0123|consen  264 RSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD-ENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLY  342 (369)
T ss_pred             ccccccccccccccCccccchhHHHHHHhcccceeeEEEEec-cCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchh
Confidence            223566788999999999999999999999999999999887 5899999999999999999999999999999999999


Q ss_pred             EEEcccCC
Q 043064          163 VDWAFSNG  170 (196)
Q Consensus       163 v~~a~~~~  170 (196)
                      |.++..+.
T Consensus       343 vav~qr~~  350 (369)
T KOG0123|consen  343 VAVAQRKE  350 (369)
T ss_pred             hhHHhhhc
Confidence            99987433

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.14  E-value=1.1e-10  Score=102.34  Aligned_cols=82  Identities=28%  Similarity=0.562  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      +.-++||||+.|+..+++.+|..+|..||+|.+|.++..      +++|||......+|.+|+..|+++.+.++.|+|.|
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            334799999999999999999999999999999988765      78999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 043064          166 AFSNGPST  173 (196)
Q Consensus       166 a~~~~~~~  173 (196)
                      |..+..+.
T Consensus       492 a~g~G~ks  499 (894)
T KOG0132|consen  492 AVGKGPKS  499 (894)
T ss_pred             eccCCcch
Confidence            98877664

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.11  E-value=2.3e-10  Score=94.77  Aligned_cols=80  Identities=20%  Similarity=0.290  Sum_probs=71.7

Q ss_pred             CCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           82 GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      .+......++|+|.|||.++|++.|++-|..||.|....|+   .+|+.+|  .|.|.++++|++|+..|++..|+|+.|
T Consensus       529 a~gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I  603 (608)
T KOG4212|consen  529 AVGAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNI  603 (608)
T ss_pred             cccccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCcee
Confidence            34456678899999999999999999999999999999884   5677776  899999999999999999999999999


Q ss_pred             EEEEc
Q 043064          162 TVDWA  166 (196)
Q Consensus       162 ~v~~a  166 (196)
                      +|.|.
T Consensus       604 ~V~y~  608 (608)
T KOG4212|consen  604 KVTYF  608 (608)
T ss_pred             eeeeC
Confidence            99874

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.10  E-value=9.7e-10  Score=93.83  Aligned_cols=87  Identities=23%  Similarity=0.375  Sum_probs=79.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .+.-++.|||++|...+...+|+.+|++||.|+-..++.+..+.-.++|+||++.+..+|.+||..||.+.|.|+.|.|.
T Consensus       401 rs~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVE  480 (940)
T KOG4661|consen  401 RSTLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVE  480 (940)
T ss_pred             ccccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeee
Confidence            45567899999999999999999999999999999999887777779999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      .++..+.
T Consensus       481 kaKNEp~  487 (940)
T KOG4661|consen  481 KAKNEPG  487 (940)
T ss_pred             ecccCcc
Confidence            8876543

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.08  E-value=7.4e-10  Score=93.33  Aligned_cols=82  Identities=26%  Similarity=0.347  Sum_probs=68.9

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ..+|||.|||.+++..+|+++|.+||.|+...|..-...++..+|+||+|.+.+.++.||.. +-..|++++|.|..-++
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            45599999999999999999999999999987765433344449999999999999999975 56779999999998766


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      ...
T Consensus       367 ~~~  369 (419)
T KOG0116|consen  367 GFR  369 (419)
T ss_pred             ccc
Confidence            543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=99.00  E-value=1.5e-09  Score=85.19  Aligned_cols=80  Identities=23%  Similarity=0.393  Sum_probs=73.8

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|+|.|||..++..+|+++|..||.+..+.+.+++ +|.+.|.|-|.|...++|..|++.||+..|+|++|++....+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            4779999999999999999999999999999999985 899999999999999999999999999999999999986554


Q ss_pred             C
Q 043064          169 N  169 (196)
Q Consensus       169 ~  169 (196)
                      .
T Consensus       162 ~  162 (243)
T KOG0533|consen  162 P  162 (243)
T ss_pred             c
Confidence            3

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.99  E-value=6e-10  Score=90.64  Aligned_cols=85  Identities=20%  Similarity=0.357  Sum_probs=76.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||++|+|.++++.|++.|.+||+|..|.++.++.++.++||+||+|.+.+....+|. ...+.|+|+.|.+.-|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            56889999999999999999999999999999999999999999999999999888888874 35677999999999888


Q ss_pred             cCCCCC
Q 043064          168 SNGPST  173 (196)
Q Consensus       168 ~~~~~~  173 (196)
                      ++....
T Consensus        84 ~r~~~~   89 (311)
T KOG4205|consen   84 SREDQT   89 (311)
T ss_pred             Cccccc
Confidence            876543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.96  E-value=2.1e-09  Score=93.63  Aligned_cols=76  Identities=20%  Similarity=0.425  Sum_probs=69.4

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTG---FVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g---~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      |||.||++.+|...|..+|..+|.|..+.|...+...   .+.|||||+|.+.++|+.|++.|+|+.|+|+.|.|.++.
T Consensus       518 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  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999999999999999999999999887664322   245999999999999999999999999999999999998

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.95  E-value=3.5e-09  Score=83.12  Aligned_cols=87  Identities=22%  Similarity=0.374  Sum_probs=79.6

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+...+||+|+...+|...+...|..||.|..+.|+.++.++.++||+||+|.+.+.++.++. |++..|.|+.+.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            456678889999999999999999999999999999999999888999999999999999999998 9999999999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .+.....+
T Consensus       175 t~~r~~~p  182 (231)
T KOG4209|consen  175 TLKRTNVP  182 (231)
T ss_pred             eeeeeecC
Confidence            98776643

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.92  E-value=1.5e-08  Score=77.51  Aligned_cols=86  Identities=20%  Similarity=0.271  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CcEeE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLD-RRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQTLT  162 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~---g~~l~  162 (196)
                      ...++|||++||.++...+|..+|..|-..+.+.|... +.....+-+||+.|.+.+.|..|+..|||..++   ++.|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34789999999999999999999999866666555432 222234579999999999999999999999986   78999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      +.+|++....
T Consensus       112 iElAKSNtK~  121 (284)
T KOG1457|consen  112 IELAKSNTKR  121 (284)
T ss_pred             eeehhcCccc
Confidence            9999887754

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.91  E-value=3e-09  Score=83.34  Aligned_cols=83  Identities=25%  Similarity=0.469  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eC--CcEeEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE-LL--TQTLTVD  164 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-l~--g~~l~v~  164 (196)
                      +.++|||+.|.+.-.|++++.+|..||.|.+|.+.+.. .|.++|++||.|.+.-+|+.||..|||.. +-  ...|.|.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            46789999999999999999999999999999998874 88899999999999999999999999875 33  4679999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.....
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            9976654

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.90  E-value=2.9e-09  Score=82.01  Aligned_cols=73  Identities=25%  Similarity=0.493  Sum_probs=67.0

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ..+||++||+.+.+.+|..||..||.|..+.+.        .||+||+|.+..+|..|+.-||+..|.|..+.|.|+...
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            459999999999999999999999999998875        578999999999999999999999999988999999764


Q ss_pred             C
Q 043064          170 G  170 (196)
Q Consensus       170 ~  170 (196)
                      .
T Consensus        74 ~   74 (216)
T KOG0106|consen   74 R   74 (216)
T ss_pred             c
Confidence            3

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.83  E-value=1.4e-08  Score=82.00  Aligned_cols=80  Identities=28%  Similarity=0.322  Sum_probs=72.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      ..+.|||+|||.++|-+++.++|+++|-|.        .|.|..+. .|..+|=|+|.|...++++.|++.|++..|.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            356799999999999999999999999875        37787774 699999999999999999999999999999999


Q ss_pred             EeEEEEccc
Q 043064          160 TLTVDWAFS  168 (196)
Q Consensus       160 ~l~v~~a~~  168 (196)
                      .|+|+.|+-
T Consensus       212 ~~rVerAkf  220 (382)
T KOG1548|consen  212 KLRVERAKF  220 (382)
T ss_pred             EEEEehhhh
Confidence            999987753

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

Probab=98.82  E-value=4.9e-08  Score=66.28  Aligned_cols=79  Identities=16%  Similarity=0.284  Sum_probs=69.6

Q ss_pred             CEEEEcCCCccCcHHHHHHhhcc--CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC----CcEeEE
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGE--YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL----TQTLTV  163 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~--~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~----g~~l~v  163 (196)
                      ++|.|+|||...|...|.+++..  .|..-.+.++.|..++-+.|||||.|.+++.|..-...++|..+.    .+.+.|
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            68999999999999999998875  366777888999888999999999999999999999999999874    577888


Q ss_pred             EEccc
Q 043064          164 DWAFS  168 (196)
Q Consensus       164 ~~a~~  168 (196)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88854

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

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.75  E-value=1.7e-08  Score=88.20  Aligned_cols=81  Identities=15%  Similarity=0.343  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR---TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~---~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ..+.|||+||++.+++..|-..|+.||+|..+.|++.+.   ....+-++||.|-+..+|++|++.|+|..+.+..+++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            468899999999999999999999999999999987752   23455689999999999999999999999999999999


Q ss_pred             Eccc
Q 043064          165 WAFS  168 (196)
Q Consensus       165 ~a~~  168 (196)
                      |+++
T Consensus       253 Wgk~  256 (877)
T KOG0151|consen  253 WGKA  256 (877)
T ss_pred             cccc
Confidence            9843

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.70  E-value=1.2e-08  Score=86.96  Aligned_cols=73  Identities=23%  Similarity=0.527  Sum_probs=66.5

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ...+..+|+|-|||..+++++|..+|+.||+|+.|..-..+     +|..||+|.+..+|+.|++.|++..+.|+.|+
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            46678899999999999999999999999999997654443     88999999999999999999999999999988

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.61  E-value=3.5e-07  Score=77.18  Aligned_cols=118  Identities=19%  Similarity=0.320  Sum_probs=83.4

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCC----------------CCCCCCCCCCCCEEEEcCCCccCcHHHHHHhh
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTD----------------GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVF  110 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F  110 (196)
                      ..|..|-+||++.+.+............+...                ....+..+.....|-+.+||+.||+++|.+||
T Consensus        45 ~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FF  124 (510)
T KOG4211|consen   45 NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFF  124 (510)
T ss_pred             CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHh
Confidence            46788999999996665544332211111100                01122233456789999999999999999999


Q ss_pred             ccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064          111 GEYGEIRN-LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus       111 ~~~G~i~~-v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +..-.+.. +.++.++ .+++.|-|||+|++.+.|++||.. |...|+.+-|.|..+
T Consensus       125 aGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  125 AGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             cCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            98744444 4556664 677899999999999999999964 777899998888643

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.51  E-value=5e-08  Score=74.46  Aligned_cols=79  Identities=19%  Similarity=0.191  Sum_probs=70.6

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ..+|||.|+...++++-|.++|-+-|+|..|.|...+ .++.+ ||||.|.+.-...-|+..+||..+.+..|.|.+-..
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            5789999999999999999999999999999998775 56656 999999999999999999999999999998876543


Q ss_pred             C
Q 043064          169 N  169 (196)
Q Consensus       169 ~  169 (196)
                      .
T Consensus        87 ~   87 (267)
T KOG4454|consen   87 N   87 (267)
T ss_pred             C
Confidence            3

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.46  E-value=7.7e-07  Score=73.63  Aligned_cols=75  Identities=28%  Similarity=0.482  Sum_probs=68.4

Q ss_pred             CCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           89 GWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        89 ~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ...|.|.||... +|.+.|..+|+.||.|.+|.|..++     +-.|+|+|.+...|+.|+..|+|+.|.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            577889999775 9999999999999999999999875     4569999999999999999999999999999999986


Q ss_pred             c
Q 043064          168 S  168 (196)
Q Consensus       168 ~  168 (196)
                      -
T Consensus       372 H  372 (492)
T KOG1190|consen  372 H  372 (492)
T ss_pred             C
Confidence            3

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.45  E-value=2.3e-07  Score=72.31  Aligned_cols=85  Identities=19%  Similarity=0.335  Sum_probs=76.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ......+||.+-|.-.++.+.|...|.+|-......+++++.+|+++||+||.|.+..++..|+..|+|..++.++|++.
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            34557889999999999999999999999877778889999999999999999999999999999999999999999876


Q ss_pred             EcccC
Q 043064          165 WAFSN  169 (196)
Q Consensus       165 ~a~~~  169 (196)
                      -...+
T Consensus       266 kS~wk  270 (290)
T KOG0226|consen  266 KSEWK  270 (290)
T ss_pred             hhhHH
Confidence            54433

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.45  E-value=3.2e-07  Score=70.77  Aligned_cols=73  Identities=21%  Similarity=0.408  Sum_probs=64.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....+.|.|.|++..+.+.+|.+.|..+|++....+.        .+++||+|...++|.+||..|++..+.++.|.+.+
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh--------ccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            4557889999999999999999999999998554442        67899999999999999999999999999999954


Q ss_pred             c
Q 043064          166 A  166 (196)
Q Consensus       166 a  166 (196)
                      .
T Consensus       168 ~  168 (216)
T KOG0106|consen  168 N  168 (216)
T ss_pred             c
Confidence            4

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=98.43  E-value=1.7e-06  Score=73.11  Aligned_cols=80  Identities=21%  Similarity=0.300  Sum_probs=67.9

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .....|-+.+|||.+|+++|.+||+.+ .|..+.+.  +.+|+..|-|||+|.+.+++++|++ .+...++.+.|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~--r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIP--RRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEe--ccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            345668889999999999999999998 57775544  4589999999999999999999997 4888899999999877


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      .+..
T Consensus        84 ~~~e   87 (510)
T KOG4211|consen   84 GGAE   87 (510)
T ss_pred             CCcc
Confidence            6554

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.43  E-value=2.1e-07  Score=79.82  Aligned_cols=84  Identities=27%  Similarity=0.393  Sum_probs=78.0

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ...+.+||++||-.+++.++.+++..||.+....++.+..+|.++||||.+|.+......|+..|||..+++++|.|+.|
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            34688999999999999999999999999999999999888999999999999999999999999999999999999987


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      ....
T Consensus       367 ~~g~  370 (500)
T KOG0120|consen  367 IVGA  370 (500)
T ss_pred             hccc
Confidence            6543

>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=98.37  E-value=1.7e-06  Score=56.51  Aligned_cols=68  Identities=16%  Similarity=0.364  Sum_probs=46.1

Q ss_pred             CEEEEcCCCccCcHHHHH----HhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           90 WIILVTGVHEEAQEDDLQ----NVFGEYG-EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~----~~F~~~G-~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ..|+|.|||.+.....++    .++..+| .|..|.          .+.|+|.|.+.+.|.+|++.|+|..+.|..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999988876554    4555664 555541          3569999999999999999999999999999999


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      |..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            973

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.36  E-value=1.9e-06  Score=69.86  Aligned_cols=83  Identities=22%  Similarity=0.277  Sum_probs=75.3

Q ss_pred             CCEEE-EcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           89 GWIIL-VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        89 ~~~l~-V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++| |++|+..+++++|+.+|..+|.|..+.++.+..++...||+||.|.+...+..++.. +...+.+.++.+.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            45566 999999999999999999999999999999999999999999999999999999876 7888999999999998


Q ss_pred             cCCCC
Q 043064          168 SNGPS  172 (196)
Q Consensus       168 ~~~~~  172 (196)
                      +.+..
T Consensus       263 ~~~~~  267 (285)
T KOG4210|consen  263 PRPKS  267 (285)
T ss_pred             CCccc
Confidence            87654

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.36  E-value=1.7e-05  Score=59.38  Aligned_cols=71  Identities=20%  Similarity=0.379  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 043064           80 GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL  157 (196)
Q Consensus        80 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~  157 (196)
                      ...++.......|.|++||+..++++|+++..+-|.|....+.++       |.+.|+|...++.+-|+..|....+.
T Consensus       106 ~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  106 RRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            445666667788999999999999999999999999998887765       47899999999999999999887653

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.33  E-value=6e-07  Score=73.12  Aligned_cols=87  Identities=26%  Similarity=0.351  Sum_probs=78.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL  156 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l  156 (196)
                      ......+|||-+||..+++++|.++|.++|.|.        .|.|.+++.|+..++-|.|.|.+...|+.|+.-+++..+
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            344567899999999999999999999999874        367788889999999999999999999999999999999


Q ss_pred             CCcEeEEEEcccCCC
Q 043064          157 LTQTLTVDWAFSNGP  171 (196)
Q Consensus       157 ~g~~l~v~~a~~~~~  171 (196)
                      .+..|+|.+|..+..
T Consensus       142 ~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  142 CGNTIKVSLAERRTG  156 (351)
T ss_pred             cCCCchhhhhhhccC
Confidence            999999999887764

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.14  E-value=8.8e-07  Score=75.64  Aligned_cols=82  Identities=22%  Similarity=0.334  Sum_probs=74.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      +.....++|+.-|...++..+|.+||+.+|.|..|.|+.++.++.++|.+||+|.+.+....|| .|.|..+.|.+|.|+
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEec
Confidence            3445678999999989999999999999999999999999999999999999999999999999 699999999999998


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      ...
T Consensus       254 ~sE  256 (549)
T KOG0147|consen  254 LSE  256 (549)
T ss_pred             ccH
Confidence            643

>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=98.14  E-value=6.5e-06  Score=56.94  Aligned_cols=70  Identities=19%  Similarity=0.461  Sum_probs=43.7

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc-----eeCCcEeEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG-----ELLTQTLTV  163 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~-----~l~g~~l~v  163 (196)
                      ++.|+|.+++..++.++|+.+|+.||.|..|.+...      ...|||.|.+.+.|+.|+..+.-.     .|.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            357899999999999999999999999999888643      236899999999999999876433     456665555


Q ss_pred             E
Q 043064          164 D  164 (196)
Q Consensus       164 ~  164 (196)
                      .
T Consensus        75 ~   75 (105)
T PF08777_consen   75 E   75 (105)
T ss_dssp             E
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.14  E-value=1.2e-05  Score=61.78  Aligned_cols=77  Identities=21%  Similarity=0.387  Sum_probs=68.4

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CcEeEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL-TQTLTVD  164 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~-g~~l~v~  164 (196)
                      ..+...+|+.|||..++.+.|..+|.+|.....++++...     .+.|||+|.+...|..|...|++..|. ...+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            4567889999999999999999999999999999888665     789999999999999999999999987 7788888


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      ++.
T Consensus       218 ~a~  220 (221)
T KOG4206|consen  218 FAK  220 (221)
T ss_pred             ccC
Confidence            774

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.13  E-value=2.6e-06  Score=65.48  Aligned_cols=68  Identities=21%  Similarity=0.406  Sum_probs=55.7

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL  157 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~  157 (196)
                      ...+.+|||.||.++++|++|+.+|+.|-....++|.-  .+|  ...||++|.+.+.|..|+..|+|..|.
T Consensus       207 ~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~~g--~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  207 ARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA--RGG--MPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             chhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec--CCC--cceEeecHHHHHHHHHHHHHhhcceec
Confidence            33467899999999999999999999997766666542  234  347999999999999999999987753

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.08  E-value=1.3e-05  Score=65.07  Aligned_cols=86  Identities=21%  Similarity=0.431  Sum_probs=65.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHH----H--HHhhccCCCeeEEEEeecCCC-CCcceE--EEEEecCHHHHHHHHHHhCCce
Q 043064           85 RSIEGWIILVTGVHEEAQEDD----L--QNVFGEYGEIRNLHLNLDRRT-GFVKGY--ALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~----L--~~~F~~~G~i~~v~i~~~~~~-g~~~g~--afv~f~~~~~a~~al~~l~~~~  155 (196)
                      +.....-+||-+||+.+..++    |  .++|++||.|..|.+.+...+ ....++  .||+|.+.++|.+||...+|..
T Consensus       110 RVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~  189 (480)
T COG5175         110 RVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL  189 (480)
T ss_pred             eeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc
Confidence            344567789999988765544    3  589999999999887654211 111222  4999999999999999999999


Q ss_pred             eCCcEeEEEEcccCC
Q 043064          156 LLTQTLTVDWAFSNG  170 (196)
Q Consensus       156 l~g~~l~v~~a~~~~  170 (196)
                      ++|+.|+..|...+-
T Consensus       190 ~DGr~lkatYGTTKY  204 (480)
T COG5175         190 LDGRVLKATYGTTKY  204 (480)
T ss_pred             ccCceEeeecCchHH
Confidence            999999999876653

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.96  E-value=7.2e-06  Score=66.80  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=65.6

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ...+||+||-|++|.++|.+.+...|  .|.++++..++.+|.++|||+|...+....+..++.|...+|.|+.-.|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            45689999999999999988887765  4677888888899999999999999999999999999999999986555

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.82  E-value=6.5e-05  Score=64.77  Aligned_cols=75  Identities=29%  Similarity=0.535  Sum_probs=61.2

Q ss_pred             CCEEEEcCCCccCc------HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CcEe
Q 043064           89 GWIILVTGVHEEAQ------EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL-TQTL  161 (196)
Q Consensus        89 ~~~l~V~nLp~~~t------e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~-g~~l  161 (196)
                      ...|+|-|+|---.      ..-|..+|+++|+|..+.++.+..+| .+||.|++|.+...|+.|++.|||+.|+ .+.+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            45688888876322      25678899999999999998886555 8999999999999999999999999976 5566


Q ss_pred             EEE
Q 043064          162 TVD  164 (196)
Q Consensus       162 ~v~  164 (196)
                      .|.
T Consensus       137 ~v~  139 (698)
T KOG2314|consen  137 FVR  139 (698)
T ss_pred             Eee
Confidence            664

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.80  E-value=1.9e-05  Score=61.76  Aligned_cols=73  Identities=12%  Similarity=0.213  Sum_probs=60.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCC--------CCcc----eEEEEEecCHHHHHHHHHHhCCce
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRT--------GFVK----GYALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~--------g~~~----g~afv~f~~~~~a~~al~~l~~~~  155 (196)
                      ..-.||+++||+.+...-|+.+|+.||.|-.|.+-....+        |.+.    .-++|+|.+...|..+...|||..
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            5678999999999999999999999999998887544323        2222    236799999999999999999999


Q ss_pred             eCCcE
Q 043064          156 LLTQT  160 (196)
Q Consensus       156 l~g~~  160 (196)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.79  E-value=8.6e-05  Score=64.39  Aligned_cols=80  Identities=18%  Similarity=0.299  Sum_probs=64.6

Q ss_pred             CCCCCCCCCEEEEcCCCccCcHHHHHHhhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---C
Q 043064           82 GPQRSIEGWIILVTGVHEEAQEDDLQNVFGE-YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL---L  157 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l---~  157 (196)
                      .|.....++.|||.||-.-.|.-+|+.++.. .|.|... |+ |    +.+.+|||.|.+.++|...+..|||..+   +
T Consensus       437 SPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  437 SPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            3446667899999999999999999999996 5556655 32 2    1367899999999999999999999975   6


Q ss_pred             CcEeEEEEcc
Q 043064          158 TQTLTVDWAF  167 (196)
Q Consensus       158 g~~l~v~~a~  167 (196)
                      .+.|.+.|+.
T Consensus       511 PK~L~adf~~  520 (718)
T KOG2416|consen  511 PKHLIADFVR  520 (718)
T ss_pred             CceeEeeecc
Confidence            7888888764

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.69  E-value=0.00011  Score=44.31  Aligned_cols=52  Identities=21%  Similarity=0.439  Sum_probs=41.6

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHH
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI  148 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al  148 (196)
                      +.|-|.+.++...+. +...|.+||+|..+.+...      ..+.+|.|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            468899999886655 4558889999999887622      457999999999999985

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.66  E-value=0.00045  Score=57.07  Aligned_cols=81  Identities=23%  Similarity=0.351  Sum_probs=71.4

Q ss_pred             CCCCCCCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           84 QRSIEGWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ....+++.+.|.+|... ++-+-|..+|-.||.|..|.+++.+     .|-|.|+..+..+.++|+.-||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            44557899999999876 6778899999999999999999876     67899999999999999999999999999999


Q ss_pred             EEEcccC
Q 043064          163 VDWAFSN  169 (196)
Q Consensus       163 v~~a~~~  169 (196)
                      |.+++..
T Consensus       357 v~~SkQ~  363 (494)
T KOG1456|consen  357 VCVSKQN  363 (494)
T ss_pred             Eeecccc
Confidence            9887654

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.62  E-value=0.00045  Score=57.05  Aligned_cols=84  Identities=23%  Similarity=0.370  Sum_probs=67.3

Q ss_pred             CCCCCCCCCEEEEcCCCc--cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--
Q 043064           82 GPQRSIEGWIILVTGVHE--EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL--  157 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~--~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~--  157 (196)
                      ++....+.+.|.++-|.+  -+|-+-|..+....|+|..|.|.+.  +|.   .|.|+|.+.+.|++|...|||..|.  
T Consensus       113 g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsG  187 (494)
T KOG1456|consen  113 GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSG  187 (494)
T ss_pred             CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhccccccccc
Confidence            344455567777665554  4888999999999999999988654  444   5899999999999999999999974  


Q ss_pred             CcEeEEEEcccCC
Q 043064          158 TQTLTVDWAFSNG  170 (196)
Q Consensus       158 g~~l~v~~a~~~~  170 (196)
                      -+.|+|.||+|..
T Consensus       188 CCTLKIeyAkP~r  200 (494)
T KOG1456|consen  188 CCTLKIEYAKPTR  200 (494)
T ss_pred             ceeEEEEecCcce
Confidence            4789999998864

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.55  E-value=0.00024  Score=59.17  Aligned_cols=77  Identities=23%  Similarity=0.233  Sum_probs=63.2

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc-EeEEEEc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ-TLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~-~l~v~~a  166 (196)
                      ++.+|.++|+|+.++|++|+.+|..-|-..+....    -++.+-++++.+.+.+.|..|+..++++.++.. .|+|+|+
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFS  488 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFS  488 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEee
Confidence            46789999999999999999999988765443221    233356899999999999999999999998755 8999998


Q ss_pred             cc
Q 043064          167 FS  168 (196)
Q Consensus       167 ~~  168 (196)
                      ++
T Consensus       489 ks  490 (492)
T KOG1190|consen  489 KS  490 (492)
T ss_pred             cc
Confidence            65

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.51  E-value=0.00015  Score=65.57  Aligned_cols=80  Identities=30%  Similarity=0.387  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~  162 (196)
                      .....+.++|++|++++....|...|..||.|..|.+-    .|  ..|++|.|.+...++.|+..|-+..|++  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~----hg--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR----HG--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc----cC--CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            67788999999999999999999999999999998764    33  3599999999999999999999999986  6799


Q ss_pred             EEEcccCC
Q 043064          163 VDWAFSNG  170 (196)
Q Consensus       163 v~~a~~~~  170 (196)
                      |.|+.+..
T Consensus       525 vdla~~~~  532 (975)
T KOG0112|consen  525 VDLASPPG  532 (975)
T ss_pred             cccccCCC
Confidence            99987644

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.50  E-value=0.00044  Score=61.20  Aligned_cols=75  Identities=16%  Similarity=0.360  Sum_probs=64.6

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRN-LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      +.|-+.|+|++++-++|.+||..|-.+-. |.+.++ ..|+..|-|.|.|++.++|.+|...|++..|..+.++|.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            37788999999999999999999966543 444443 6899999999999999999999999999999999988764

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.50  E-value=4.6e-05  Score=68.42  Aligned_cols=110  Identities=16%  Similarity=0.243  Sum_probs=84.2

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCC
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR  126 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~  126 (196)
                      .++-+|.+|+.|-..........  +.....         .....|+|.|+|+..|.+.|+.+++.+|.++++.++.. .
T Consensus       705 ~~~~rG~~Y~~F~~~~~~~aaV~--f~d~~~---------~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r  772 (881)
T KOG0128|consen  705 EKRFRGKAYVEFLKPEHAGAAVA--FRDSCF---------FGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-R  772 (881)
T ss_pred             ccccccceeeEeecCCchhhhhh--hhhhhh---------hhhhhhheeCCCCCCchHHHHhhccccCCccccchhhh-h
Confidence            45678999999975444433211  111111         11456999999999999999999999999999988777 4


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064          127 TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus       127 ~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .|+++|.+||.|.+..++.+++.......+.-..+.|+.+.|
T Consensus       773 ~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  773 AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            899999999999999999999987777777767777776554

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.44  E-value=0.00053  Score=59.25  Aligned_cols=65  Identities=15%  Similarity=0.350  Sum_probs=53.3

Q ss_pred             HHHHHhhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRR---TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~---~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ++++.-+++||.|..|.++.+..   ..-..|-.||+|.+.+++++|+..|+|.++.++.+...|-..
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            45566678999999999987721   223456689999999999999999999999999999988654

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.33  E-value=0.00033  Score=58.69  Aligned_cols=71  Identities=25%  Similarity=0.468  Sum_probs=57.9

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeec---CCC--CC--------cceEEEEEecCHHHHHHHHHHh
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLD---RRT--GF--------VKGYALIEYENFEEAQNAITAM  151 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~---~~~--g~--------~~g~afv~f~~~~~a~~al~~l  151 (196)
                      ...++++|.+-|||.+-.-+.|.++|+.+|.|+.|+|...   ..+  +.        .+-+|+|+|...+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3467899999999999888999999999999999999766   222  11        1457999999999999999887


Q ss_pred             CCce
Q 043064          152 NGGE  155 (196)
Q Consensus       152 ~~~~  155 (196)
                      +...
T Consensus       307 ~~e~  310 (484)
T KOG1855|consen  307 NPEQ  310 (484)
T ss_pred             chhh
Confidence            5443

>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=97.33  E-value=0.0018  Score=44.29  Aligned_cols=77  Identities=18%  Similarity=0.148  Sum_probs=50.4

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEE-EeecC------CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc-E
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH-LNLDR------RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ-T  160 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~-i~~~~------~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~-~  160 (196)
                      .+.|.|-+.|+. ....+...|++||.|.+.. +..+.      .......+..|.|.++.+|.+||. .||..|.|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            456888899988 4567888999999997764 11000      001124588999999999999995 599999885 4


Q ss_pred             eEEEEcc
Q 043064          161 LTVDWAF  167 (196)
Q Consensus       161 l~v~~a~  167 (196)
                      +-|.+..
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            5566664

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.

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.24  E-value=0.0046  Score=50.66  Aligned_cols=84  Identities=19%  Similarity=0.331  Sum_probs=63.8

Q ss_pred             CCCCCCCCCEEEEcCCCc----cCc-------HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q 043064           82 GPQRSIEGWIILVTGVHE----EAQ-------EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA  150 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~----~~t-------e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~  150 (196)
                      .+......++|.|.||=.    ..+       .++|.+-..+||.|.+|.+.-.    -+.|.+-|.|.+.+.|..||+.
T Consensus       258 ~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~  333 (382)
T KOG1548|consen  258 DPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQT  333 (382)
T ss_pred             ccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHH
Confidence            345556678899998832    122       2455666778999999877521    1378899999999999999999


Q ss_pred             hCCceeCCcEeEEEEcccC
Q 043064          151 MNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus       151 l~~~~l~g~~l~v~~a~~~  169 (196)
                      |+|..++|+.|..+....+
T Consensus       334 m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  334 MDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             hcCeeecceEEEEEEeCCc
Confidence            9999999999998765433

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.16  E-value=0.00063  Score=56.37  Aligned_cols=78  Identities=23%  Similarity=0.294  Sum_probs=65.2

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCC-eeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGE-IRN--LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~--v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .....|-+++||...+.++|.++|..|.. |..  |.++.+ ..|...|-|||+|.+.+.|..|....+++....+.|.|
T Consensus       278 ~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEv  356 (508)
T KOG1365|consen  278 RSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEV  356 (508)
T ss_pred             CCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEE
Confidence            33567899999999999999999998854 333  667666 57899999999999999999999998888888888888


Q ss_pred             EE
Q 043064          164 DW  165 (196)
Q Consensus       164 ~~  165 (196)
                      --
T Consensus       357 fp  358 (508)
T KOG1365|consen  357 FP  358 (508)
T ss_pred             ee
Confidence            53

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.14  E-value=0.0027  Score=46.17  Aligned_cols=59  Identities=20%  Similarity=0.331  Sum_probs=45.3

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCC
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~  171 (196)
                      .+|...|..||.+.-++++.+        ..+|+|.+-+.|-+|+. ++|..+.|+.|+|....|.+-
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPDWL  109 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE------
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCccHH
Confidence            367788889999888887743        47999999999999994 899999999999998877764

; PDB: 1UFW_A 2DNR_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.98  E-value=0.0027  Score=54.46  Aligned_cols=67  Identities=18%  Similarity=0.300  Sum_probs=60.4

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHH
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFG-EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA  150 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~  150 (196)
                      +.-.+.+||||++||.-++..+|-.+|. -||.|..+-|-.|+.-+.++|-|-|+|.+..+-.+||..
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3445679999999999999999999999 599999999999988889999999999999999999964

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.81  E-value=0.0034  Score=53.91  Aligned_cols=63  Identities=19%  Similarity=0.381  Sum_probs=46.9

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCC---CCCcce---EEEEEecCHHHHHHHHHH
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR---TGFVKG---YALIEYENFEEAQNAITA  150 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~---~g~~~g---~afv~f~~~~~a~~al~~  150 (196)
                      .-.++|||++||++++|+.|...|..||.+. |.|+....   -.-++|   |+|+.|++......-|..
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            3468899999999999999999999999863 45542111   112455   999999998777766544

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.78  E-value=0.0014  Score=54.96  Aligned_cols=76  Identities=18%  Similarity=0.304  Sum_probs=59.7

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCCcEeEEEEccc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE-LLTQTLTVDWAFS  168 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-l~g~~l~v~~a~~  168 (196)
                      .++||+||.+.++..+|..+|...----+-.++..      .||+||.+.+...|.+|++.+++.. +.|+++.|.+.-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            35999999999999999999985411111112221      5899999999999999999999875 8999999998877


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      +..
T Consensus        76 kkq   78 (584)
T KOG2193|consen   76 KKQ   78 (584)
T ss_pred             HHH
Confidence            654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.67  E-value=0.0032  Score=52.38  Aligned_cols=75  Identities=19%  Similarity=0.368  Sum_probs=58.1

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE-EEc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR---TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV-DWA  166 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~---~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v-~~a  166 (196)
                      .|.|.||.+.+|.+++..||...|.|..+.|.....   .....-.|||.|.+...+..|.. |.++++-++-|.| -|+
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEecC
Confidence            699999999999999999999999999988764321   12345689999999999998875 6666655555444 443

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.48  E-value=0.0014  Score=51.59  Aligned_cols=61  Identities=18%  Similarity=0.331  Sum_probs=48.2

Q ss_pred             HHHHhhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064          105 DLQNVFG-EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus       105 ~L~~~F~-~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +|...|. +||+|..+.+..+. .--..|-+||.|...++|++|+..|||.-+.|++|...+.
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            4444445 89999988665432 2234677999999999999999999999999999998764

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.40  E-value=0.011  Score=49.32  Aligned_cols=73  Identities=19%  Similarity=0.237  Sum_probs=54.5

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccC----CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEY----GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~----G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .-.|-+++||+++++.++.++|..-    |....|.++.. .+|+..|-|||.|...++|+.||.. |...|+-+.|.+
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIEl  237 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIEL  237 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHH
Confidence            3456678999999999999999742    23445555554 4889999999999999999999964 555555544443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.33  E-value=0.00024  Score=64.00  Aligned_cols=69  Identities=20%  Similarity=0.268  Sum_probs=59.8

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL  157 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~  157 (196)
                      ..++||+||+..+.+.+|...|..+|.+..+.+..+...++.+|.||+.|...+.+.+|+....+..++
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            467899999999999999999999999888877766678999999999999999999999765555544

>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=96.31  E-value=0.0095  Score=45.06  Aligned_cols=81  Identities=12%  Similarity=0.167  Sum_probs=50.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhcc-CCCe---eEEEEeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCceeCC---
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGE-YGEI---RNLHLNLDRRT--GFVKGYALIEYENFEEAQNAITAMNGGELLT---  158 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~-~G~i---~~v~i~~~~~~--g~~~g~afv~f~~~~~a~~al~~l~~~~l~g---  158 (196)
                      ...+|.|++||+++|++++...++. ++..   ..+.-.....+  -....-|||.|.+.+++..-+..++|+.+..   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999987776 5554   22221111111  1234569999999999999999999987532   


Q ss_pred             --cEeEEEEccc
Q 043064          159 --QTLTVDWAFS  168 (196)
Q Consensus       159 --~~l~v~~a~~  168 (196)
                        ....|.+|--
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3566777643

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.25  E-value=0.0085  Score=47.26  Aligned_cols=61  Identities=20%  Similarity=0.289  Sum_probs=53.6

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM  151 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l  151 (196)
                      ..|||.||+..++.+.|...|+.||+|....+..| ..++..+-++|.|...-.|.+|+..+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~   92 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRC   92 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHh
Confidence            67999999999999999999999999988666666 36777888999999999999998776

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.22  E-value=0.018  Score=46.43  Aligned_cols=64  Identities=17%  Similarity=0.203  Sum_probs=50.4

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCc-ceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRRTGFV-KGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~~g~~-~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      .++++...+||.|..|.|...+..-.. ---.||+|...+.|.+|+--|||..++|+.++..|-.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            466777789999999887665432211 1237999999999999999999999999999887754

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.18  E-value=0.03  Score=36.76  Aligned_cols=56  Identities=18%  Similarity=0.337  Sum_probs=42.0

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG  153 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~  153 (196)
                      .+..+|+ .|..+...+|..+|+.||.|. |.++-+       .-|||.....+.|..++..+..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            4666776 999999999999999999974 455543       2599999999999999988764

; 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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.04  E-value=0.046  Score=33.89  Aligned_cols=55  Identities=24%  Similarity=0.318  Sum_probs=43.5

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccC---CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEY---GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM  151 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~---G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l  151 (196)
                      ...|+|.++. +++.++++.+|..|   .....|.|+-|.       -|-|.|.+...|.+||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3569999985 57889999999988   234678888663       3679999999999999754

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.03  E-value=0.0057  Score=52.07  Aligned_cols=77  Identities=18%  Similarity=0.287  Sum_probs=60.9

Q ss_pred             CCCCEEEEcCCCccC-cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~-te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      .+.+.|-+.-.|+.+ +-.+|...|.+||.|..|.+-..      .-.|.|+|.+..+|-.|.. .++..|+++.|+|.|
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFW  442 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEE
Confidence            344556666666664 55899999999999999987544      3458999999999977764 689999999999999


Q ss_pred             cccCC
Q 043064          166 AFSNG  170 (196)
Q Consensus       166 a~~~~  170 (196)
                      -.+.+
T Consensus       443 hnps~  447 (526)
T KOG2135|consen  443 HNPSP  447 (526)
T ss_pred             ecCCc
Confidence            88744

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.00  E-value=0.0064  Score=54.13  Aligned_cols=75  Identities=13%  Similarity=0.046  Sum_probs=62.6

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRN-LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      +..|||..||..+++..+..+|+..-.|++ |.|... -+++.++.|||.|...+++..|+..-+.+.++.+.|+|.
T Consensus       434 g~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  434 GGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             cceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            678999999999999999999998666666 666555 377888999999999888888876667777888889986

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.96  E-value=0.0028  Score=51.74  Aligned_cols=84  Identities=23%  Similarity=0.323  Sum_probs=63.6

Q ss_pred             CCCCEEEEcCCCccCcHH-HH--HHhhccCCCeeEEEEeecCC----CCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           87 IEGWIILVTGVHEEAQED-DL--QNVFGEYGEIRNLHLNLDRR----TGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~-~L--~~~F~~~G~i~~v~i~~~~~----~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      .....+||-+|+..+..+ .|  ...|.+||.|..|.+..+..    .+. ..-++|+|...++|..||...+|..+.|+
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~-~~s~yITy~~~eda~rci~~v~g~~~dg~  153 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGG-TCSVYITYEEEEDADRCIDDVDGFVDDGR  153 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCC-CCcccccccchHhhhhHHHHhhhHHhhhh
Confidence            344668888888775443 33  36888999999998876541    122 22389999999999999999999999999


Q ss_pred             EeEEEEcccCCC
Q 043064          160 TLTVDWAFSNGP  171 (196)
Q Consensus       160 ~l~v~~a~~~~~  171 (196)
                      .|+..+..++-.
T Consensus       154 ~lka~~gttkyc  165 (327)
T KOG2068|consen  154 ALKASLGTTKYC  165 (327)
T ss_pred             hhHHhhCCCcch
Confidence            988887766653

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.87  E-value=0.067  Score=38.77  Aligned_cols=75  Identities=16%  Similarity=0.305  Sum_probs=55.8

Q ss_pred             CCCCCCEEEEcCCCccCcH----HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           85 RSIEGWIILVTGVHEEAQE----DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      ...+-.+|.|.-|..++..    ..+...++.||+|.+|.+.     |  +.-|.|.|.+..+|-.|+..++. ..-|..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            3455678888877666533    4455667789999998763     2  34599999999999999988876 556778


Q ss_pred             eEEEEcc
Q 043064          161 LTVDWAF  167 (196)
Q Consensus       161 l~v~~a~  167 (196)
                      +.+.|-.
T Consensus       154 ~qCsWqq  160 (166)
T PF15023_consen  154 FQCSWQQ  160 (166)
T ss_pred             EEeeccc
Confidence            8888754

>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=95.86  E-value=0.025  Score=43.00  Aligned_cols=63  Identities=17%  Similarity=0.184  Sum_probs=45.8

Q ss_pred             cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCcEeEEEEcccCC
Q 043064          102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN--GGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       102 te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~--~~~l~g~~l~v~~a~~~~  170 (196)
                      ....|+.+|..|+.+..+.++..      -+-..|.|.+.+.|..|...|+  +..+.|..|+|.|+.+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            34789999999999888766643      3347899999999999999999  899999999999996544

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.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.80  E-value=0.0027  Score=57.75  Aligned_cols=80  Identities=13%  Similarity=0.211  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      .+.+||++||+..+++.+|+..|..+|.|..|.|-... -+.-.-|+||.|.+..++..|+..+.+..|..-.+++.+..
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            46889999999999999999999999999999986553 33335589999999999999999999988877677777765


Q ss_pred             c
Q 043064          168 S  168 (196)
Q Consensus       168 ~  168 (196)
                      +
T Consensus       450 ~  450 (975)
T KOG0112|consen  450 P  450 (975)
T ss_pred             c
Confidence            4

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=95.58  E-value=0.0053  Score=47.44  Aligned_cols=109  Identities=18%  Similarity=0.259  Sum_probs=78.6

Q ss_pred             ccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcC----CCccCcHHHHHHhhccC
Q 043064           38 LKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTG----VHEEAQEDDLQNVFGEY  113 (196)
Q Consensus        38 ~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~te~~L~~~F~~~  113 (196)
                      +|..|..+.-.+.| |+||.|. .+-..-++...+++......+..      .+++-++    |...++++.+...|++-
T Consensus        37 ~kv~ip~~~d~~~k-Fa~v~f~-~E~sv~~a~~L~ng~~l~~~e~q------~~~r~G~shapld~r~~~ei~~~v~s~a  108 (267)
T KOG4454|consen   37 YKVGIPSGQDQEQK-FAYVFFP-NENSVQLAGQLENGDDLEEDEEQ------RTLRCGNSHAPLDERVTEEILYEVFSQA  108 (267)
T ss_pred             EEEeCCCCccCCCc-eeeeecc-cccchhhhhhhcccchhccchhh------cccccCCCcchhhhhcchhhheeeeccc
Confidence            44444444444556 9999998 45555666667776665543332      2355566    67788999999999999


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q 043064          114 GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus       114 G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  155 (196)
                      +++..+++..+. .|.++.+.|+.+.-....-.++....+..
T Consensus       109 ~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l~  149 (267)
T KOG4454|consen  109 GPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGLE  149 (267)
T ss_pred             CCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhcccC
Confidence            999999998875 58888899999988877777776665543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.33  E-value=0.0015  Score=54.89  Aligned_cols=112  Identities=19%  Similarity=0.292  Sum_probs=77.8

Q ss_pred             cCcccccCCCcHHHHHHhhhhcccCCCCCC-----CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEe-ec
Q 043064           51 KGRGFREEADSERHSRLADRNFESLGTDGG-----PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN-LD  124 (196)
Q Consensus        51 kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-~~  124 (196)
                      .||.|+...+..-+.+.....-....+.+.     ..-++...++++.|.|+|+...++-|..|+..||.+..|..+ .+
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~  116 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTD  116 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccc
Confidence            489999887444444322211111222221     112233346779999999999999999999999999888553 33


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064          125 RRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus       125 ~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..+.    ..-|+|...+.+..||..|++..+....++|.|.
T Consensus       117 ~eta----vvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen  117 SETA----VVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             hHHH----HHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            2221    2347899999999999999999999999999885

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=94.48  E-value=0.077  Score=46.22  Aligned_cols=82  Identities=18%  Similarity=0.209  Sum_probs=56.5

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhc-cCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---C-CcEeEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFG-EYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL---L-TQTLTV  163 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~-~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l---~-g~~l~v  163 (196)
                      .+++.|.|+|-..|-.-|.+.-. ..|.-..+.++.|-.+..+.|||||.|.+.+++....+.+||..+   + .+.+.+
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            34455566665544444333322 245555677777766777899999999999999999999999874   3 466778


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .||+-..
T Consensus       468 tYArIQG  474 (549)
T KOG4660|consen  468 TYARIQG  474 (549)
T ss_pred             ehhhhhc
Confidence            8876544

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.96  E-value=0.043  Score=48.68  Aligned_cols=73  Identities=10%  Similarity=0.072  Sum_probs=61.6

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      +...+..++||+|+...+...-++.++..+|.|..+...         -|+|+.|..+.....|+..++-..++|+.+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~---------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRD---------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhh---------hhcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            344456789999999999999999999999988776543         28999999999999999999988898888776


Q ss_pred             EE
Q 043064          164 DW  165 (196)
Q Consensus       164 ~~  165 (196)
                      .-
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            53

>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=93.76  E-value=1.6  Score=30.38  Aligned_cols=74  Identities=18%  Similarity=0.159  Sum_probs=49.7

Q ss_pred             CEEEEcCCCcc-CcHHHHHHhhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CcEeEEE
Q 043064           90 WIILVTGVHEE-AQEDDLQNVFGEY-GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQTLTVD  164 (196)
Q Consensus        90 ~~l~V~nLp~~-~te~~L~~~F~~~-G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~---g~~l~v~  164 (196)
                      ..|.|--+|+. ++-+.|..+.+.+ ..|..++|+++.  ..++-.+++.|.+...|..-...+||..++   ...++|-
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            44555455555 5555666555555 456778888763  224556889999999999999999999864   3445544


Q ss_pred             E
Q 043064          165 W  165 (196)
Q Consensus       165 ~  165 (196)
                      |
T Consensus        91 f   91 (110)
T PF07576_consen   91 F   91 (110)
T ss_pred             E
Confidence            4

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

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=93.76  E-value=0.043  Score=50.07  Aligned_cols=74  Identities=19%  Similarity=0.229  Sum_probs=61.3

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCcEeEEEEcccC
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE--LLTQTLTVDWAFSN  169 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~--l~g~~l~v~~a~~~  169 (196)
                      .++.|.+-..+-..|..+++.||.+.+.+.+++      ...|.|.|.+.+.|..|+..|+|..  ..|-+.+|.+|++-
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            444555557778899999999999999887766      3579999999999999999999997  45888999999876


Q ss_pred             CC
Q 043064          170 GP  171 (196)
Q Consensus       170 ~~  171 (196)
                      +-
T Consensus       375 ~~  376 (1007)
T KOG4574|consen  375 PM  376 (1007)
T ss_pred             cc
Confidence            53

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.75  E-value=0.26  Score=40.04  Aligned_cols=64  Identities=20%  Similarity=0.229  Sum_probs=47.3

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      ...|-|-+.|+.- -..|..+|++||.|.+....   .+   -.+.+|.|.+..+|++||. .||..|+|..
T Consensus       197 D~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~---~n---gNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP---SN---GNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             cceEEEeccCccc-hhHHHHHHHhhCeeeeeecC---CC---CceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            3456666777653 35577899999998775433   23   3489999999999999995 5888887753

>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=93.68  E-value=0.48  Score=30.29  Aligned_cols=67  Identities=16%  Similarity=0.353  Sum_probs=38.6

Q ss_pred             EEEEc-CCCccCcHHHHHHhhccCCC-----eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           91 IILVT-GVHEEAQEDDLQNVFGEYGE-----IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        91 ~l~V~-nLp~~~te~~L~~~F~~~G~-----i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ++||. +--..++..+|..++...+.     |-.|.|.        ..|+||+-.. +.|..++..|++..+.|++|+|.
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--------~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--------DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---------SS-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--------eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            35552 22335788889888887644     4456665        3378998874 57899999999999999999998


Q ss_pred             Ec
Q 043064          165 WA  166 (196)
Q Consensus       165 ~a  166 (196)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            65

; PDB: 2G0C_A 3MOJ_B.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=93.20  E-value=0.072  Score=43.40  Aligned_cols=81  Identities=14%  Similarity=0.015  Sum_probs=64.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..+++|++++.+.+.+.++..++..+|.+..+.+.....+..+++++++.|...+.+..|+.....+.+.+..+...+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999888899999987776665555678889999999999999999997655556666665554443


Q ss_pred             c
Q 043064          168 S  168 (196)
Q Consensus       168 ~  168 (196)
                      .
T Consensus       167 ~  167 (285)
T KOG4210|consen  167 R  167 (285)
T ss_pred             c
Confidence            3

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

Probab=92.97  E-value=0.23  Score=38.62  Aligned_cols=93  Identities=17%  Similarity=0.206  Sum_probs=57.3

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-----------------C--------------CCCCCCCCCEEEE
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFESLGTDGG-----------------P--------------GPQRSIEGWIILV   94 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~--------------~~~~~~~~~~l~V   94 (196)
                      .+++++|++|+.|.+ ...+..+...++.....+.                 .              ..........+++
T Consensus       152 ~~~~~~g~~~v~f~~-~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (306)
T COG0724         152 ETGKSRGFAFVEFES-EESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYV  230 (306)
T ss_pred             ccCccCceEEEEecC-HHHHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhccccccccccccccceeec
Confidence            356899999999994 4444434434432211110                 0              0112334678899


Q ss_pred             cCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEec
Q 043064           95 TGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE  139 (196)
Q Consensus        95 ~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~  139 (196)
                      .+++..++...+..+|..+|.+....+...........+.++.+.
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (306)
T COG0724         231 GNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNE  275 (306)
T ss_pred             cccccccchhHHHHhccccccceeeeccCCCCCcccccccccchh
Confidence            999999999999999999999977666554333333333333333

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=92.20  E-value=0.32  Score=42.62  Aligned_cols=70  Identities=11%  Similarity=0.184  Sum_probs=53.0

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhcc--CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCcEeE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGE--YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLT  162 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~--~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~l~g~~l~  162 (196)
                      ...+.|.|+-||..+..++++.||..  +-++++|.+-.+-       -=||+|.+..+|+.|.+.|.-  .+|.|++|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            34577778999999999999999985  6677888776442       148999999999999876643  236666654


Q ss_pred             E
Q 043064          163 V  163 (196)
Q Consensus       163 v  163 (196)
                      .
T Consensus       246 A  246 (684)
T KOG2591|consen  246 A  246 (684)
T ss_pred             h
Confidence            3

>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=91.33  E-value=1.4  Score=27.67  Aligned_cols=55  Identities=22%  Similarity=0.361  Sum_probs=42.0

Q ss_pred             cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064          100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus       100 ~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .++-.+++..+..|+- ..  |..++ +    | -||.|.+..+|++|....++..+.+..|.+
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-DR--IRDDR-T----G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-ce--EEecC-C----E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3577899999999953 33  33443 2    2 489999999999999999999887777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=91.00  E-value=0.96  Score=38.78  Aligned_cols=69  Identities=14%  Similarity=0.249  Sum_probs=56.7

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEY-GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT  158 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~-G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g  158 (196)
                      +++.|+|-.+|..++-.+|-.|...+ -.|..++|+++.. . ++=..+|.|.+..+|..-.+.+||..++.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~-p-nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM-P-NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC-C-ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            38899999999999999999998875 4688899998532 2 23346899999999999999999998653

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=90.50  E-value=0.26  Score=37.87  Aligned_cols=66  Identities=18%  Similarity=0.247  Sum_probs=41.7

Q ss_pred             cccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcCCCcc-CcHHHHHHhhcc-CCCe
Q 043064           39 KSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEE-AQEDDLQNVFGE-YGEI  116 (196)
Q Consensus        39 r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~te~~L~~~F~~-~G~i  116 (196)
                      |+.    .++.+||||||+|+ ....+.++...|+..-..+          +.|.+.=||+. .-+..+...+.. +..+
T Consensus        84 Rnk----rTGNSKgYAFVEFE-s~eVA~IaAETMNNYLl~e----------~lL~c~vmppe~~v~~~~~k~~~~~~~~~  148 (214)
T KOG4208|consen   84 RNK----RTGNSKGYAFVEFE-SEEVAKIAAETMNNYLLME----------HLLECHVMPPEQKVEKNLKKVSGTPFKPG  148 (214)
T ss_pred             ccc----ccCCcCceEEEEec-cHHHHHHHHHHhhhhhhhh----------heeeeEEeCchhhhhhhhhhhcCCcCCCC
Confidence            665    45689999999999 6777777777777765433          44666677776 444444433332 3444


Q ss_pred             eEE
Q 043064          117 RNL  119 (196)
Q Consensus       117 ~~v  119 (196)
                      ..+
T Consensus       149 ~~~  151 (214)
T KOG4208|consen  149 KTV  151 (214)
T ss_pred             Ccc
Confidence            333

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=86.77  E-value=0.33  Score=38.29  Aligned_cols=57  Identities=16%  Similarity=0.136  Sum_probs=32.1

Q ss_pred             CCCCcCCccCCCCCCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCC
Q 043064           15 DLMDEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLG   76 (196)
Q Consensus        15 d~~ded~~~~~d~~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~   76 (196)
                      ++|.|++.++.--.-++...+-..++.    .++.+|||+||.|.+ ..++..+...+++..
T Consensus       199 ed~~E~dL~eLf~~fg~i~rvylardK----~TG~~kGFAFVtF~s-RddA~rAI~~LnG~g  255 (270)
T KOG0122|consen  199 EDMREDDLEELFRPFGPITRVYLARDK----ETGLSKGFAFVTFES-RDDAARAIADLNGYG  255 (270)
T ss_pred             cccChhHHHHHhhccCccceeEEEEcc----ccCcccceEEEEEec-HHHHHHHHHHccCcc
Confidence            344444444433333444444445555    466899999999994 444444445555544

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=85.58  E-value=3.3  Score=33.57  Aligned_cols=47  Identities=13%  Similarity=0.106  Sum_probs=34.9

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCe-eEEEEeecCCCCCcceEEEEEecCH
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEI-RNLHLNLDRRTGFVKGYALIEYENF  141 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i-~~v~i~~~~~~g~~~g~afv~f~~~  141 (196)
                      ..-|+|+||+.++.-.+|+..+.+.+-+ .++.|.-      +.|-||++|.+.
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            3459999999999999999999886532 3444432      256799999764

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.56  E-value=4.2  Score=36.12  Aligned_cols=83  Identities=20%  Similarity=0.306  Sum_probs=61.4

Q ss_pred             CCCCCCCCEEEEcCCCcc-CcHHHHHHhhccC----CCeeEEEEeecC----------CCCC------------------
Q 043064           83 PQRSIEGWIILVTGVHEE-AQEDDLQNVFGEY----GEIRNLHLNLDR----------RTGF------------------  129 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~----G~i~~v~i~~~~----------~~g~------------------  129 (196)
                      |+....+++|-|-||.|+ +...+|..+|+.|    |.|.+|.|....          .+|.                  
T Consensus       168 ~~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~  247 (650)
T KOG2318|consen  168 PVLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDD  247 (650)
T ss_pred             cccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccch
Confidence            344556788999999997 7889999999876    578888765432          0111                  


Q ss_pred             -------------------cceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEEEE
Q 043064          130 -------------------VKGYALIEYENFEEAQNAITAMNGGELLT--QTLTVDW  165 (196)
Q Consensus       130 -------------------~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~~  165 (196)
                                         ..=||.|+|.+...|....+.++|..+..  ..|-+.|
T Consensus       248 ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  248 EEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                               01278899999999999999999999864  4444444

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=84.41  E-value=0.55  Score=36.83  Aligned_cols=25  Identities=36%  Similarity=0.502  Sum_probs=19.2

Q ss_pred             ccCCCCCCCcCcccccCCCcHHHHH
Q 043064           42 ITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        42 ~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      |+...+.|+||||||.|.+.+.+.|
T Consensus        45 itd~~t~rskGyGfVTf~d~~aa~r   69 (247)
T KOG0149|consen   45 ITDKNTGRSKGYGFVTFRDAEAATR   69 (247)
T ss_pred             EeccCCccccceeeEEeecHHHHHH
Confidence            4455788999999999996655555

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=81.85  E-value=1.6  Score=32.98  Aligned_cols=75  Identities=21%  Similarity=0.257  Sum_probs=51.0

Q ss_pred             EEEEcCCCccCcH-----HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc-EeEEE
Q 043064           91 IILVTGVHEEAQE-----DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ-TLTVD  164 (196)
Q Consensus        91 ~l~V~nLp~~~te-----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~-~l~v~  164 (196)
                      .+.+.+|+..+-.     .....+|.+|-+.....+++.      .++.-|.|.+.+.|..|...++...|.|+ .++.-
T Consensus        12 ~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs------frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~y   85 (193)
T KOG4019|consen   12 AIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS------FRRVRINFSNPEAAADARIKLHSTSFNGKNELKLY   85 (193)
T ss_pred             eeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh------hceeEEeccChhHHHHHHHHhhhcccCCCceEEEE
Confidence            3666677665322     334455665554444344432      34566899999999999999999999988 88888


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.+.-.
T Consensus        86 faQ~~~~   92 (193)
T KOG4019|consen   86 FAQPGHP   92 (193)
T ss_pred             EccCCCc
Confidence            8876543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	196
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		1e-34
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		9e-34
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		6e-33
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		7e-33
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-32
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-31
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-31
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		4e-30
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-10
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-09
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-09
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-08
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		1e-07
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-07
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		3e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		4e-07
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		4e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		5e-07
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-07
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		1e-06
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-06
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		3e-06
2khc_A	118	Bruno Rrm3+ Length = 118		3e-06
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		4e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		4e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		5e-06
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-06
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		5e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		6e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		6e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		9e-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		9e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		9e-06
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		1e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		1e-05
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		1e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		2e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		5e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		5e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		5e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		6e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		7e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		1e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-04
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		3e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		4e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		4e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		5e-04
1wf1_A	110	Solution Structure Of Rrm Domain In Rna-Binding Pro		5e-04
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		8e-04

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score =  142 bits (358), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 68/128 (53%), Positives = 90/128 (70%), Gaps = 8/128 (6%)
Query: 48  KKTKGRGFREEADSERHSRLADRNFESLGTDGG----PGPQRSIEGWIILVTGVHEEAQE 103
           K  KGRGF     S+ ++R A  ++E +  +      PGPQRS+EGWI+ VT +HEEAQE
Sbjct: 31  KHRKGRGF----GSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQE 86
Query: 104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           D++Q  F +YGEI+N+HLNLDRRTGF KGYAL+EYE  ++A  A  A+NG E++ QT+ V
Sbjct: 87  DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
Query: 164 DWAFSNGP 171
           DW F  GP
Sbjct: 147 DWCFVKGP 154

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score =  139 bits (350), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 60/102 (58%), Positives = 82/102 (80%), Gaps = 1/102 (0%)
Query: 71  NFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF 129
           +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG+
Sbjct: 4   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63
Query: 130 VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           +KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F  GP
Sbjct: 64  LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score =  137 bits (344), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 58/91 (63%), Positives = 73/91 (80%)
Query: 81  PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN 140
           PGPQRS+EGWI+ VT +HEEAQED++Q  F +YGEI+N+HLNLDRRTGF KGYAL+EYE 
Sbjct: 18  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77
Query: 141 FEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
            ++A  A  A+NG E++ QT+ VDW F  GP
Sbjct: 78  HKQALAAKEALNGAEIMGQTIQVDWCFVKGP 108

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score =  136 bits (343), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 57/91 (62%), Positives = 75/91 (82%)
Query: 81  PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN 140
           PGPQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG++KGY L+EYE 
Sbjct: 1   PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 141 FEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           ++EAQ A+  +NG +L+ Q ++VDW F  GP
Sbjct: 61  YKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 91

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score =  135 bits (339), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 58/98 (59%), Positives = 80/98 (81%), Gaps = 1/98 (1%)
Query: 71  NFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF 129
           +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG+
Sbjct: 3   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
Query: 130 VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF 167
           +KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F
Sbjct: 63  LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score =  132 bits (331), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 55/89 (61%), Positives = 73/89 (82%)
Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           PQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++
Sbjct: 1   PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 143 EAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           EAQ A+  +NG +L+ Q ++VDW F  GP
Sbjct: 61  EAQAAMEGLNGQDLMGQPISVDWCFVRGP 89

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score =  131 bits (330), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 55/89 (61%), Positives = 73/89 (82%)
Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           PQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++
Sbjct: 1   PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 143 EAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           EAQ A+  +NG +L+ Q ++VDW F  GP
Sbjct: 61  EAQAAMEGLNGQDLMGQPISVDWCFVRGP 89

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score =  127 bits (319), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 53/85 (62%), Positives = 71/85 (83%)
Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           PQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG++KGY L+EYE ++
Sbjct: 1   PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 143 EAQNAITAMNGGELLTQTLTVDWAF 167
           EAQ A+  +NG +L+ Q ++VDW F
Sbjct: 61  EAQAAMEGLNGQDLMGQPISVDWCF 85

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 37/103 (35%), Positives = 58/103 (56%), Gaps = 4/103 (3%)
Query: 76  GTDGGPGP-QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  GP +R+ +   I VT + E+ +E DLQ +F  +G I  ++L  D+ TG  KG+A
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWA---FSNGPSTG 174
            I +   E+A  AI  ++G       L V+WA    ++GPS+G
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 48/77 (62%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  VH++  +DD+++VF  +G+I++  L  D  TG  KGY  IEYE  + +Q+A+++M
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 152 NGGELLTQTLTVDWAFS 168
           N  +L  Q L V  A +
Sbjct: 173 NLFDLGGQYLRVGKAVT 189

>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 = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 48/77 (62%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  VH++  +DD+++VF  +G+I++  L  D  TG  KGY  IEYE  + +Q+A+++M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 152 NGGELLTQTLTVDWAFS 168
           N  +L  Q L V  A +
Sbjct: 188 NLFDLGGQYLRVGKAVT 204

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 57.4 bits (137), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 47/77 (61%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  VH++  +DD+++VF  +G+I++  L  D  TG  KGY  IEYE  + +Q+A+++ 
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 152 NGGELLTQTLTVDWAFS 168
           N  +L  Q L V  A +
Sbjct: 172 NLFDLGGQYLRVGKAVT 188

>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 = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 47/88 (53%), Gaps = 2/88 (2%)
Query: 81  PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN 140
           P   RS+    + V  +  EA E+ L+++F E G + +  L  DR TG  KGY   EY++
Sbjct: 2   PAVDRSLRS--VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 141 FEEAQNAITAMNGGELLTQTLTVDWAFS 168
            E A +A+  +NG E   + L VD A S
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAAS 87

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 50/88 (56%), Gaps = 5/88 (5%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+  +  E  L+ VF +YG+I  + +  DR T   +G+  + +EN ++A++A+ AM
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 152 NGGELLTQTLTVDWAFS-----NGPSTG 174
           NG  +  + + VD A       +GPS+G
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/99 (29%), Positives = 52/99 (52%), Gaps = 5/99 (5%)
Query: 75  LGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           LG+   P P        + V G+     E DL+ VF +YG I ++ +  D+++   +G+A
Sbjct: 3   LGSRANPDPN-----CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 57
Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPST 173
            + +EN ++A+ A    NG EL  + + VD++ +  P T
Sbjct: 58  FVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 96

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 49/92 (53%), Gaps = 4/92 (4%)
Query: 76  GTDGGPGPQ-RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  GP  RS     + V G+ E+  E+ L+  F   G +R   +  DR TG  KG+ 
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFG 57
Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
            +++ + E+A+ A  AM  GE+    +T+DWA
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/102 (33%), Positives = 53/102 (51%), Gaps = 5/102 (4%)
Query: 55  FREEADSERHSRLAD----RNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           F  E DS+R  ++ +    RN     +   PG + SI+   + VT +     +D L  +F
Sbjct: 52  FTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE-SIKDTNLYVTNLPRTITDDQLDTIF 110
Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN 152
           G+YG I   ++  D+ TG  +G A + Y   EEAQ AI+A+N
Sbjct: 111 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 5/89 (5%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 151 MNGGELLTQTLTVDWA-----FSNGPSTG 174
           MN  EL  +T+ V+ A       +GPS+G
Sbjct: 74  MNESELFGRTIRVNLAKPMRIKESGPSSG 102

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 41/125 (32%), Positives = 63/125 (50%), Gaps = 13/125 (10%)
Query: 55  FREEADSERHSRLAD----RNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVF 110
           F  E DS+R  ++ +    RN     +   PG + SI+   + VT +     +D L  +F
Sbjct: 63  FTSEXDSQRAIKVLNGITVRNKRLKVSYARPGGE-SIKDTNLYVTNLPRTITDDQLDTIF 121
Query: 111 GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN-----GGELLTQTLTVDW 165
           G+YG I   ++  D+ TG  +G A + Y   EEAQ AI+A+N     GG   +Q L+V  
Sbjct: 122 GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG---SQPLSVRL 178
Query: 166 AFSNG 170
           A  +G
Sbjct: 179 AEEHG 183

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEI-RNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I +  +  E  E  L + F  +G I +   +  D  TG  KGYA I + +F+ +  AI A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 151 MNGGELLTQTLTVDWAFS-----NGPSTG 174
           MNG  L  + +TV +AF      +GPS+G
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSKGSGPSSG 96

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 3/90 (3%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +D+ +++FG  G+I +  L  D+ TG   GY  + Y +  +A  AI  +
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNM 181
           NG +L T+T+ V +A    PS+   +  N+
Sbjct: 67  NGLKLQTKTIKVSYA---RPSSASIRDANL 93

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G++ E  E  L+ VFG++G I  + L  DR T   +G+A I +EN  +A+NA   M
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 152 NGGELLTQTLTVDWA 166
           NG  L  + + V+ A
Sbjct: 69  NGKSLHGKAIKVEQA 83

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/100 (29%), Positives = 51/100 (51%), Gaps = 5/100 (5%)
Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           S G    P P        + V G+     E DL+ VF +YG I ++ +  D+++   +G+
Sbjct: 5   SSGNRANPDPN-----CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59
Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPST 173
           A + +EN ++A+ A    NG EL  + + VD++ +  P T
Sbjct: 60  AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHT 99

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 55/105 (52%), Gaps = 8/105 (7%)
Query: 76  GTDGGPGPQRSIEGWIIL-VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  GP   ++G I L V  +      D L+ VF +YG + ++++  +  T   +G+A
Sbjct: 1   GSSGSSGPD--VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA 58
Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS-----NGPSTG 174
            + + +  +AQ+A  AM+G EL  + L V  A       +GPS+G
Sbjct: 59  FVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 43/75 (57%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +D+ +++FG  G+I +  L  D+ TG   GY  + Y +  +A  AI  +
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 152 NGGELLTQTLTVDWA 166
           NG +L T+T+ V +A
Sbjct: 67  NGLKLQTKTIKVSYA 81

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 50/90 (55%), Gaps = 3/90 (3%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +++ +++FG  GEI +  L  D+ TG   GY  + Y + ++A+ AI  +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNM 181
           NG  L T+T+ V +A    PS+   +  N+
Sbjct: 65  NGLRLQTKTIKVSYA---RPSSASIRDANL 91

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 79  GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY 138
           G  GP R      + V  +H    ED L+ +F  +G I ++ L +D  TG  KGY  I +
Sbjct: 22  GSAGPMR------LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 139 ENFEEAQNAITAMNGGELLTQTLTV 163
            + E A+ A+  +NG EL  + + V
Sbjct: 76  SDSECAKKALEQLNGFELAGRPMKV 100

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 8/90 (8%)
Query: 86  SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           SI+   + VT +     +D L  +FG+YG I   ++  D+ TG  +G A + Y   EEAQ
Sbjct: 10  SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 69
Query: 146 NAITAMN-----GGELLTQTLTVDWAFSNG 170
            AI+A+N     GG   +Q L+V  A  +G
Sbjct: 70  EAISALNNVIPEGG---SQPLSVRLAEEHG 96

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 51/102 (50%), Gaps = 5/102 (4%)
Query: 70  RNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF 129
           R    +G    P P        + V G+     E DL+ VF +YG I ++ +  D+++  
Sbjct: 32  RGSRHVGNRANPDPN-----CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR 86
Query: 130 VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
            +G+A + +EN ++A+ A    NG EL  + + VD++ +  P
Sbjct: 87  SRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E   +D+++ F  +G+I +  +  D  TG  KGY  + + N  +A+NAI  M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 152 NGGELLTQTLTVDWAF-----SNGPSTG 174
            G  L  + +  +WA       +GPS+G
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPSGPSSG 105

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 103 EDDLQNVFGEYGEIRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
           +D +  +F  YG+I+ + + ++R      KGYA +E+EN +EA+ A+  M+GG++  Q +
Sbjct: 18  KDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
Query: 162 TVDWAFSNGP 171
           T     +  P
Sbjct: 78  TATAVLAPWP 87

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 43/76 (56%)
Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           EG  + +  + +E  + DL + F  +G + +  + +D++T   K +  + ++N + AQ A
Sbjct: 39  EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 148 ITAMNGGELLTQTLTV 163
           I AMNG ++ T+ L V
Sbjct: 99  IKAMNGFQVGTKRLKV 114

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 151 MNGGELLTQTLTVDWA 166
           MN  EL  +T+ V+ A
Sbjct: 67  MNESELFGRTIRVNLA 82

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 151 MNGGELLTQTLTVDWA 166
           MN  EL  +T+ V+ A
Sbjct: 69  MNESELFGRTIRVNLA 84

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  
Sbjct: 4   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 151 MNGGELLTQTLTVDWA 166
           MN  EL  +T+ V+ A
Sbjct: 64  MNESELFGRTIRVNLA 79

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 43/81 (53%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+ +   + +++ +F +YG I    + LD+ TG  +G   I ++   EA+ AI  +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 152 NGGELLTQTLTVDWAFSNGPS 172
           NG + L     +   F+N PS
Sbjct: 64  NGQKPLGAAEPITVKFANNPS 84

>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 = 47.4 bits (111), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 32/103 (31%), Positives = 55/103 (53%), Gaps = 7/103 (6%)
Query: 76  GTDGGPGPQR---SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKG 132
           G+ G  G  R   S+E   + ++G+     +++L+ +   +G +++L L +  R G  KG
Sbjct: 1   GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRL-VTNRAGKPKG 59
Query: 133 YALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN-GPSTG 174
            A +EYEN  +A  A+  M+G  +    + V  A SN GPS+G
Sbjct: 60  LAYVEYENESQASQAVMKMDGMTIKENIIKV--AISNSGPSSG 100

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 3/90 (3%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +D+L+++F   GE+ +  L  D+  G   GY  + Y   ++A+ AI  +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNM 181
           NG  L ++T+ V +A    PS+   K  N+
Sbjct: 65  NGLRLQSKTIKVSYA---RPSSEVIKDANL 91

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 43/76 (56%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 151 MNGGELLTQTLTVDWA 166
           MN  EL  +T+ V+ A
Sbjct: 125 MNESELFGRTIRVNLA 140

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 3/90 (3%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +D+L+++F   GE+ +  L  D+  G   GY  + Y   ++A+ AI  +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNM 181
           NG  L ++T+ V +A    PS+   K  N+
Sbjct: 65  NGLRLQSKTIKVSYA---RPSSEVIKDANL 91

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 5/92 (5%)
Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           EG  + +  + +E  + DL  +F  +G + +  + +D++T   K +  + Y+N   AQ A
Sbjct: 24  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 148 ITAMNGGELLTQTLTVDWAFS-----NGPSTG 174
           I +MNG ++  + L V    S     +GPS+G
Sbjct: 84  IQSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +H    ED L+ +F  +G+I N+ L  D  TG  KGY  I + + E A+ A+  +
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 152 NGGELLTQTLTVDWAF-----SNGPSTG 174
           NG EL  + + V          +GPS+G
Sbjct: 68  NGFELAGRPMRVGHVTERLDGGSGPSSG 95

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 40/73 (54%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V+ +  E  L+  F  YG I+ +H+   +R+G  +GYA IEYE+  +  +A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 152 NGGELLTQTLTVD 164
           +G ++  + + VD
Sbjct: 165 DGKKIDGRRVLVD 177

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 83  PQRSIEGWIIL-VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF 141
           P   +EG   L V  +      D L+ VF +YG + ++++  DR T   +G+A + + + 
Sbjct: 40  PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 142 EEAQNAITAMNGGELLTQTLTVDWA 166
            +A++A+ AM+G  L  + L V  A
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQMA 124

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 40/77 (51%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  +     E  L+ +F  YG I ++ +  DR T   +GY  +++++   AQ AI  +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 152 NGGELLTQTLTVDWAFS 168
           NG  +L + L V  A S
Sbjct: 105 NGFNILNKRLKVALAAS 121

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 40/73 (54%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V+ +  E  L+  F  YG I+ +H+   +R+G  +GYA IEYE+  +  +A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 152 NGGELLTQTLTVD 164
           +G ++  + + VD
Sbjct: 165 DGKKIDGRRVLVD 177

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/113 (28%), Positives = 53/113 (46%), Gaps = 14/113 (12%)
Query: 76  GTDGGPG-PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN--------LHLNLDRR 126
           G+ G  G P    +   I V G+++    DDL + F + G ++         +H+ LD+ 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 127 TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA-----FSNGPSTG 174
           TG  KG A + YE+   A+ A+   +G +     L V  A      ++GPS+G
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 42/75 (56%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +D+L+++F   GE+ +  L  D+  G   GY  + Y   ++A+ AI  +
Sbjct: 7   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 152 NGGELLTQTLTVDWA 166
           NG  L ++T+ V +A
Sbjct: 67  NGLRLQSKTIKVSYA 81

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 5/85 (5%)
Query: 90  WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
             + V G+     E DL+ VF +YG I ++ +  D+++   +G+A + +EN ++A+ A  
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 150 AMNGGELLTQTLTVDWAFSNGPSTG 174
             NG EL  + + V     +GPS+G
Sbjct: 76  RANGMELDGRRIRV-----SGPSSG 95

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 39/81 (48%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E   +D++  F  +G I +  +  D  TG  KGY  + + N  +A+NAI  M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 152 NGGELLTQTLTVDWAFSNGPS 172
            G  L  + +  +WA    P+
Sbjct: 78  GGQWLGGRQIRTNWATRKPPA 98

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 44/79 (55%)
Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           +G  ++V  + +   +D+L+++F   GE+ +  L  D+  G   GY  + Y   ++A+ A
Sbjct: 18  QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 148 ITAMNGGELLTQTLTVDWA 166
           I  +NG  L ++T+ V +A
Sbjct: 78  INTLNGLRLQSKTIKVSYA 96

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 5/88 (5%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+ E+  E  L  +F + G + N H+  DR TG  +GY  +E+ + E+A  AI  M
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 152 NGGELLTQTLTVDWAFSN-----GPSTG 174
           +  +L  + + V+ A ++     GPS+G
Sbjct: 78  DMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 43/75 (57%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  ++    ++ L+N F ++    + H+  D +TG  +GY  + + + ++AQNA+ +M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 152 NGGELLTQTLTVDWA 166
            G +L  + L ++WA
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     + DL  +   YG+I +    LD+ T   KGY  +++++   AQ A+TA+
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 152 NGGELLTQTLTVDWAFSNGPSTG 174
               +  Q      A  +GPS+G
Sbjct: 68  KASGVQAQ-----MAKQSGPSSG 85

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 43.9 bits (102), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/85 (25%), Positives = 45/85 (52%), Gaps = 5/85 (5%)
Query: 82  GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF 141
           GP R     ++ +  +  +  E+ + ++    G + NL +  D +TG  KGYA IE+ + 
Sbjct: 1   GPSR-----VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDL 55
Query: 142 EEAQNAITAMNGGELLTQTLTVDWA 166
           E + +A+  +NG +L ++ L   ++
Sbjct: 56  ESSASAVRNLNGYQLGSRFLKCGYS 80

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/89 (30%), Positives = 50/89 (56%), Gaps = 7/89 (7%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  ++++  EDD++ +F  +G I    + L    G  KG A ++Y +  EAQ AI A+
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 152 NGGELL---TQTLTVDWAFSN---GPSTG 174
           +G + +   + +L V +A ++   GPS+G
Sbjct: 77  HGSQTMPGASSSLVVKFADTDKESGPSSG 105

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 42/76 (55%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ +  +  +  E+ + ++    G + NL +  D +TG  KGYA IE+ + E + +A+  
Sbjct: 6   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 151 MNGGELLTQTLTVDWA 166
           +NG +L ++ L   ++
Sbjct: 66  LNGYQLGSRFLKCGYS 81

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 42/76 (55%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ +  +  +  E+ + ++    G + NL +  D +TG  KGYA IE+ + E + +A+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 151 MNGGELLTQTLTVDWA 166
           +NG +L ++ L   ++
Sbjct: 64  LNGYQLGSRFLKCGYS 79

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V  + +   ED L+  F   G I N+ + +D+    V  YA +EY    +A  A+  
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQT 60
Query: 151 MNGGELLTQTLTVDWAFSNGPST 173
           +NG ++    + ++WAF +  S+
Sbjct: 61  LNGKQIENNIVKINWAFQSQQSS 83

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 87  IEGWIIL-VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           +EG   L V  +      D L+ VF +YG + ++++  DR T   +G+A + + +  +A+
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 146 NAITAMNGGELLTQTLTVDWA 166
           +A+ AM+G  L  + L V  A
Sbjct: 127 DAMDAMDGAVLDGRELRVQMA 147

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 36/75 (48%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 177 NGMQLGDKKLLVQRA 191

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 36/75 (48%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 99  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 159 NGMQLGDKKLLVQRA 173

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 36/75 (48%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 157 NGMQLGDKKLLVQRA 171

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 50/88 (56%), Gaps = 8/88 (9%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  + +  D+++VF +YG IR++ L  +RR G    +A +E+E+  +A++A+   
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGG--PPFAFVEFEDPRDAEDAVYGR 81
Query: 152 NGGELLTQTLTVDWAFS-----NGPSTG 174
           +G +     L V++  S     +GPS+G
Sbjct: 82  DGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           E+ +  +F + G+I+ + + LD+      G+  +EY +  +A+NA+  +NG  L  + + 
Sbjct: 53  EEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR 112
Query: 163 VDW--AFSNGPSTG 174
            DW   F  G   G
Sbjct: 113 TDWDAGFKEGRQYG 126

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 36/75 (48%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 64  NGMQLGDKKLLVQRA 78

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/81 (25%), Positives = 42/81 (51%)
Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + ++  + +L  +F   G I    +  D +TG+  GYA +++ +  ++Q AI  +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 152 NGGELLTQTLTVDWAFSNGPS 172
           NG  +  + L V +A   G S
Sbjct: 66  NGITVRNKRLKVSYARPGGES 86

>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein Np_057951 Length = 110

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 13/79 (16%)
Query: 101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
            ++ D++ +F +YG +    ++        KGYA ++Y N   A+ A+   NG  L  QT
Sbjct: 40  VKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLGENGRVLAGQT 91
Query: 161 LTVDWAFS-----NGPSTG 174
           L ++ A       +GPS+G
Sbjct: 92  LDINMAGEPKPDRSGPSSG 110

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 76  GTDGGPGPQRSIEGWI-ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G +R+++    ++V G+  +  E DL+  F  +GE+  + +  D +TG  KG+ 
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 135 LIEYENFE 142
            + +  +E
Sbjct: 61  FVRFTEYE 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	196
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-45
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-45
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-45
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-43
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-28
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-20
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-19
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-19
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-19
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	1e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-18
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-18
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-18
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	8e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-18
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	9e-18
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-17
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-17
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-17
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-10
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-17
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	9e-14
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-17
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-16
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-16
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-16
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-16
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-10
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-15
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-15
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-15
2div_A	99	TRNA selenocysteine associated protein; structural	4e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-15
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-15
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-15
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	9e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	9e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-14
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-12
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-13
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-13
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-13
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	8e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	8e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-12
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-11
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	7e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-10
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-10
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-10
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	8e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-08
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-08
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	2e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	5e-05
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-08
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	7e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	9e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	1e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	6e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	9e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	6e-06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	6e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	6e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	9e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	2e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-05
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-05
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-05
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	3e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	4e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-04
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-04

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  144 bits (365), Expect = 3e-45
 Identities = 60/104 (57%), Positives = 82/104 (78%), Gaps = 1/104 (0%)

Query: 69  DRNFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRT 127
             +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRT
Sbjct: 2   REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61

Query: 128 GFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           G++KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F  GP
Sbjct: 62  GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>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 =  145 bits (368), Expect = 5e-45
 Identities = 74/178 (41%), Positives = 100/178 (56%), Gaps = 17/178 (9%)

Query: 7   DALDFE--DDDLMDEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERH 64
           D LD +  ++  +DEDG   +                      K  KGRGF  ++++   
Sbjct: 3   DVLDIDNAEEFEVDEDGDQGIVRLKEKA---------------KHRKGRGFGSDSNTREA 47

Query: 65  SRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLD 124
               +R       +  PGPQRS+EGWI+ VT +HEEAQED++Q  F +YGEI+N+HLNLD
Sbjct: 48  IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 107

Query: 125 RRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMR 182
           RRTGF KGYAL+EYE  ++A  A  A+NG E++ QT+ VDW F  GP       K  R
Sbjct: 108 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165

>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 =  144 bits (365), Expect = 6e-45
 Identities = 70/126 (55%), Positives = 92/126 (73%), Gaps = 7/126 (5%)

Query: 71  NFESLGTDGG-PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF 129
           +++S+  DG  PGPQRS+EGWI+ VTGVHEEA E+D+ + F EYGEI+N+HLNLDRRTG+
Sbjct: 3   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62

Query: 130 VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRS 189
           +KGY L+EYE ++EAQ A+  +NG +L+ Q ++VDW F  GP       K  R G   RS
Sbjct: 63  LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP------PKGKRRGGRRRS 116

Query: 190 RSPRRR 195
           RSP RR
Sbjct: 117 RSPDRR 122

>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 =  139 bits (352), Expect = 3e-43
 Identities = 59/104 (56%), Positives = 76/104 (73%)

Query: 68  ADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRT 127
            +R       +  PGPQRS+EGWI+ VT +HEEAQED++Q  F +YGEI+N+HLNLDRRT
Sbjct: 5   YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64

Query: 128 GFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           GF KGYAL+EYE  ++A  A  A+NG E++ QT+ VDW F  GP
Sbjct: 65  GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP 108

>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 =  101 bits (254), Expect = 2e-28
 Identities = 37/103 (35%), Positives = 58/103 (56%), Gaps = 4/103 (3%)

Query: 76  GTDGGPGP-QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  GP +R+ +   I VT + E+ +E DLQ +F  +G I  ++L  D+ TG  KG+A
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWA---FSNGPSTG 174
            I +   E+A  AI  ++G       L V+WA    ++GPS+G
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103

>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 = 80.9 bits (200), Expect = 3e-20
 Identities = 29/112 (25%), Positives = 50/112 (44%), Gaps = 13/112 (11%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN--------LHLNLDRRT 127
            +     P    +   I V G+++    DDL + F + G ++         +H+ LD+ T
Sbjct: 2   SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61

Query: 128 GFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA-----FSNGPSTG 174
           G  KG A + YE+   A+ A+   +G +     L V  A      ++GPS+G
Sbjct: 62  GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 79.7 bits (197), Expect = 6e-20
 Identities = 14/88 (15%), Positives = 37/88 (42%), Gaps = 5/88 (5%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY 138
           GG  P + +         +++  +E  L+++  +YGE+  + + L  RT    G A + +
Sbjct: 1   GGQIPLKEV-----TFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLF 55

Query: 139 ENFEEAQNAITAMNGGELLTQTLTVDWA 166
            +   A+  +  ++   ++   +     
Sbjct: 56  TSTRGAKETVKNLHLTSVMGNIIHAQLD 83

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 79.1 bits (195), Expect = 3e-19
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  M
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125

Query: 152 NGGELLTQTLTVDWA 166
           N  EL  +T+ V+ A
Sbjct: 126 NESELFGRTIRVNLA 140

>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 = 76.8 bits (190), Expect = 4e-19
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  M
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69

Query: 152 NGGELLTQTLTVDWA 166
           N  EL  +T+ V+ A
Sbjct: 70  NESELFGRTIRVNLA 84

>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 = 76.9 bits (190), Expect = 5e-19
 Identities = 20/89 (22%), Positives = 46/89 (51%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + +  +  +  E+ + ++    G + NL +  D +TG  KGYA IE+ + E + +A+  +
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKN 180
           NG +L ++ L   ++ ++  S    +  +
Sbjct: 65  NGYQLGSRFLKCGYSSNSDISGVSLEHHH 93

>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 = 5e-19
 Identities = 25/107 (23%), Positives = 53/107 (49%), Gaps = 8/107 (7%)

Query: 76  GTDGGPG-PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR-TGFVKGY 133
           G+ G  G   +      ILV  +  +A + +++ +F  +GE++ + L      TG  +G+
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 134 ALIEYENFEEAQNAITAM-NGGELLTQTLTVDWA-----FSNGPSTG 174
             +++   ++A+ A  A+ +   L  + L ++WA       +GPS+G
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107

>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 = 76.9 bits (190), Expect = 6e-19
 Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 6/104 (5%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  GP        + V  +      D L+ VF +YG + ++++  +  T   +G+A 
Sbjct: 1   GSSGSSGPDVD-GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAF 59

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWA-----FSNGPSTG 174
           + + +  +AQ+A  AM+G EL  + L V  A       +GPS+G
Sbjct: 60  VRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103

>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 = 76.5 bits (189), Expect = 8e-19
 Identities = 30/88 (34%), Positives = 48/88 (54%), Gaps = 5/88 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  M
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74

Query: 152 NGGELLTQTLTVDWAF-----SNGPSTG 174
           N  EL  +T+ V+ A       +GPS+G
Sbjct: 75  NESELFGRTIRVNLAKPMRIKESGPSSG 102

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 78.5 bits (194), Expect = 1e-18
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176

Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 177 NGMQLGDKKLLVQRA 191

>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 = 57.0 bits (138), Expect = 1e-10
 Identities = 17/106 (16%), Positives = 37/106 (34%), Gaps = 6/106 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN-----LDRRTGFVKGYALIEYENFEEAQN 146
           + V  +     E+ + + F     +  L        L  +    K +A +E+ + +E   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 147 AITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSP 192
           A+ A +G     Q+L +       P  G  +  ++       +  P
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVP 111

>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 = 75.8 bits (187), Expect = 3e-18
 Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 5/86 (5%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +  +     E DL ++F  + E +   +     TG ++G A I + N E A  A+  +NG
Sbjct: 30  LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG 89

Query: 154 GELLTQTLTVDWAFS-----NGPSTG 174
            +L  + L +++  +     +GPS+G
Sbjct: 90  YKLYGKILVIEFGKNKKQRSSGPSSG 115

>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 = 74.9 bits (185), Expect = 3e-18
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR-TGFVKGYALIEYENFEEAQNAITA 150
           + +  +     +D +  +F  YG+I+ + + ++R      KGYA +E+EN +EA+ A+  
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 151 MNGGELLTQTLTVDWA 166
           M+GG++  Q +T    
Sbjct: 67  MDGGQIDGQEITATAV 82

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 75.5 bits (186), Expect = 5e-18
 Identities = 26/123 (21%), Positives = 48/123 (39%)

Query: 44  GGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQE 103
           G +              S   S    +         G  P        + V  +      
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSP 61

Query: 104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
           D L+ VF +YG + ++++  DR T   +G+A + + +  +A++A+ AM+G  L  + L V
Sbjct: 62  DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

Query: 164 DWA 166
             A
Sbjct: 122 QMA 124

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 74.2 bits (183), Expect = 6e-18
 Identities = 28/101 (27%), Positives = 54/101 (53%), Gaps = 2/101 (1%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           S G+ G      S+E   + ++G+     +++L+ +   +G +++L L  +R  G  KG 
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGL 60

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG 174
           A +EYEN  +A  A+  M+G  +    + V  + ++GPS+G
Sbjct: 61  AYVEYENESQASQAVMKMDGMTIKENIIKVAIS-NSGPSSG 100

>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 = 76.1 bits (188), Expect = 8e-18
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 157 NGMQLGDKKLLVQRA 171

>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 = 54.9 bits (133), Expect = 5e-10
 Identities = 17/91 (18%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN-----LDRRTGFVKGYALIEYENFEEAQN 146
           + V  +     E+ + + F     +  L        L  +    K +A +E+ + +E   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 147 AITAMNGGELLTQTLTVDWAFSNGPSTGPFK 177
           A+ A +G     Q+L +       P  G  K
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 = 73.8 bits (182), Expect = 8e-18
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 1/93 (1%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           S G+ G  G     +  +  V+ +      +DL  +F +YG++  + +  D+ T   KG 
Sbjct: 2   SSGSSGMSGGLAPSKSTVY-VSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV 60

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
           A I + + + AQN   A+N  +L  + +    A
Sbjct: 61  AFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 = 73.7 bits (182), Expect = 8e-18
 Identities = 29/88 (32%), Positives = 45/88 (51%), Gaps = 5/88 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +H    ED L+ +F  +G+I N+ L  D  TG  KGY  I + + E A+ A+  +
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67

Query: 152 NGGELLTQTLTVDWA-----FSNGPSTG 174
           NG EL  + + V          +GPS+G
Sbjct: 68  NGFELAGRPMRVGHVTERLDGGSGPSSG 95

>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 = 73.8 bits (182), Expect = 9e-18
 Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 6/99 (6%)

Query: 82  GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF 141
           G   S     + V  +   + E+DL+ +F  YG +  LH  +D  T   KG+A + +   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 142 EEAQNAITAMNGGELLTQTLTVDWA------FSNGPSTG 174
           E A  A   ++G     + L V  +        +GPS+G
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 75.2 bits (185), Expect = 1e-17
 Identities = 26/142 (18%), Positives = 57/142 (40%), Gaps = 5/142 (3%)

Query: 54  GFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEY 113
           G  +   S+ +  L+    +    D     +   +   + V  +     E+ +  +F + 
Sbjct: 4   GLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKS 63

Query: 114 GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPST 173
           G+I+ + + LD+      G+  +EY +  +A+NA+  +NG  L  + +  DW      + 
Sbjct: 64  GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD-----AG 118

Query: 174 GPFKRKNMRPGRTHRSRSPRRR 195
               R+  R     + R   R+
Sbjct: 119 FKEGRQYGRGRSGGQVRDEYRQ 140

>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 = 73.4 bits (181), Expect = 1e-17
 Identities = 27/67 (40%), Positives = 39/67 (58%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
           EA E+ L+++F E G + +  L  DR TG  KGY   EY++ E A +A+  +NG E   +
Sbjct: 19  EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR 78

Query: 160 TLTVDWA 166
            L VD A
Sbjct: 79  ALRVDNA 85

>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 = 73.4 bits (181), Expect = 2e-17
 Identities = 31/101 (30%), Positives = 53/101 (52%), Gaps = 6/101 (5%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY 138
            GP  +R+ +   + V G+ E+  E  L  +F + G + N H+  DR TG  +GY  +E+
Sbjct: 6   SGPISERNQDA-TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 139 ENFEEAQNAITAMNGGELLTQTLTVDWAF-----SNGPSTG 174
            + E+A  AI  M+  +L  + + V+ A       +GPS+G
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>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 = 73.1 bits (180), Expect = 2e-17
 Identities = 31/107 (28%), Positives = 51/107 (47%), Gaps = 9/107 (8%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  G  +  +   + +  +     E DL+ +F E+G+I  L +  DR TG  KG A 
Sbjct: 1   GSSGSSG-MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59

Query: 136 IEYENFEEAQNAITAMNGGELL---TQTLTVDWAFS-----NGPSTG 174
           + Y   E A  A +A++  + L    + + V  A S     +GPS+G
Sbjct: 60  LTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>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 = 73.1 bits (180), Expect = 2e-17
 Identities = 24/75 (32%), Positives = 39/75 (52%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +H    ED L+ +F  +G I ++ L +D  TG  KGY  I + + E A+ A+  +
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

Query: 152 NGGELLTQTLTVDWA 166
           NG EL  + + V   
Sbjct: 89  NGFELAGRPMKVGHV 103

>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 = 76.2 bits (188), Expect = 4e-17
 Identities = 19/87 (21%), Positives = 32/87 (36%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +     +   + +   +G +    L    RTG  KGY   EY   + A  A + + G
Sbjct: 100 VANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG 159

Query: 154 GELLTQTLTVDWAFSNGPSTGPFKRKN 180
             L  +TL V W  +   +      + 
Sbjct: 160 KPLGPRTLYVHWTDAGQLTPALLHSRC 186

>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 = 4e-14
 Identities = 17/94 (18%), Positives = 27/94 (28%), Gaps = 11/94 (11%)

Query: 102 QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
             D L              L   +  G +KG+A++EYE  E A+ A    +G  L    L
Sbjct: 198 DVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 256

Query: 162 TVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRR 195
            V +                         + +  
Sbjct: 257 RVSFC----------APGPPGRSMLAALIAAQAT 280

>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 = 56.9 bits (138), Expect = 4e-10
 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 7/75 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           IL+ G+  +    ++ ++  +Y  ++   ++        KG A +   N E+A+ AI A 
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY------KGTAFVTLLNGEQAEAAINAF 77

Query: 152 NGGELLTQTLTVDWA 166
           +   L  + L+V   
Sbjct: 78  HQSRLRERELSVQLQ 92

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 74.7 bits (184), Expect = 5e-17
 Identities = 30/84 (35%), Positives = 48/84 (57%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  VH++  +DD+++VF  +G+I++  L  D  TG  KGY  IEYE  + +Q+A+++M
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 152 NGGELLTQTLTVDWAFSNGPSTGP 175
           N  +L  Q L V  A +       
Sbjct: 188 NLFDLGGQYLRVGKAVTPPMPLLT 211

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 66.2 bits (162), Expect = 9e-14
 Identities = 25/95 (26%), Positives = 44/95 (46%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  ++ E  ED ++  F  +G I+++ ++ D  T   KG+A +EYE  E AQ A+  MN 
Sbjct: 33  VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92

Query: 154 GELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHR 188
             L  + + V    + G +     +        +R
Sbjct: 93  VMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127

>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 = 73.3 bits (180), Expect = 6e-17
 Identities = 30/122 (24%), Positives = 52/122 (42%), Gaps = 1/122 (0%)

Query: 46  APKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWI-ILVTGVHEEAQED 104
           A K  K        D E     A + F              +EG   + V  +      D
Sbjct: 26  AEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPD 85

Query: 105 DLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD 164
            L+ VF +YG + ++++  DR T   +G+A + + +  +A++A+ AM+G  L  + L V 
Sbjct: 86  TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 145

Query: 165 WA 166
            A
Sbjct: 146 MA 147

>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 = 71.5 bits (176), Expect = 7e-17
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 1/92 (1%)

Query: 76  GTDGGPGPQRSIEGWIIL-VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G + + +    L V G+     E DL+ VF +YG I ++ +  D+++   +G+A
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
            + +EN ++A+ A    NG EL  + + V   
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGP 92

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 71.2 bits (175), Expect = 1e-16
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 4/97 (4%)

Query: 70  RNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF 129
               +       GP+    G  + +  + +E  + DL + F  +G + +  + +D++T  
Sbjct: 25  AAAAAAAGKQIEGPE----GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL 80

Query: 130 VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
            K +  + ++N + AQ AI AMNG ++ T+ L V   
Sbjct: 81  SKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>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 = 71.7 bits (176), Expect = 2e-16
 Identities = 22/75 (29%), Positives = 39/75 (52%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  +     E  L+ +F  YG I ++ +  DR T   +GY  +++++   AQ AI  +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 152 NGGELLTQTLTVDWA 166
           NG  +L + L V  A
Sbjct: 105 NGFNILNKRLKVALA 119

>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 = 70.4 bits (173), Expect = 2e-16
 Identities = 20/86 (23%), Positives = 42/86 (48%), Gaps = 7/86 (8%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +  +  E  +  +F + G  ++  +  +  +     Y  +E+    +A  A+ AMNG
Sbjct: 20  VGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNG 77

Query: 154 GELLTQTLTVDWAFS-----NGPSTG 174
            ++L + + V+WA +     +GPS+G
Sbjct: 78  RKILGKEVKVNWATTPSSQKSGPSSG 103

>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 = 70.5 bits (173), Expect = 2e-16
 Identities = 27/102 (26%), Positives = 45/102 (44%), Gaps = 10/102 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E   +D++  F  +G I +  +  D  TG  KGY  + + N  +A+NAI  M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPR 193
            G  L  + +  +WA           RK   P  T+ S + +
Sbjct: 78  GGQWLGGRQIRTNWA----------TRKPPAPKSTYESNTKQ 109

>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 = 70.4 bits (173), Expect = 2e-16
 Identities = 29/107 (27%), Positives = 54/107 (50%), Gaps = 6/107 (5%)

Query: 74  SLGTDGGPGPQRS-IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKG 132
           +  + G  G Q+   EG  + +  + +E  + DL  +F  +G + +  + +D++T   K 
Sbjct: 9   TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68

Query: 133 YALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS-----NGPSTG 174
           +  + Y+N   AQ AI +MNG ++  + L V    S     +GPS+G
Sbjct: 69  FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115

>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 = 69.4 bits (171), Expect = 3e-16
 Identities = 19/64 (29%), Positives = 39/64 (60%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           ++ L+N F ++    + H+  D +TG  +GY  + + + ++AQNA+ +M G +L  + L 
Sbjct: 15  DETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 74

Query: 163 VDWA 166
           ++WA
Sbjct: 75  INWA 78

>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 = 70.0 bits (172), Expect = 3e-16
 Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEE 143
           I V G+ E    + + + F + G I+         ++L  DR TG +KG A + +++   
Sbjct: 16  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75

Query: 144 AQNAITAMNGGELLTQTLTVDWA 166
           A+ AI   +G E     + V +A
Sbjct: 76  AKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 70.4 bits (173), Expect = 3e-16
 Identities = 36/105 (34%), Positives = 55/105 (52%), Gaps = 5/105 (4%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G++ E  E  L+ VFG++G I  + L  DR T   +G+A I +EN  +A+NA   M
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
           NG  L  + + V+ A    PS     R+  RP  + R+RSP    
Sbjct: 69  NGKSLHGKAIKVEQA--KKPSFQSGGRR--RPPASSRNRSPSGSL 109

>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 = 70.5 bits (173), Expect = 3e-16
 Identities = 29/116 (25%), Positives = 53/116 (45%), Gaps = 5/116 (4%)

Query: 56  REEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGE 115
                S    +   R    +G    P P   +      V G+     E DL+ VF +YG 
Sbjct: 18  GSHMASMTGGQQMGRGSRHVGNRANPDPNCCL-----GVFGLSLYTTERDLREVFSKYGP 72

Query: 116 IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP 171
           I ++ +  D+++   +G+A + +EN ++A+ A    NG EL  + + VD++ +  P
Sbjct: 73  IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>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 = 69.1 bits (170), Expect = 4e-16
 Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  V   A  ++L+  F   G +  + +  D+ +G  KG+A IE+ + E  + ++ A+
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67

Query: 152 NGGELLTQTLTVDWAFSNGP 171
           +      + + V    +N P
Sbjct: 68  DESLFRGRQIKVIPKRTNRP 87

>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 = 6e-16
 Identities = 21/84 (25%), Positives = 40/84 (47%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  + ++  + +L  +F   G I    +  D +TG+  GYA +++ +  ++Q AI  +NG
Sbjct: 8   VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67

Query: 154 GELLTQTLTVDWAFSNGPSTGPFK 177
             +  + L V +A   G S     
Sbjct: 68  ITVRNKRLKVSYARPGGESIKDTN 91

>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 = 66.8 bits (164), Expect = 2e-14
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           VT +     +D L  +FG+YG I   ++  D+ TG  +G A + Y   EEAQ AI+A+N 
Sbjct: 94  VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153

Query: 154 GELL--TQTLTVDWA 166
                 +Q L+V  A
Sbjct: 154 VIPEGGSQPLSVRLA 168

>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 = 69.3 bits (170), Expect = 7e-16
 Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 90  WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
            I+ +  +  +   +++ ++FG+YG IR + +     T   +G A + YE+  +A+NA+ 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVD 65

Query: 150 AMNGGELLTQTLTVDWA 166
            ++G  +  + L V + 
Sbjct: 66  HLSGFNVSNRYLVVLYY 82

>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 = 69.7 bits (171), Expect = 7e-16
 Identities = 23/87 (26%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V   +   DL+  F   G I  + +  D+ +G  KGYA IE+        A+ AM
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AM 97

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKR 178
           +      +T+ V    +N P      R
Sbjct: 98  DETVFRGRTIKVLPKRTNMPGISSTDR 124

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 68.9 bits (169), Expect = 8e-16
 Identities = 23/106 (21%), Positives = 50/106 (47%), Gaps = 9/106 (8%)

Query: 61  SERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH 120
               S L  R    + T+    P+R      + V+ +    ++ DL+ +FG++G+I ++ 
Sbjct: 8   HHHSSGLVPR-GSHMNTENKSQPKR------LHVSNIPFRFRDPDLRQMFGQFGKILDVE 60

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
           +  + R    KG+  + +EN  +A  A   ++G  +  + + V+ A
Sbjct: 61  IIFNERGS--KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 68.6 bits (168), Expect = 9e-16
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 76  GTDGGPG--PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           G+ G  G  P+R      + +  +    Q + L ++  +YG + +               
Sbjct: 1   GSSGSSGSVPKRQ-RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AV 56

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
             + Y + ++A+ A+  +NG +L   TL V + 
Sbjct: 57  VNVTYSSKDQARQALDKLNGFQLENFTLKVAYI 89

>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 = 68.4 bits (168), Expect = 1e-15
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 12/87 (13%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +  +      DDL+ +FG+          L  +     GYA ++Y +   A  AI  ++G
Sbjct: 13  IGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPDQNWAIRAIETLSG 66

Query: 154 -GELLTQTLTVDWAF-----SNGPSTG 174
             EL  + + VD++      S+GPS+G
Sbjct: 67  KVELHGKIMEVDYSVSKKLRSSGPSSG 93

>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 = 70.3 bits (173), Expect = 1e-15
 Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           +L   +     ED+L+ VF +  EIR     L  + G  KG A IE+++  +A+  +   
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEK 156

Query: 152 NGGELLTQTLTVDWA 166
            G E+  +++++ + 
Sbjct: 157 QGAEIDGRSVSLYYT 171

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 15/93 (16%), Positives = 39/93 (41%), Gaps = 9/93 (9%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +  ++      +L+    E     +L + +D RTG  + +  +++E+ E+ + A+  + G
Sbjct: 18  IGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKAL-ELTG 75

Query: 154 GELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRT 186
            ++    + ++              K +R  RT
Sbjct: 76  LKVFGNEIKLEKPK-------GRDSKKVRAART 101

>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 = 67.9 bits (167), Expect = 1e-15
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           + G+     + DL  +   YG+I +    LD+ T   KGY  +++++   AQ A+TA+  
Sbjct: 10  IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69

Query: 154 GELLTQTLTVDWAFSNGPSTG 174
             +  Q         +GPS+G
Sbjct: 70  SGVQAQMAKQ-----SGPSSG 85

>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 = 69.1 bits (170), Expect = 3e-15
 Identities = 24/84 (28%), Positives = 44/84 (52%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  + +   +++ +++FG  GEI +  L  D+ TG   GY  + Y + ++A+ AI  +NG
Sbjct: 7   VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66

Query: 154 GELLTQTLTVDWAFSNGPSTGPFK 177
             L T+T+ V +A  +  S     
Sbjct: 67  LRLQTKTIKVSYARPSSASIRDAN 90

>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 = 63.0 bits (154), Expect = 6e-13
 Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G+ +   + +L+ +F +YG I    + +D+ TG  +G   I ++   EA+ AI  +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 152 NGGEL--LTQTLTVDWA 166
           NG +    T+ +TV +A
Sbjct: 151 NGQKPSGATEPITVKFA 167

>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 = 68.7 bits (169), Expect = 3e-15
 Identities = 19/68 (27%), Positives = 39/68 (57%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
              ++ L+N F ++    + H+  D +TG  +GY  + + + ++AQNA+ +M G +L  +
Sbjct: 98  NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157

Query: 160 TLTVDWAF 167
            L ++WA 
Sbjct: 158 PLRINWAA 165

>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 = 1e-11
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 98  HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL 157
            +   ED L+  F   G I N+ + +D+       YA +EY    +A  A+  +NG ++ 
Sbjct: 9   DKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIE 67

Query: 158 TQTLTVDWAFSNGPS 172
              + ++WAF +  S
Sbjct: 68  NNIVKINWAFQSQQS 82

>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 = 66.8 bits (164), Expect = 4e-15
 Identities = 21/75 (28%), Positives = 34/75 (45%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  E     +   F  +G I +  +  D  TG  KGY  + + N  +A+NAI  M
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 152 NGGELLTQTLTVDWA 166
            G  L  + +  +WA
Sbjct: 69  GGQWLGGRQIRTNWA 83

>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 = 67.0 bits (164), Expect = 4e-15
 Identities = 24/104 (23%), Positives = 47/104 (45%), Gaps = 10/104 (9%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGE-IRNLHLNLDRRTGFVKGYA 134
           G+ G  G   S+  W   +  +     E+ +   F   GE + ++ +  +R TG   GY 
Sbjct: 1   GSSGSSGMAASL--W---MGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYC 55

Query: 135 LIEYENFEEAQNAITAMNG----GELLTQTLTVDWAFSNGPSTG 174
            +E+ +   A+  +  +NG    G    +   +++A  +GPS+G
Sbjct: 56  FVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSSG 99

>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 = 66.9 bits (164), Expect = 4e-15
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +    +E+ L  +F + G +  + +  DR  G  K +  + +++ E    AI  +NG
Sbjct: 21  VGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNG 79

Query: 154 GELLTQTLTVDWAFS 168
             L  + + V    S
Sbjct: 80  IRLYGRPINVSGPSS 94

>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 = 66.9 bits (164), Expect = 4e-15
 Identities = 28/88 (31%), Positives = 50/88 (56%), Gaps = 5/88 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+  +  E  L+ VF +YG+I  + +  DR T   +G+  + +EN ++A++A+ AM
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74

Query: 152 NGGELLTQTLTVDWAF-----SNGPSTG 174
           NG  +  + + VD A       +GPS+G
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRSGPSSG 102

>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 = 66.9 bits (164), Expect = 5e-15
 Identities = 21/88 (23%), Positives = 48/88 (54%), Gaps = 7/88 (7%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+ +    ++ DL+ +FG++G+I ++ +  + R    KG+  + +EN  +A  A   +
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 75

Query: 152 NGGELLTQTLTVDWA-----FSNGPSTG 174
           +G  +  + + V+ A      ++GPS+G
Sbjct: 76  HGTVVEGRKIEVNNATARVMTNSGPSSG 103

>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 = 66.5 bits (163), Expect = 5e-15
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 11/82 (13%)

Query: 98  HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL 157
            E+     L+  F  +G I +L ++        +  A + YE  E A  A+  +NG ++ 
Sbjct: 22  GEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVE 75

Query: 158 TQTLTVDWAFS-----NGPSTG 174
           +  L V+ A       +GPS+G
Sbjct: 76  SVQLKVNIARKQPMLDSGPSSG 97

>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 = 66.0 bits (162), Expect = 6e-15
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
            A  + ++ +F ++G++ N+ L  DR T   KG+  +E +  E    AI  ++  + + +
Sbjct: 12  SATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGR 70

Query: 160 TLTVDWA 166
           T+ V  A
Sbjct: 71  TIRVTEA 77

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.2 bits (162), Expect = 7e-15
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +  +   A E DL  +F  +G I +     +      KG   I+Y+  E+A   I A+  
Sbjct: 32  IGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALAN 85

Query: 154 GELLTQTLTVDWA 166
                + L   W 
Sbjct: 86  FPFQGRNLRTGWG 98

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 65.9 bits (161), Expect = 9e-15
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 91  IILVTGV------HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEA 144
            I+V G            +  L ++F + G++ N+   +D  TG  KG+  +E  +  +A
Sbjct: 8   YIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDA 67

Query: 145 QNAITAMNGGEL 156
           +  I + +G  L
Sbjct: 68  KKIIKSFHGKRL 79

>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 = 65.7 bits (161), Expect = 9e-15
 Identities = 23/105 (21%), Positives = 49/105 (46%), Gaps = 12/105 (11%)

Query: 76  GTDGGPGPQRSIEGWI-ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G +++      + V  +  +  E++++ +F +YG+   + ++ D      KG+ 
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWA-----FSNGPSTG 174
            I  E    A+ A   ++   L  + L V +A      ++GPS+G
Sbjct: 55  FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSSG 99

>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 = 66.2 bits (162), Expect = 1e-14
 Identities = 26/107 (24%), Positives = 47/107 (43%), Gaps = 1/107 (0%)

Query: 62  ERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHL 121
            R  +L D+    L   G  G      G  +LV+ +     + D+Q +F E+G ++   +
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

Query: 122 NLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS 168
           + DR +G   G A + +E   +A  A+   NG  L  + + +    S
Sbjct: 62  HYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS 107

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 65.9 bits (161), Expect = 1e-14
 Identities = 25/121 (20%), Positives = 46/121 (38%), Gaps = 18/121 (14%)

Query: 84  QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN--------LHLNLDRRTGFVKGYAL 135
           Q + +   I V G+ E    + + + F + G I+         ++L  DR TG +KG A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRR 195
           + +++   A+ AI   +G E     + V +A           R+          R     
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA----------TRRADFNRGGGNGRGGLEH 111

Query: 196 Y 196
           +
Sbjct: 112 H 112

>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 = 65.4 bits (160), Expect = 2e-14
 Identities = 22/101 (21%), Positives = 45/101 (44%), Gaps = 5/101 (4%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           S   +     ++      +L   +     ED+L+ VF +  EIR     L  + G  KG 
Sbjct: 1   SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGI 55

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG 174
           A IE+++  +A+  +    G E+  +++++ +    G + G
Sbjct: 56  AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 67.8 bits (165), Expect = 2e-14
 Identities = 14/116 (12%), Positives = 34/116 (29%), Gaps = 4/116 (3%)

Query: 56  REEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGE 115
            E+           RN      +     +      ++       E  E++   +  E G 
Sbjct: 90  LEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGV 149

Query: 116 IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL----LTQTLTVDWAF 167
            R   + +           L+E+++  +A   +  +N  ++         T+   F
Sbjct: 150 KRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLCF 205

>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 = 60.5 bits (146), Expect = 8e-12
 Identities = 24/119 (20%), Positives = 42/119 (35%), Gaps = 15/119 (12%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
           G   P       +++V G+ +     D + NVF  YG +  +     +      G A++E
Sbjct: 1   GADSP-------VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVE 48

Query: 138 YENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
             +      AIT +N   +  Q + V    S  P+  P +   +  G          R 
Sbjct: 49  MADGYAVDRAITHLNNNFMFGQKMNVCV--SKQPAIMPGQSYGLEDGSCSYKDFSESRN 105

>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 = 65.4 bits (160), Expect = 2e-14
 Identities = 21/114 (18%), Positives = 47/114 (41%), Gaps = 14/114 (12%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY 138
           G  G     +  ++ V  +     E+ L+  F ++G++  +          +K YA I +
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHF 52

Query: 139 ENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSP 192
           +  + A  A+  MNG +L  + + + +A        P +++  R  +   +  P
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFA------KPPDQKRKERKAQRQAASGP 100

>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 = 64.9 bits (159), Expect = 2e-14
 Identities = 31/89 (34%), Positives = 46/89 (51%), Gaps = 6/89 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEI-RNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I +  +  E  E  L + F  +G I +   +  D  TG  KGYA I + +F+ +  AI A
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 151 MNGGELLTQTLTVDWAFS-----NGPSTG 174
           MNG  L  + +TV +AF      +GPS+G
Sbjct: 68  MNGQYLCNRPITVSYAFKKDSKGSGPSSG 96

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 64.7 bits (158), Expect = 3e-14
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 82  GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYE 139
           G         I++  +      D +      Y    + N+ L  D++T   +G+A ++  
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61

Query: 140 NFEEAQNAITAMNGGELLT----QTLTVDWA 166
           +  +A   +  +           +T+ VD+A
Sbjct: 62  SAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 64.6 bits (158), Expect = 3e-14
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 11/89 (12%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I+ V  +     E+ ++  F               R   ++ YA + + N E+A  A+ A
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVEAMKA 70

Query: 151 MNGGELLTQTLTVDWA-----FSNGPSTG 174
           +NG  L    + V  A      S+GPS+G
Sbjct: 71  LNGKVLDGSPIEVTLAKPVDKDSSGPSSG 99

>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 = 67.3 bits (165), Expect = 3e-14
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 2/88 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I +  + +      L + F  +G I +  +  D      KGY  + +E  E A+ AI  M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRK 179
           NG  L  + + V    S          +
Sbjct: 164 NGMLLNDRKVFVGRFKSRKEREAELGAR 191

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 98  HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL 157
           H +  E  L   F   G I ++ +  D  T    GYA + ++   +A+ A+  MN   + 
Sbjct: 24  HPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK 83

Query: 158 TQTLTVDWAFSNGPST 173
            + + + W+    PS 
Sbjct: 84  GKPVRIMWS-QRDPSL 98

>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 = 64.2 bits (157), Expect = 5e-14
 Identities = 28/106 (26%), Positives = 54/106 (50%), Gaps = 8/106 (7%)

Query: 76  GTDGGPGPQ-RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G + R      + V  ++++  E+D+  +F  +G I    +      G  KG A
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59

Query: 135 LIEYENFEEAQNAITAMNGGELL---TQTLTVDWAFS---NGPSTG 174
            +++ +  EAQ AI A++G + +   + +L V +A +   +GPS+G
Sbjct: 60  FVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSSG 105

>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 = 64.7 bits (158), Expect = 5e-14
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 1/106 (0%)

Query: 61  SERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH 120
            ++  R  D+    L   G  G +    G  +LV+ +     + D+Q +F E+G ++   
Sbjct: 7   GQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 66

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
           ++ DR +G   G A + +E   +A  A+    G  L  + + +   
Sbjct: 67  VDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 111

>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 = 66.1 bits (162), Expect = 5e-14
 Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 3/90 (3%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFV--KGYALIEYENFEEAQNAITAM 151
           V  V     E DL+ +F +YG +  +++  DR       KG   + +   + A  A  A+
Sbjct: 8   VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67

Query: 152 NGGELLTQTLTVDWA-FSNGPSTGPFKRKN 180
           +  ++L           ++       + + 
Sbjct: 68  HNMKVLPGMHHPIQMKPADSEKNNAVEDRK 97

>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 = 64.6 bits (158), Expect = 1e-13
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 4/76 (5%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +  + ++  E+D++ +F  +G+I    +      G  +G A + +     AQ AI AM+ 
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQ 158

Query: 154 GELL---TQTLTVDWA 166
            + +   +  + V +A
Sbjct: 159 AQTMEGCSSPMVVKFA 174

>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 = 63.9 bits (156), Expect = 6e-14
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 11/86 (12%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
             G+     +  ++  F  +G+I  + +  +      KGY+ + +   E A +AI ++NG
Sbjct: 30  CGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG 83

Query: 154 GELLTQTLTVDWA-----FSNGPSTG 174
             +    +   W       ++GPS+G
Sbjct: 84  TTIEGHVVKCYWGKESPDMTSGPSSG 109

>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 = 63.8 bits (156), Expect = 6e-14
 Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 8/98 (8%)

Query: 82  GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF 141
              RS     + V G+ E+  E+ L+  F      R   +  DR TG  KG+  +++ + 
Sbjct: 8   PNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---IVTDRETGSSKGFGFVDFNSE 64

Query: 142 EEAQNAITAMNGGELLTQTLTVDWA-----FSNGPSTG 174
           E+A+ A  AM  GE+    +T+DWA       +GPS+G
Sbjct: 65  EDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSSG 102

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 63.4 bits (155), Expect = 7e-14
 Identities = 26/100 (26%), Positives = 48/100 (48%), Gaps = 9/100 (9%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  G  +      I V  +  +     L++ F E G +  L+ ++    G  KG  +
Sbjct: 1   GSSGSSGACQ------IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGV 52

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWA-FSNGPSTG 174
           +++E+ E A+ A   MNG +L  + + V     ++GPS+G
Sbjct: 53  VKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPSSG 92

>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 = 63.9 bits (156), Expect = 7e-14
 Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 11/103 (10%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           P    EG  + +  +  +++E+ L  V  ++G+++ + + L   T   KG A  ++   E
Sbjct: 9   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68

Query: 143 EAQNAITAMN------GGELLTQTLTVDWAFS-----NGPSTG 174
            AQ  + A +      G +L  + L VD A +     +GPS+G
Sbjct: 69  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSSG 111

>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 = 63.5 bits (155), Expect = 8e-14
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 9/86 (10%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           ++ +   A E+ LQ VF +   I+        + G  KGYA IE+ +FE+A+ A+ + N 
Sbjct: 20  LSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFASFEDAKEALNSCNK 75

Query: 154 GELLTQTLTVDWA-----FSNGPSTG 174
            E+  + + ++        ++GPS+G
Sbjct: 76  REIEGRAIRLELQGPRGSPNSGPSSG 101

>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 = 66.2 bits (161), Expect = 9e-14
 Identities = 21/119 (17%), Positives = 50/119 (42%), Gaps = 7/119 (5%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
                       ++LV+ ++ E      L  +FG YG+++ + +  ++     K  AL++
Sbjct: 24  IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQ 78

Query: 138 YENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
             +  +AQ A++ +NG +L  + + +  +        P + +  +        SP  R+
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQL-PREGQEDQGLTKDYGNSPLHRF 136

>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 = 56.5 bits (136), Expect = 3e-10
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 5/85 (5%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
                    + ++ +     E+DL+ +F   G +        +     +  ALI+  + E
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVE 200

Query: 143 EAQNAITAMNGGELL-TQTLTVDWA 166
           EA  A+  ++  +L     L V ++
Sbjct: 201 EAVQALIDLHNHDLGENHHLRVSFS 225

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 63.5 bits (155), Expect = 1e-13
 Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 8/75 (10%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V     + QE +L  +FG +G ++ + +        + G+A +E+E  E A  AI  +
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85

Query: 152 NGGELLTQTLTVDWA 166
           +G     Q L V ++
Sbjct: 86  HGKSFANQPLEVVYS 100

>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 = 63.4 bits (155), Expect = 1e-13
 Identities = 21/101 (20%), Positives = 34/101 (33%), Gaps = 12/101 (11%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I +  + +      L + F  +G I +  +  D      KGY  + +E  E A+ AI  M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEKM 65

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSP 192
           NG  L  + + V             K +  R          
Sbjct: 66  NGMLLNDRKVFVGRF----------KSRKEREAELGARAKE 96

>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 = 65.5 bits (159), Expect = 2e-13
 Identities = 24/193 (12%), Positives = 48/193 (24%), Gaps = 27/193 (13%)

Query: 3   NAEVDALDFEDDDLMDEDGTADVDASSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSE 62
           N E +    +  DL D+  +   +   +P           T G               + 
Sbjct: 7   NQEAEYGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTG 66

Query: 63  RHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYG--EIRNLH 120
           +   L                          +  +     ++DL       G  +I  + 
Sbjct: 67  KRIAL-------------------------YIGNLTWWTTDEDLTEAVHSLGVNDILEIK 101

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKN 180
              +R  G  KG+AL+   +   ++  +  +   EL  Q   V        S    + + 
Sbjct: 102 FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 161

Query: 181 MRPGRTHRSRSPR 193
                        
Sbjct: 162 TTQSGQMSGEGKA 174

>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 = 64.5 bits (157), Expect = 2e-13
 Identities = 21/106 (19%), Positives = 49/106 (46%), Gaps = 7/106 (6%)

Query: 92  ILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           +LV+ ++ E      L  +FG YG+++ + +  ++     K  AL++  +  +AQ A++ 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 151 MNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
           +NG +L  + + +  +        P + +  +        SP  R+
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQL-PREGQEDQGLTKDYGNSPLHRF 105

>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 = 58.4 bits (141), Expect = 4e-11
 Identities = 18/123 (14%), Positives = 40/123 (32%), Gaps = 6/123 (4%)

Query: 46  APKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIE-GWIILVTGVHEEAQED 104
           +  +        + D        +         G    Q        + ++ +     E+
Sbjct: 76  SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEE 135

Query: 105 DLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL-TQTLTV 163
           DL+ +F   G +        +     +  ALI+  + EEA  A+  ++  +L     L V
Sbjct: 136 DLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV 191

Query: 164 DWA 166
            ++
Sbjct: 192 SFS 194

>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 = 62.2 bits (152), Expect = 3e-13
 Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  + +   ++ L+  F  +G I +  + ++   G  KG+  + + + EEA  A+T MNG
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 154 GELLTQTLTVDWAF-----SNGPSTG 174
             + T+ L V  A       +GPS+G
Sbjct: 78  RIVATKPLYVALAQRKEERQSGPSSG 103

>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 = 62.3 bits (152), Expect = 3e-13
 Identities = 24/120 (20%), Positives = 43/120 (35%), Gaps = 8/120 (6%)

Query: 76  GTDGGPGPQRSIE-GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G  ++   G  + V  +  +     L+ VF   G +    +  D+  G  +G  
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRR 194
            + +E   EA  AI+  NG  L  + + V       P      + +  P    +   P  
Sbjct: 60  TVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP------KGDFFPPERPQQSGPSS 113

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 63.7 bits (155), Expect = 4e-13
 Identities = 26/144 (18%), Positives = 52/144 (36%), Gaps = 10/144 (6%)

Query: 28  SSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSI 87
            +    P+    +   GG  +       +   D  +H              G  G +   
Sbjct: 36  VNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDS---------GCGGGEGVE 86

Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
            G  +LV+ +     + D+Q +F E+G ++   ++ DR +G   G A + +E   +A  A
Sbjct: 87  TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 145

Query: 148 ITAMNGGELLTQTLTVDWAFSNGP 171
           +    G  L  + + +    S   
Sbjct: 146 MKQYKGVPLDGRPMDIQLVASQID 169

>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 = 61.1 bits (149), Expect = 4e-13
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 2/66 (3%)

Query: 103 EDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
           ++DL       G  +I  +    +R  G  KG+AL+   +   ++  +  +   EL  Q 
Sbjct: 15  DEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN 74

Query: 161 LTVDWA 166
             V  +
Sbjct: 75  PVVTPS 80

>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 = 61.1 bits (149), Expect = 6e-13
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 9/83 (10%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V G+        L   F  +G IR +    D   G    +A I+YE+ + AQ A   M G
Sbjct: 22  VGGLGPNTSLAALAREFDRFGSIRTI----DHVKG--DSFAYIQYESLDAAQAACAKMRG 75

Query: 154 GEL--LTQTLTVDWAFSNGPSTG 174
             L    + L VD+A  +GPS+G
Sbjct: 76  FPLGGPDRRLRVDFA-KSGPSSG 97

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 61.2 bits (149), Expect = 6e-13
 Identities = 18/102 (17%), Positives = 41/102 (40%), Gaps = 13/102 (12%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +   A + +L+  F  YG +R + +  +       G+A +E+E+  +A++A+  ++G
Sbjct: 5   VGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGLDG 59

Query: 154 GELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRR 195
             +    + V+ +            +  R  R    R     
Sbjct: 60  KVICGSRVRVELSTG--------MPRRSRFDRPPARRKLLEV 93

>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 = 60.7 bits (148), Expect = 6e-13
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 8/84 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  V       +L+++F   G +    +        VK YA +  E   +A+ AI  +
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIAQL 63

Query: 152 NGGELLTQTLTVDWAFSNGPSTGP 175
           NG E+  + + V+ +      +GP
Sbjct: 64  NGKEVKGKRINVELSTKGQKKSGP 87

>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 = 64.6 bits (158), Expect = 7e-13
 Identities = 10/73 (13%), Positives = 30/73 (41%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +T       + +++++  +   +         R    + +A I+  + E+A+  +  +NG
Sbjct: 122 MTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG 181

Query: 154 GELLTQTLTVDWA 166
            ++   TL    +
Sbjct: 182 LKIEGYTLVTKVS 194

>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 = 64.2 bits (157), Expect = 9e-13
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRR-TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL 161
           E+ L+  F  +G I  +++   ++   F    A + +EN + A+ A+  MN   L  + +
Sbjct: 225 ENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREI 283

Query: 162 TVDWAFS 168
           +V  A  
Sbjct: 284 SVSLADK 290

>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 = 60.0 bits (146), Expect = 3e-11
 Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 78  DGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
                  R+ E   +LV  + +   ++ +   F   G I ++ +           +A IE
Sbjct: 30  KANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIE 87

Query: 138 YENFEEAQNAITAMNG 153
           +  ++ A  AIT  + 
Sbjct: 88  FARYDGALAAITKTHK 103

>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 = 60.7 bits (148), Expect = 7e-13
 Identities = 19/80 (23%), Positives = 41/80 (51%), Gaps = 13/80 (16%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
           EA E +++++F +YG++    +        +K Y  +  E+   A++AI  ++  +L   
Sbjct: 19  EATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70

Query: 160 TLTVDWAF-----SNGPSTG 174
            + V+ +      S+GPS+G
Sbjct: 71  NINVEASKNKSKASSGPSSG 90

>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 = 60.7 bits (148), Expect = 8e-13
 Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 8/91 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFV---KGYALIEYENFEEAQNAI 148
           + +  ++    E+ L+ VF + G I++  ++  +    V    G+  +EY+  E+AQ A+
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67

Query: 149 TAMNGGELLTQTLTVDWAF-----SNGPSTG 174
             + G  +    L V  +      ++GPS+G
Sbjct: 68  KQLQGHTVDGHKLEVRISERATKPASGPSSG 98

>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 = 61.2 bits (149), Expect = 8e-13
 Identities = 23/88 (26%), Positives = 46/88 (52%), Gaps = 8/88 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V  +  + +  D+++VF +YG IR++ L   R       +A +E+E+  +A++A+   
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAVYGR 81

Query: 152 NGGELLTQTLTVDWA-----FSNGPSTG 174
           +G +     L V++        +GPS+G
Sbjct: 82  DGYDYDGYRLRVEFPRSGRGTGSGPSSG 109

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 61.2 bits (149), Expect = 8e-13
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           +    +    +  DL++ F   G++R++ +  DR +   KG A +E+   +    AI  +
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 152 NGGELLTQTLTVDWAFSNGP 171
            G  LL   + V  + +   
Sbjct: 87  TGQRLLGVPIIVQASQAEKN 106

>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 = 61.0 bits (148), Expect = 1e-12
 Identities = 18/100 (18%), Positives = 32/100 (32%), Gaps = 6/100 (6%)

Query: 80  GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE 139
           G          +IL   +       ++Q  F  +G +  + L     T  V      E+ 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIV------EFL 54

Query: 140 NFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRK 179
              EA+ A   +   +     L ++WA        P K+ 
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKD 94

>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 = 60.7 bits (148), Expect = 1e-12
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 7/85 (8%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           ++ +     E +L+N+   +G++ +  +  D  +G  +G      E+ E+ +  I   NG
Sbjct: 30  ISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNG 88

Query: 154 GELLTQTLTVDWA------FSNGPS 172
             + T              FS   S
Sbjct: 89  KFIKTPPGVSAPTEPLLCKFSGPSS 113

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 59.7 bits (145), Expect = 1e-12
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 91  IILVTG--VHEEAQEDDLQNV----FGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEA 144
           +I+V         + + L+NV    F ++G+I N         G  KGY  +EY +   A
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHA 60

Query: 145 QNAITAMNGGEL 156
            +A+   +G +L
Sbjct: 61  VDAVKNADGYKL 72

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 61.5 bits (149), Expect = 2e-12
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 2/88 (2%)

Query: 103 EDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT 160
           +  L  V    G  ++  L    +R  G  KGYA +   +       +  + G  L  + 
Sbjct: 69  DQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK 128

Query: 161 LTVDWAFSNGPSTGPFKRKNMRPGRTHR 188
           + V  A     S    + +     R  R
Sbjct: 129 VDVRPATRQNLSQFEAQARKRECVRVPR 156

>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 = 59.6 bits (145), Expect = 3e-12
 Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 3/100 (3%)

Query: 76  GTDGGPGPQRSIEG-WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G      G  II V  +      D++ + F  Y  I           G   G A
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG 174
           ++ +E+ +EA  A+  +N   + ++ + +     +GPS+G
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLV--LGSGPSSG 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 = 58.4 bits (142), Expect = 5e-12
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
                +L+  F EYG +    +        VK YA +  E  E+A  AI  ++  E   +
Sbjct: 21  TCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDAVEAIRGLDNTEFQGK 72

Query: 160 TLTVDWA-----FSNGPSTG 174
            + V  +      ++GPS+G
Sbjct: 73  RMHVQLSTSRLRTASGPSSG 92

>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 = 58.2 bits (141), Expect = 6e-12
 Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 12/88 (13%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ILV  + +++   ++ ++  +Y                 K  A +   N E+AQNAI   
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 152 NGGELLTQTLTVDWA-----FSNGPSTG 174
           +      + L V          +GPS+G
Sbjct: 61  HQYSFRGKDLIVQLQPTDALLCSGPSSG 88

>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 = 58.4 bits (142), Expect = 6e-12
 Identities = 15/80 (18%), Positives = 41/80 (51%), Gaps = 7/80 (8%)

Query: 91  IILVTGVHEEAQEDDLQ----NVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQN 146
            I +  ++E+ ++D+L+     +F  +G+I ++ ++   +    +G A + ++    A N
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATN 66

Query: 147 AITAMNGGELLTQTLTVDWA 166
           A+ +M G     + + + +A
Sbjct: 67  ALRSMQGFPFYDKPMRIQYA 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 = 58.3 bits (141), Expect = 9e-12
 Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 82  GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGE-IRNLHLNLDRR-TGFVKGYALIEYE 139
           G   S     + + G+ +  + +++     +  E + ++ +          +G+A +EYE
Sbjct: 1   GSSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYE 60

Query: 140 NFEEAQNAITAMNGG--ELLTQTLTVDWA 166
           +   A  A   +  G  +L    + VDWA
Sbjct: 61  SHRAAAMARRKLMPGRIQLWGHQIAVDWA 89

>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 = 57.7 bits (140), Expect = 9e-12
 Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 9/92 (9%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  G  ++I    + V G+ +   E DL+N F ++GEIR + +   ++  F++    
Sbjct: 1   GSSGSSGEDKTIT--TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQ---- 54

Query: 136 IEYENFEEAQNAITAM-NGGELLTQTLTVDWA 166
             +   + A+ A     N   +  + L V W 
Sbjct: 55  --FATRQAAEVAAEKSFNKLIVNGRRLNVKWG 84

>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 = 58.0 bits (141), Expect = 9e-12
 Identities = 12/81 (14%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +  ++      +L+    E     +L + +D RTG  + +  +++E+ E+ + A+  + G
Sbjct: 22  IGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEKAL-ELTG 79

Query: 154 GELLTQTLTVDWAFSNGPSTG 174
            ++    + ++       + G
Sbjct: 80  LKVFGNEIKLEKPKGRDGTRG 100

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 57.2 bits (139), Expect = 2e-11
 Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 19/92 (20%)

Query: 99  EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
           +   ++DL  +F  YG I  +++           +  I+++N +  ++AI   +      
Sbjct: 21  KNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECESQEMNFG 72

Query: 159 QTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSR 190
           + L ++ +             N RP   H   
Sbjct: 73  KKLILEVS-----------SSNARPQFDHGDH 93

>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 = 57.8 bits (140), Expect = 2e-11
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 13/81 (16%)

Query: 99  EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
              ++ D++ +F +YG +    +         KGYA ++Y N   A+ A+   NG  L  
Sbjct: 38  ALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAG 89

Query: 159 QTLTVDWAFS-----NGPSTG 174
           QTL ++ A       +GPS+G
Sbjct: 90  QTLDINMAGEPKPDRSGPSSG 110

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 57.4 bits (139), Expect = 2e-11
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V     E  ++ +  +F ++G+I N         G  KGY  +EY +   A +A+   +G
Sbjct: 26  VGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADG 83

Query: 154 GEL 156
            +L
Sbjct: 84  YKL 86

>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 = 60.3 bits (145), Expect = 2e-11
 Identities = 20/109 (18%), Positives = 50/109 (45%), Gaps = 9/109 (8%)

Query: 92  ILVTGVHEEAQEDDL----QNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           I +  ++E+ ++D+L      +F ++G+I ++ +    R+  ++G A + ++    A NA
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 68

Query: 148 ITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
           + +M G     + + + +A +   S    K K     R  +    + + 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKT--DSDIIAKMKGTFVERDRKREKRKPKS 115

>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 = 57.2 bits (137), Expect = 3e-10
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
              +    I+ +T + EE  E  L  +F ++   + + L   R        A +E++N  
Sbjct: 201 LSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEV 255

Query: 143 EAQNAITAMNGGELL-TQTLTVDWA 166
           +A  A  A+ G ++     + + +A
Sbjct: 256 QAGAARDALQGFKITQNNAMKISFA 280

>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 = 56.6 bits (137), Expect = 3e-11
 Identities = 11/68 (16%), Positives = 30/68 (44%), Gaps = 8/68 (11%)

Query: 99  EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
           +   ++DL  +F  YG I  +++           +  I+++N +  ++AI   +      
Sbjct: 33  KNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFG 84

Query: 159 QTLTVDWA 166
           + L ++ +
Sbjct: 85  KKLILEVS 92

>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 = 56.9 bits (137), Expect = 3e-11
 Identities = 25/121 (20%), Positives = 49/121 (40%), Gaps = 22/121 (18%)

Query: 62  ERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHL 121
            +H+ L     E++         +S+   ++   G+      + L  V  + G +  L +
Sbjct: 8   AKHTLLRHEGIETV-----SYATQSL---VVANGGLGNGVSRNQLLPVLEKCGLVDALLM 59

Query: 122 NLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQTLTVDWAF-----SNGPST 173
             +      K Y+   Y   EE++ A   +NG E++    Q +T+   F      +GPS+
Sbjct: 60  PPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSGPSS 113

Query: 174 G 174
           G
Sbjct: 114 G 114

>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 = 57.5 bits (139), Expect = 3e-11
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 98  HEEAQEDDLQNVFGEYGEIRNLHLNL-----DRRTGFVKGYALIEYENFEEAQNAITAMN 152
            +  QE DL+ +FG Y +  +    +       + G +KG A I   N + A  A+   N
Sbjct: 54  AKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN 113

Query: 153 GGELLTQTLTVDWA 166
           G  L  + + V +A
Sbjct: 114 GYVLFGKPMVVQFA 127

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 57.2 bits (138), Expect = 4e-11
 Identities = 19/94 (20%), Positives = 38/94 (40%), Gaps = 7/94 (7%)

Query: 77  TDGGPGPQRSIEGWIILVTGVHEEAQEDDLQ----NVFGEYGEIRNLHLNLDRRTGFVKG 132
            D G  P  +    ++L+T ++ E  ++ LQ     +    G+I ++ +     +    G
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDNSG 73

Query: 133 YALIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
            A I +   E AQ  + A  G       L + ++
Sbjct: 74  KAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS 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 = 58.9 bits (143), Expect = 5e-11
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           V  +  +  E+D + +F  YGE   + +N DR      G+  I  E+   A+ A   ++G
Sbjct: 27  VGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAELDG 80

Query: 154 GELLTQTLTVDWA 166
             L ++ L + +A
Sbjct: 81  TILKSRPLRIRFA 93

>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 = 57.0 bits (138), Expect = 2e-10
 Identities = 18/106 (16%), Positives = 37/106 (34%), Gaps = 9/106 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +      + L+  F ++G +    + +D   G   G   +E+     A+ A+   
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERC 157

Query: 152 NGGE-LLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
             G  LLT T              P ++ +   G   +     ++Y
Sbjct: 158 GDGAFLLTTTPRPVIVE-------PMEQFDDEDGLPEKLMQKTQQY 196

>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 = 56.8 bits (137), Expect = 7e-11
 Identities = 24/141 (17%), Positives = 53/141 (37%), Gaps = 27/141 (19%)

Query: 48  KKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWI---------------- 91
           K  KG    E  D+    ++  +     G DG      + + +                 
Sbjct: 10  KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDS 69

Query: 92  ------ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
                 + V  +     + +L+  FG YG +R++ +  +       G+A +E+E+  +A 
Sbjct: 70  CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAA 124

Query: 146 NAITAMNGGELLTQTLTVDWA 166
           +A+  ++G  L    + V+ +
Sbjct: 125 DAVRELDGRTLCGCRVRVELS 145

>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 = 55.2 bits (133), Expect = 1e-10
 Identities = 25/110 (22%), Positives = 45/110 (40%), Gaps = 17/110 (15%)

Query: 76  GTDGGPGPQRSIE-GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G    +    ++ V G+ E   E DL     ++G I  + +         K  A
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQA 54

Query: 135 LIEYENFEEAQNAITAMNGGELLT--QTLTVDWAFS--------NGPSTG 174
           L+E+EN + A+  +T      +    Q    +++ S        +GPS+G
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ 159
              + D+  +F +   IR++ L  D+ T   KG+  +E++  +  + A+   +G  L  +
Sbjct: 26  NTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDR 83

Query: 160 TLTVDWA 166
           +L VD A
Sbjct: 84  SLRVDIA 90

>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 = 55.3 bits (133), Expect = 2e-10
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 11/92 (11%)

Query: 94  VTGVHEEAQEDDL---QNVFGEYGEIRNLHLNLDRRTGFVK---GYALIEYENFEEAQNA 147
           V G+ +   + ++      FG++G+I  + +N        +     A + Y   E+A  A
Sbjct: 20  VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79

Query: 148 ITAMNGGELLTQTLTVDWA-----FSNGPSTG 174
           I  +N   +  +TL            +GPS+G
Sbjct: 80  IQCVNNVVVDGRTLKASLGTTKYCSYSGPSSG 111

>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 = 54.2 bits (131), Expect = 2e-10
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 1/92 (1%)

Query: 76  GTDGGPGPQRSIEG-WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G      G  +I V  +      D++ + F  Y  I           G   G A
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWA 166
           ++ +E+ +EA  A+  +N   + ++ + +   
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>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 = 54.4 bits (131), Expect = 3e-10
 Identities = 23/120 (19%), Positives = 44/120 (36%), Gaps = 17/120 (14%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ GGP  +RS     ++V+G+       DL++   E G++    +  D       G  +
Sbjct: 4   GSSGGPPSRRS--ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRR 195
           +E+   E+   A+  ++  +  +      +           K    R     RSRS    
Sbjct: 55  VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR--------VKVDGPRSPSYGRSRSSGPS 106

>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 = 51.5 bits (124), Expect = 2e-09
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+     E ++++ F  YG ++ + +  D RTG  KGY  + + N  + Q  +   
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV--E 68

Query: 152 NGGELLTQTLTVDWA 166
           +      + L +  A
Sbjct: 69  SQINFHGKKLKLGPA 83

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 51.3 bits (123), Expect = 3e-09
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 78  DGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
           +    P ++    ++ + G+ +   E DL     E+G I  + +         K  AL+E
Sbjct: 10  ENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVE 63

Query: 138 YENFEEAQNAITAMNGGELLT--QTLTVDWAFS 168
           +E+   A NA+      ++        V+++ S
Sbjct: 64  FEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 51.3 bits (123), Expect = 3e-09
 Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           + G   +A  DD++    + G++ N+ +       F KG   + +++ E A+  +    G
Sbjct: 16  IKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFV-ETPG 73

Query: 154 GELLTQTLTVDWA 166
            +     L + + 
Sbjct: 74  QKYKETDLLILFK 86

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 50.6 bits (121), Expect = 8e-09
 Identities = 21/115 (18%), Positives = 41/115 (35%), Gaps = 9/115 (7%)

Query: 80  GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE 139
           GP  +RS     ++V+G+       DL++   E G++    +  D       G  ++E+ 
Sbjct: 9   GPPSRRS--ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFV 59

Query: 140 NFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRR 194
             E+   A+  ++  +  +      +                R     RSRS  R
Sbjct: 60  RKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSRSR 114

>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 = 49.9 bits (120), Expect = 9e-09
 Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRRT-GFVKGYALIEYENFEEAQNAITAMNGGELLT 158
           +  E+ ++  F     I  + L  +      +KG+   E+E+ +   +A+ ++N   L  
Sbjct: 30  DVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN 87

Query: 159 QTLTVDWA 166
           + + VD A
Sbjct: 88  RRIRVDVA 95

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+  + +  + +  F ++G I +  L LD+ TG  +G+  + Y++ +         
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QN 148

Query: 152 NGGELLTQTLTVDWAFS 168
              +   + + +  A  
Sbjct: 149 KFIDFKDRKIEIKRAEP 165

>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 = 42.9 bits (102), Expect = 1e-05
 Identities = 14/61 (22%), Positives = 31/61 (50%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G++ +  ED+L+  FG+YG + +L +  D  TG  +G+  + +E        +   
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 152 N 152
           +
Sbjct: 66  H 66

>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 = 49.6 bits (119), Expect = 1e-08
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 100 EAQEDDLQNVFGEYGEIRNLHLNLDRR-TGFVKGYALIEYENFEEAQNAITAMNGGELLT 158
           +  E+ ++  F     I  + L  +      +KG+   E+E+ +   +A+ ++N   L  
Sbjct: 26  DVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN 83

Query: 159 QTLTVDWA-----FSNGPSTG 174
           + + VD A       +GPS+G
Sbjct: 84  KRIRVDVADQAQDKDSGPSSG 104

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 20/88 (22%), Positives = 36/88 (40%), Gaps = 10/88 (11%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEY 138
           G      S   W++L   +  +     L+ +  ++G + + H  L+      +G AL +Y
Sbjct: 1   GAMAWGSS---WLLL-KNLTAQIDGPTLRTLCMQHGPLVSFHPYLN------QGIALCKY 50

Query: 139 ENFEEAQNAITAMNGGELLTQTLTVDWA 166
              EEA  A  A+N   L   T+  +  
Sbjct: 51  TTREEANKAQMALNNCVLANTTIFAESP 78

>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 = 49.5 bits (118), Expect = 2e-08
 Identities = 17/108 (15%), Positives = 36/108 (33%), Gaps = 8/108 (7%)

Query: 61  SERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH 120
           S  H           G+  G      +   +I +  +  +  E ++ ++   +G++ NL 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL 62

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAIT--AMNGGELLTQTLTVDWA 166
           +         K  A IE    E A   +         L  Q + + ++
Sbjct: 63  MLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS 104

>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 = 50.4 bits (121), Expect = 3e-08
 Identities = 22/113 (19%), Positives = 46/113 (40%), Gaps = 9/113 (7%)

Query: 78  DGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
           +    P   +    I V G+ E+ +E  L++ F +YG+I  + +  DR +G  +G+A + 
Sbjct: 93  EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152

Query: 138 YENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSR 190
           +++ +     +       +      V  A S        K++      + R R
Sbjct: 153 FDDHDSVDKIV-IQKYHTVNGHNCEVRKALS--------KQEMASASSSQRGR 196

>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 = 41.1 bits (97), Expect = 5e-05
 Identities = 16/91 (17%), Positives = 38/91 (41%), Gaps = 1/91 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  E  ++ L++ F ++G + +  +  D  T   +G+  + Y   EE   A+   
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 74

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMR 182
              ++  + +    A S   S  P     ++
Sbjct: 75  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 105

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 48.3 bits (115), Expect = 4e-08
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 5/75 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +A+  DL+    E G +      L       +  A + Y +   AQ A++ +
Sbjct: 22  VYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSCL 76

Query: 152 NGGELLTQTLTVDWA 166
            G  L T TL V  A
Sbjct: 77  QGLRLGTDTLRVALA 91

>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 = 50.2 bits (119), Expect = 4e-08
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G   +A  DD++    + G++ N+ +       F KG   + +++ E A+  +   
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVETP 170

Query: 152 N---GGELLTQTLTVDW 165
                   L      D+
Sbjct: 171 GQKYKETDLLILFKDDY 187

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.9 bits (114), Expect = 7e-08
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 8/78 (10%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           +I +  +  +  E ++ ++   +G++ NL +         K  A IE    E A   +  
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY 71

Query: 151 --MNGGELLTQTLTVDWA 166
                  L  Q + + ++
Sbjct: 72  YTSVTPVLRGQPIYIQFS 89

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 49.8 bits (118), Expect = 8e-08
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 6/76 (7%)

Query: 95  TGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG 154
             +     E  ++ VF   G+I  +           K    ++++    A+ A  AM+  
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQ 202

Query: 155 ELLTQTLTVDWAFSNG 170
            LL  +         G
Sbjct: 203 TLLLPSDKEWDDRREG 218

>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 = 47.0 bits (112), Expect = 9e-08
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN-----LDRRTGFVKGYALIEYENFEEAQN 146
           + V  +     E+ + + F     +  L        L  +    K +A +E+ + +E   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 147 AITAMNGGELLTQTLTV 163
           A+ A +G     Q+L +
Sbjct: 69  AM-AFDGIIFQGQSLKI 84

>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 = 47.5 bits (113), Expect = 9e-08
 Identities = 15/91 (16%), Positives = 37/91 (40%), Gaps = 13/91 (14%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT- 149
           ++ +  +  E  E ++  +   +G++ N+ +         K  A +E    E A   +  
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNY 70

Query: 150 -AMNGGELLTQTLTVDWA-----FSNGPSTG 174
            +     L  Q + + ++      ++GPS+G
Sbjct: 71  YSAVTPHLRNQPIYIQYSNHKELKTSGPSSG 101

>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 = 47.4 bits (113), Expect = 1e-07
 Identities = 18/120 (15%), Positives = 38/120 (31%), Gaps = 8/120 (6%)

Query: 76  GTDGGPGP-QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G    +       +T +     + D+           N    L    G   G A
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRR 194
           L++++N ++A+ +   ++  +L  +   V         T    R+  +         P  
Sbjct: 61  LVQFKNEDDARKSE-RLHRKKLNGREAFVH------VVTLEDMREIEKNPPAQGKSGPSS 113

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 46.5 bits (111), Expect = 1e-07
 Identities = 15/102 (14%), Positives = 38/102 (37%), Gaps = 19/102 (18%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+G         L   F  +G + ++   +D+  G    +A++E  +    +  + + 
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVV--MDKDKG---VFAIVEMGDVGAREAVL-SQ 64

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPR 193
           +   L    L V             + +  +  ++  S+SP+
Sbjct: 65  SQHSLGGHRLRV-------------RPREQKEFQSPASKSPK 93

>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 = 49.1 bits (116), Expect = 2e-07
 Identities = 26/105 (24%), Positives = 46/105 (43%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  V+ +  E  L+  F  YG I+ +H+   +R+G  +GYA IEYE+  +  +A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
           +G ++  + + VD            +R     G T R  +     
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIR 209

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.8 bits (108), Expect = 6e-07
 Identities = 17/107 (15%), Positives = 39/107 (36%), Gaps = 7/107 (6%)

Query: 76  GTDGGPGPQRSIEGWIILVT--GVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
                 G   + +  ++ +    +      D L  +F ++G +  +              
Sbjct: 13  AAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----Q 68

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKN 180
           AL++Y +   AQ+A  +++G  +     T+   FS   ++   K  N
Sbjct: 69  ALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK-LTSLNVKYNN 114

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 44.6 bits (106), Expect = 9e-07
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 12/94 (12%)

Query: 92  ILVTGVHEEAQEDDLQNVFGE-YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           + V  +  +  +  L   F + Y   R   + LD+ TG  KGY  +++ +  E + A+T 
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70

Query: 151 MNGGELL-TQTLTVDWAFS---------NGPSTG 174
             G   L ++ + +  A           +GPS+G
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVESGPSSG 104

>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 = 43.6 bits (104), Expect = 1e-06
 Identities = 14/57 (24%), Positives = 31/57 (54%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           I V G+  +  E+ ++  FG +GE+ ++ L +D +T   +G+  I ++  E  +  +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 18/103 (17%), Positives = 31/103 (30%), Gaps = 6/103 (5%)

Query: 61  SERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLH 120
           S  H           G+     P +      I +  + E     DL+++  E        
Sbjct: 3   SSHHHHHHSSGLVPRGSHMSKLPAKRYR---ITMKNLPEGCSWQDLKDLARENSLE---T 56

Query: 121 LNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV 163
                 T    G   +E+ + E    A+  +N  E     +TV
Sbjct: 57  TFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 18/111 (16%), Positives = 40/111 (36%), Gaps = 8/111 (7%)

Query: 70  RNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF 129
           +     G    P     +   ++ +         D L  V    G+++ + +        
Sbjct: 8   KRITRPGNTDDPSGGNKV--LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-- 63

Query: 130 VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKN 180
               A++E+E+   AQ A  A+NG ++     T+   ++  P+     R +
Sbjct: 64  ---QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR-PTRLNVIRND 110

>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 = 45.1 bits (106), Expect = 2e-06
 Identities = 15/95 (15%), Positives = 37/95 (38%), Gaps = 8/95 (8%)

Query: 76  GTDGGPGPQRSIEGWIILVT--GVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
                 G   + +  ++ +    +      D L  +F ++G +  +              
Sbjct: 31  AAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----Q 86

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQ--TLTVDWA 166
           AL++Y +   AQ+A  +++G  +     TL +D++
Sbjct: 87  ALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121

>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 = 42.6 bits (101), Expect = 6e-06
 Identities = 21/100 (21%), Positives = 45/100 (45%), Gaps = 6/100 (6%)

Query: 80  GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE 139
           G       +   I V G+     E +L+  F ++G +  + +  D      +G+  I +E
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 140 NFEEAQNAITAMNGGELLTQTLTVDWAF-----SNGPSTG 174
           + E++ +    M+  +++ + + V  A      S+GPS+G
Sbjct: 61  D-EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSGPSSG 99

>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 = 42.6 bits (101), Expect = 6e-06
 Identities = 23/105 (21%), Positives = 49/105 (46%), Gaps = 8/105 (7%)

Query: 76  GTDGGPGPQRSIEGWI-ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G +R+++    ++V G+  +  E DL+  F  +GE+  + +  D +TG  KG+ 
Sbjct: 1   GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS-----NGPSTG 174
            + +  +E     ++  +   +  +        S     +GPS+G
Sbjct: 61  FVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSGPSSG 103

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 42.3 bits (100), Expect = 6e-06
 Identities = 16/95 (16%), Positives = 33/95 (34%), Gaps = 4/95 (4%)

Query: 80  GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE 139
           G           + + G      E ++            + +  +   G   GY  +++ 
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFS 58

Query: 140 NFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTG 174
           N EE + A+   N   +  + + V     +GPS+G
Sbjct: 59  NEEEVKQALK-CNREYMGGRYIEVFRE-KSGPSSG 91

>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 = 42.5 bits (100), Expect = 7e-06
 Identities = 15/105 (14%), Positives = 36/105 (34%), Gaps = 7/105 (6%)

Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
            G+ + + G+  EA+   + + F +   + +         G   G   +E+ N  + + A
Sbjct: 24  AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83

Query: 148 ITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSP 192
           +   +   +  + + V       P T     + +   R      P
Sbjct: 84  L-CRHKQYMGNRFIQVH------PITKKGMLEKIDMIRKRLQSGP 121

>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 = 42.3 bits (100), Expect = 8e-06
 Identities = 20/77 (25%), Positives = 33/77 (42%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  G Q+      I V G+     +  L+  F  +G+I    +  DR+TG  +GY  
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 136 IEYENFEEAQNAITAMN 152
           +   +   A+ A    N
Sbjct: 64  VTMADRAAAERACKDPN 80

>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 = 42.0 bits (99), Expect = 9e-06
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 76  GTDGGPGPQ-RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G   +S  G  + + G+   A E+D+ N F        +H+ +    G V G A
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEA 58

Query: 135 LIEYENFEEAQNAITAMNGGEL 156
            +E+   E+A  A+ A +   +
Sbjct: 59  DVEFATHEDAVAAM-AKDKANM 79

>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 = 42.2 bits (99), Expect = 1e-05
 Identities = 15/98 (15%), Positives = 32/98 (32%), Gaps = 7/98 (7%)

Query: 65  SRLADRNFESLGTDGG------PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN 118
           S L  R        GG           S     + + G+     ++++   F     + N
Sbjct: 12  SGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPN 71

Query: 119 LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL 156
                    G + G A +++ + E A+ A+   +   +
Sbjct: 72  GITLPVDPEGKITGEAFVQFASQELAEKAL-GKHKERI 108

>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 = 42.0 bits (99), Expect = 1e-05
 Identities = 21/108 (19%), Positives = 45/108 (41%), Gaps = 14/108 (12%)

Query: 78  DGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
             G     + +   + V G+   A E+D+++ F     +  +HL  D   G   G  L++
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVK 62

Query: 138 YENFEEAQNAITAMNGGELLTQTLTVDWA-----------FSNGPSTG 174
           + + ++   A+   N   ++ + + V  A            ++GPS+G
Sbjct: 63  FLSPQDTFEALK-RNRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109

>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 Length = 104

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 11/55 (20%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 99  EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +E  E+    +  +YGE+  +++  D     + G   +++   E+A+ A+  +N 
Sbjct: 37  DEFFEEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

>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 = 41.4 bits (97), Expect = 2e-05
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 76  GTDGGPGPQ---RSIEGWIILVTGVHEEAQEDDLQNVFGEY---GEIRNLHLNLDRRTGF 129
           G+ G  G        EG+++ + G+      +D+QN   +      +  +H    R  G 
Sbjct: 1   GSSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GR 59

Query: 130 VKGYALIEYENFEEAQNAITAMNGGEL 156
             G A +E E+ ++ + A+   +   +
Sbjct: 60  QSGEAFVELESEDDVKLAL-KKDRESM 85

>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 = 41.8 bits (98), Expect = 2e-05
 Identities = 23/108 (21%), Positives = 48/108 (44%), Gaps = 5/108 (4%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR-NLHLNLDRRTGFVKGYA 134
           G+       +S  G  + + G+  +A E+D+ N F     +R ++ +  D R     G A
Sbjct: 33  GSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRV---TGEA 89

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMR 182
            +E+   EEA  A+ + +   +  + + +    + G S G +  + M+
Sbjct: 90  DVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 40.9 bits (95), Expect = 2e-05
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
           +D L  +  +YGE+ NL L+  +      G A++E+   + A+ A+    G  L+   L 
Sbjct: 31  KDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVG--LVDNPLK 83

Query: 163 VDWAFSNGPST 173
           + W        
Sbjct: 84  ISWLEGQPQDA 94

>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 = 40.5 bits (95), Expect = 3e-05
 Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 76  GTDGGPGPQRSIEGW-IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G          + + G+     ++++   F     + N         G   G A
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 135 LIEYENFEEAQNAITAMNGGEL 156
            +++ + E A+ A+   +   +
Sbjct: 61  FVQFASQEIAEKALK-KHKERI 81

>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 = 39.5 bits (93), Expect = 5e-05
 Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G +     + +     + V G+  +  + DL++ F ++GE+ +  + +D  TG  +G+  
Sbjct: 1   GINASKNEEDA---GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGF 57

Query: 136 IEYENFEEAQNAITAMN 152
           I +++    +  +    
Sbjct: 58  ILFKDAASVEKVLDQKE 74

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 38.2 bits (90), Expect = 1e-04
 Identities = 11/57 (19%), Positives = 29/57 (50%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           I V G+      +D+++ F ++G++ +  L  D+ T   +G+  + +E+ +  +   
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 15/108 (13%), Positives = 35/108 (32%), Gaps = 6/108 (5%)

Query: 45  GAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQED 104
           G+                  + +     + +G           EG+++ + G+      +
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMT--GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVE 59

Query: 105 DLQNVFGEY---GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           D+QN   +         +H    R  G   G A +E  + ++ + A+ 
Sbjct: 60  DVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK 106

>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* Length = 345

 Score = 39.4 bits (91), Expect = 3e-04
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 9/92 (9%)

Query: 96  GVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG-- 153
           G+      + L  V  + G +  L +  +      K Y+   Y   EE++ A   +NG  
Sbjct: 27  GLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKE 80

Query: 154 -GELLTQTLTVDWAFSNGPSTGPFKRKNMRPG 184
             + L Q +T+   F         + + + PG
Sbjct: 81  VVDDLGQKITLYLNFVEKVQWKELRPQALPPG 112

>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 Length = 114

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 10/51 (19%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +DD+     ++G +  +H+ +D+ +     Y  ++  +   A  A+ A++G
Sbjct: 31  KDDVIEECNKHGGV--IHIYVDKNSAQGNVY--VKCPSIAAAIAAVNALHG 77

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 36.7 bits (86), Expect = 4e-04
 Identities = 9/59 (15%), Positives = 27/59 (45%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           + + G+  +  ++ L+  FG++GE++   +  D  T   +G+  + + +       +  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 13/93 (13%)

Query: 76  GTDGGPGPQRSIEG---------WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN---L 123
           G+ G  G   S E           I+ + G+   A  +++   FG++  I         +
Sbjct: 1   GSSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFV 60

Query: 124 DRRTGFVKGYALIEYENFEEAQNAITAMNGGEL 156
               G   G A + +   E AQNA+   +   L
Sbjct: 61  TYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLL 92

>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 = 36.4 bits (85), Expect = 6e-04
 Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 5/57 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAI 148
           + V     +  ED+L+  F +YG++ ++ +    R      +A + + + + AQ+  
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLC 59

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	196
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.94
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.9
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.89
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.87
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.87
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.86
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.86
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.86
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.86
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.86
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.86
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.85
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.85
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.85
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.85
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.85
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.85
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.84
2div_A	99	TRNA selenocysteine associated protein; structural	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.84
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.84
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.84
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.84
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.84
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.84
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.84
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.84
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.84
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.83
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.83
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.83
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.82
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.82
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.82
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.82
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.82
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.82
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.82
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.82
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.81
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.81
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.81
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.81
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.81
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.81
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.81
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.81
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.8
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.8
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.8
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.79
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.79
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.79
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.79
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.79
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.79
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.79
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.79
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.79
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.78
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.78
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.78
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.78
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.78
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.78
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.78
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.78
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.78
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.77
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.77
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.77
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.77
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.77
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.77
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.77
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.76
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.76
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.76
1x5p_A	97	Negative elongation factor E; structure genomics,	99.76
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.75
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.75
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.75
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.75
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.74
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.74
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.73
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.73
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.73
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.73
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.73
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.72
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.72
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.72
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.72
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.71
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.7
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.69
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.65
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.65
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.65
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.65
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.63
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.62
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.6
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.59
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.57
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.57
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.53
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.53
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.52
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.5
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.43
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.37
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.26
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.23
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.98
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.96
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.65
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.19
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.83
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.77
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.42
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.32
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.26
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.04
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.98
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.19
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.02
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.31
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.22
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	94.02
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	93.44
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	91.74
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	90.25
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	90.0
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	87.92
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	87.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	86.21
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	85.35
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	83.9
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	83.48
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	83.0
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	82.41
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	82.28
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	81.6
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	81.53
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	80.84
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	80.72

>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=99.94  E-value=3e-26  Score=170.76  Aligned_cols=93  Identities=62%  Similarity=1.140  Sum_probs=83.3

Q ss_pred             CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           80 GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        80 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      .+.+....+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..||+..|.|+
T Consensus        63 ~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  142 (165)
T 1rk8_A           63 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ  142 (165)
T ss_dssp             ---CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            44566677789999999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EeEEEEcccCCCC
Q 043064          160 TLTVDWAFSNGPS  172 (196)
Q Consensus       160 ~l~v~~a~~~~~~  172 (196)
                      .|.|.|+.++.+.
T Consensus       143 ~l~V~~a~~~~~~  155 (165)
T 1rk8_A          143 TIQVDWCFVKGPK  155 (165)
T ss_dssp             ECEEEESEECC--
T ss_pred             EEEEEEecCCCCC
Confidence            9999999887754

>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=99.90  E-value=3.9e-23  Score=141.35  Aligned_cols=82  Identities=27%  Similarity=0.513  Sum_probs=78.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..+++|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.|++|+|.||
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            34688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 043064          167 FS  168 (196)
Q Consensus       167 ~~  168 (196)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            76

>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=99.89  E-value=4e-23  Score=146.92  Aligned_cols=93  Identities=61%  Similarity=1.204  Sum_probs=86.0

Q ss_pred             CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           80 GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        80 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      .+.+....+.++|||+|||+.+|+++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.||+..|.|+
T Consensus        13 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             -CCBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            34455667789999999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EeEEEEcccCCCC
Q 043064          160 TLTVDWAFSNGPS  172 (196)
Q Consensus       160 ~l~v~~a~~~~~~  172 (196)
                      .|.|.|+.++...
T Consensus        93 ~l~v~~a~~~~~~  105 (126)
T 3ex7_B           93 PISVDWCFVRGPP  105 (126)
T ss_dssp             BCEEEESEESSSC
T ss_pred             EEEEEEecCCCCC
Confidence            9999999988765

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

Probab=99.89  E-value=3.3e-22  Score=147.47  Aligned_cols=123  Identities=22%  Similarity=0.341  Sum_probs=98.8

Q ss_pred             CCcCcccccCCCcHHHHHHhhhhccc-C-------------------CCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHH
Q 043064           49 KTKGRGFREEADSERHSRLADRNFES-L-------------------GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQN  108 (196)
Q Consensus        49 ~~kG~gf~~~~~~~~~~~~~~~~~~~-~-------------------~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~  108 (196)
                      +++|||||.|.+...+.+.. ..++. .                   ..............++|||+|||+.+++++|+.
T Consensus        11 ~~~G~~fV~f~~~~~A~~al-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~   89 (158)
T 2kn4_A           11 TLKGETTTEAVDAATAEKVF-KQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRR   89 (158)
T ss_dssp             SCEEEEEEECSSHHHHHHHH-HHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCHHHHHH
T ss_pred             cccchhHHHHHHHHhHHHHH-HhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            68999999999655554432 11110 0                   000011122334578999999999999999999


Q ss_pred             hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCC
Q 043064          109 VFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       109 ~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~  172 (196)
                      +|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|.|+.|.|.|+.+..+.
T Consensus        90 ~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           90 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             HHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             HHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            9999999999999999889999999999999999999999999999999999999999876544

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

Probab=99.87  E-value=5.1e-21  Score=133.89  Aligned_cols=90  Identities=26%  Similarity=0.459  Sum_probs=83.9

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+
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            33456789999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++...
T Consensus        89 V~~a~~~~~~   98 (115)
T 2dgo_A           89 TNWATRKPPA   98 (115)
T ss_dssp             EEESSCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999887765

>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=99.87  E-value=1.4e-21  Score=137.34  Aligned_cols=86  Identities=31%  Similarity=0.440  Sum_probs=80.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|++|++.||+..|.|+.|+|.|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456889999999999999999999999999999999987 999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.+....
T Consensus        83 a~~~~~~   89 (116)
T 2fy1_A           83 AKKPSFQ   89 (116)
T ss_dssp             CCCSSCS
T ss_pred             CCCCCCC
Confidence            9876654

>2dgs_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=5.1e-21  Score=130.43  Aligned_cols=87  Identities=17%  Similarity=0.352  Sum_probs=81.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||. |++..|.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999998 99999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2dgs_A           85 RAEPRDSK   92 (99)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCccc
Confidence            99877654

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

Probab=99.86  E-value=5.2e-21  Score=131.32  Aligned_cols=88  Identities=34%  Similarity=0.522  Sum_probs=82.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45567999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99887654

>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=99.86  E-value=4.1e-21  Score=130.86  Aligned_cols=88  Identities=24%  Similarity=0.325  Sum_probs=82.4

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        84 ~a~~~~~~   91 (99)
T 1whw_A           84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             EcCCCccc
Confidence            99887654

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

Probab=99.86  E-value=2.8e-21  Score=134.56  Aligned_cols=83  Identities=14%  Similarity=0.251  Sum_probs=78.9

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++|++.|||..|.|+.|+|.++
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            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 043064          167 FSN  169 (196)
Q Consensus       167 ~~~  169 (196)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

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

Probab=99.86  E-value=4.4e-21  Score=129.65  Aligned_cols=86  Identities=29%  Similarity=0.396  Sum_probs=81.2

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.|+
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            35689999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 043064          167 FSNGPS  172 (196)
Q Consensus       167 ~~~~~~  172 (196)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            877654

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

Probab=99.86  E-value=7.7e-21  Score=129.74  Aligned_cols=89  Identities=26%  Similarity=0.419  Sum_probs=82.4

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+..||+..|.|+.|+
T Consensus        11 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3445667899999999999999999999999999999999997 899999999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++..+
T Consensus        90 v~~a~~~~~~   99 (100)
T 2do4_A           90 VAISNSGPSS   99 (100)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCCCCCC
Confidence            9999887653

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

Probab=99.86  E-value=2.8e-21  Score=133.30  Aligned_cols=92  Identities=62%  Similarity=1.216  Sum_probs=85.0

Q ss_pred             CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           80 GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        80 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      .+.+....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+
T Consensus        14 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   93 (106)
T 1p27_B           14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   93 (106)
T ss_dssp             -CCBCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            34455667789999999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EeEEEEcccCCC
Q 043064          160 TLTVDWAFSNGP  171 (196)
Q Consensus       160 ~l~v~~a~~~~~  171 (196)
                      .|.|.|+.++++
T Consensus        94 ~l~V~~a~~~~~  105 (106)
T 1p27_B           94 PISVDWCFVRGP  105 (106)
T ss_dssp             BCEEEESEESSC
T ss_pred             EEEEEeecCCCC
Confidence            999999988764

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

Probab=99.86  E-value=3.8e-22  Score=134.34  Aligned_cols=84  Identities=19%  Similarity=0.392  Sum_probs=77.4

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC-CceeCCcEeEEEEc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYG-EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN-GGELLTQTLTVDWA  166 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~-~~~l~g~~l~v~~a  166 (196)
                      +++|||+|||+.+|+++|+++|++|| .|.+|.|+.++.++.++|||||+|.+.++|++||+.++ +..|+|++|+|.||
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 89999999999999999999999999999999998875 56799999999999


Q ss_pred             ccCCCC
Q 043064          167 FSNGPS  172 (196)
Q Consensus       167 ~~~~~~  172 (196)
                      .|++..
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            887654

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

Probab=99.86  E-value=2.8e-21  Score=132.66  Aligned_cols=90  Identities=23%  Similarity=0.333  Sum_probs=83.2

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ++...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34456689999999999999999999999999999999999988899999999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.+....
T Consensus        87 V~~a~~~~~~   96 (103)
T 2dnm_A           87 VQVARYGRRD   96 (103)
T ss_dssp             EEECSSCCSC
T ss_pred             EEECCcCCCC
Confidence            9999876544

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

Probab=99.86  E-value=1.3e-20  Score=132.15  Aligned_cols=90  Identities=22%  Similarity=0.343  Sum_probs=82.6

Q ss_pred             CCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           82 GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      .+....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..|++ .|.|+.|
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l   88 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKA   88 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEEC
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEE
Confidence            345566789999999999999999999999999999999999988999999999999999999999999998 8999999


Q ss_pred             EEEEcccCCCC
Q 043064          162 TVDWAFSNGPS  172 (196)
Q Consensus       162 ~v~~a~~~~~~  172 (196)
                      +|.|+.+....
T Consensus        89 ~V~~a~~~~~~   99 (116)
T 2cqd_A           89 NVNLAYLGAKP   99 (116)
T ss_dssp             EEEESTTTCCC
T ss_pred             EEEEcccCCCc
Confidence            99999876543

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

Probab=99.86  E-value=3.8e-21  Score=127.86  Aligned_cols=84  Identities=25%  Similarity=0.397  Sum_probs=77.0

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||..+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.|+
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            35688999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      .+++
T Consensus        84 ~~kp   87 (87)
T 3bs9_A           84 TRKP   87 (87)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            8764

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

Probab=99.86  E-value=4.7e-21  Score=131.23  Aligned_cols=88  Identities=30%  Similarity=0.463  Sum_probs=82.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567889999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99877654

>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=99.86  E-value=6.6e-21  Score=125.55  Aligned_cols=82  Identities=24%  Similarity=0.514  Sum_probs=78.3

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      +++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..|.|+.|+|.|+.+
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            36899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q 043064          169 NG  170 (196)
Q Consensus       169 ~~  170 (196)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.86  E-value=9.9e-21  Score=131.48  Aligned_cols=92  Identities=24%  Similarity=0.399  Sum_probs=84.5

Q ss_pred             CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC------Cc
Q 043064           81 PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN------GG  154 (196)
Q Consensus        81 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~------~~  154 (196)
                      +.+....+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||      +.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A            7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            334455678899999999999999999999999999999999998899999999999999999999999999      99


Q ss_pred             eeCCcEeEEEEcccCCCC
Q 043064          155 ELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       155 ~l~g~~l~v~~a~~~~~~  172 (196)
                      .|.|+.|+|.|+.++...
T Consensus        87 ~~~g~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           87 KLDGRQLKVDLAVTRDEA  104 (111)
T ss_dssp             ESSSCEEEEECCCCCCCC
T ss_pred             EEcCEEEEEEECCCCccC
Confidence            999999999999877654

>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=99.86  E-value=8.2e-21  Score=130.69  Aligned_cols=90  Identities=27%  Similarity=0.350  Sum_probs=83.4

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34456688999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++...
T Consensus        89 v~~a~~~~~~   98 (105)
T 1x5u_A           89 VNKASAHNKN   98 (105)
T ss_dssp             EEETTTTSCC
T ss_pred             EEECCCCCcC
Confidence            9999877653

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

Probab=99.86  E-value=3.6e-21  Score=130.35  Aligned_cols=86  Identities=31%  Similarity=0.494  Sum_probs=81.1

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNL-HLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      .+.++|||+|||+.+++++|+.+|++||.|..| .|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.|
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 9999988999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9877654

>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=99.85  E-value=4.8e-21  Score=132.99  Aligned_cols=93  Identities=62%  Similarity=1.140  Sum_probs=85.7

Q ss_pred             CCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           80 GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        80 ~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      .+.+....+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|..|+..|||..|.|+
T Consensus        17 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   96 (110)
T 1oo0_B           17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   96 (110)
T ss_dssp             -CCBCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            34556677789999999999999999999999999999999999988999999999999999999999999999999999


Q ss_pred             EeEEEEcccCCCC
Q 043064          160 TLTVDWAFSNGPS  172 (196)
Q Consensus       160 ~l~v~~a~~~~~~  172 (196)
                      .|+|.|+.++.++
T Consensus        97 ~l~V~~a~~~~~~  109 (110)
T 1oo0_B           97 TIQVDWCFVKGPK  109 (110)
T ss_dssp             ECEEEESEESSCC
T ss_pred             EEEEEEcccCCCC
Confidence            9999999887653

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

Probab=99.85  E-value=7.8e-21  Score=146.07  Aligned_cols=125  Identities=31%  Similarity=0.378  Sum_probs=101.8

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC-----C-------------CCCCCCEEEEcCCCccCcHHHHHH
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP-----Q-------------RSIEGWIILVTGVHEEAQEDDLQN  108 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~-------------~~~~~~~l~V~nLp~~~te~~L~~  108 (196)
                      +++++||+||.|.+. ..+..+...++.....+....     .             .....++|||+|||..+++++|++
T Consensus        66 ~g~~~g~afV~f~~~-~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~  144 (216)
T 2qfj_A           66 TMKHKGFAFVEYEVP-EAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKS  144 (216)
T ss_dssp             C-CCCSEEEEEESSH-HHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHH
T ss_pred             CCccCceEEEEeCCH-HHHHHHHHHccCCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHH
Confidence            457899999999954 444444445555544443211     0             123458999999999999999999


Q ss_pred             hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCC
Q 043064          109 VFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       109 ~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~  172 (196)
                      +|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..||+..|+|+.|.|.|+.+.+..
T Consensus       145 ~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          145 VFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             HHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             HHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            9999999999999999889999999999999999999999999999999999999999877543

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

Probab=99.85  E-value=1.2e-20  Score=138.92  Aligned_cols=120  Identities=22%  Similarity=0.413  Sum_probs=98.5

Q ss_pred             CCCcCcccccCCCcHHHHHHhhhhcccCCCCCC---------CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeE
Q 043064           48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG---------PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN  118 (196)
Q Consensus        48 ~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~  118 (196)
                      .+++|+|||.|.+.+. +..+...+++....+.         .......+.++|||+|||..+++++|+++|++||.|..
T Consensus        38 ~~~~g~afV~f~~~~~-a~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~  116 (166)
T 3md3_A           38 NKNVNYAFVEYHQSHD-ANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLS  116 (166)
T ss_dssp             -CCEEEEEEEESSHHH-HHHHHHHHTTCEETTEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEE
T ss_pred             CCCCCEEEEEeCCHHH-HHHHHHHcCCCccCCCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeE
Confidence            4688999999995444 4434344444333221         12234456789999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064          119 LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus       119 v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      +.++.++.++.++|||||+|.+.++|.+|+..|||..|+|+.|+|.||.+
T Consensus       117 ~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            99999988999999999999999999999999999999999999999863

>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=99.85  E-value=1.1e-20  Score=139.10  Aligned_cols=88  Identities=20%  Similarity=0.394  Sum_probs=82.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|.|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 043064          166 AFSNGPST  173 (196)
Q Consensus       166 a~~~~~~~  173 (196)
                      +.+.....
T Consensus       116 a~~~~~~~  123 (156)
T 1h2v_Z          116 DAGFKEGR  123 (156)
T ss_dssp             ESCCCTTC
T ss_pred             CCCCCCcC
Confidence            98766543

>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=99.85  E-value=1.6e-20  Score=131.47  Aligned_cols=87  Identities=26%  Similarity=0.406  Sum_probs=81.5

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9877653

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

Probab=99.85  E-value=9.3e-21  Score=129.75  Aligned_cols=88  Identities=27%  Similarity=0.485  Sum_probs=82.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.||+..|.|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99877653

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

Probab=99.85  E-value=2.6e-21  Score=131.24  Aligned_cols=84  Identities=18%  Similarity=0.300  Sum_probs=77.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCC--eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc----eeCC
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGE--IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG----ELLT  158 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~--i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~----~l~g  158 (196)
                      ....-.+|||+|||+.+|+++|+++|++||.  +..|.+++++.+|+++|||||+|.+.++|++|++.||+.    .|+|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            3445678999999999999999999999995  678999999999999999999999999999999999986    5999


Q ss_pred             cEeEEEEccc
Q 043064          159 QTLTVDWAFS  168 (196)
Q Consensus       159 ~~l~v~~a~~  168 (196)
                      ++|.|.||++
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999964

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

Probab=99.85  E-value=1.7e-20  Score=129.49  Aligned_cols=90  Identities=21%  Similarity=0.442  Sum_probs=83.1

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCcE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLD-RRTGFVKGYALIEYENFEEAQNAITAM-NGGELLTQT  160 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-~~~g~~~g~afv~f~~~~~a~~al~~l-~~~~l~g~~  160 (196)
                      +....+.++|||+|||+.+++++|+.+|++||.|..|.|+.+ +.++.++|||||+|.+.++|++||..| |+..|.|+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~   88 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR   88 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCB
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCE
Confidence            345567889999999999999999999999999999999988 779999999999999999999999999 999999999


Q ss_pred             eEEEEcccCCCC
Q 043064          161 LTVDWAFSNGPS  172 (196)
Q Consensus       161 l~v~~a~~~~~~  172 (196)
                      |+|.|+.++...
T Consensus        89 l~v~~a~~~~~~  100 (107)
T 2cph_A           89 LVLEWADSEVTV  100 (107)
T ss_dssp             CEEEECCCCCCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999887654

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

Probab=99.85  E-value=6.3e-20  Score=128.03  Aligned_cols=87  Identities=22%  Similarity=0.290  Sum_probs=80.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+..||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34557889999999999999999999999999999999986 69999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.+..+.
T Consensus        90 ~a~~~~~~   97 (114)
T 2do0_A           90 MDERALPK   97 (114)
T ss_dssp             ECSCCCCC
T ss_pred             EcccCCCC
Confidence            99765544

>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=99.85  E-value=4.3e-21  Score=145.41  Aligned_cols=133  Identities=21%  Similarity=0.364  Sum_probs=97.3

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-------------CCCCCCCCCCEEEEcCCCc
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGG-------------PGPQRSIEGWIILVTGVHE   99 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~l~V~nLp~   99 (196)
                      ..+..+++.    .+++++|||||.|.+.+.+.. +... +.....+.             ..+......++|||+|||+
T Consensus        41 ~~v~i~~~~----~~g~~~g~afV~f~~~~~A~~-A~~~-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~  114 (196)
T 1l3k_A           41 TDCVVMRDP----NTKRSRGFGFVTYATVEEVDA-AMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKE  114 (196)
T ss_dssp             EEEEEEECT----TTCCEEEEEEEEESSHHHHHH-HHHT-CSCEETTEECEEEECCC-----------CCSEEEEECCTT
T ss_pred             EEEEEEEcC----CCCCccceEEEEeCCHHHHHH-HHhc-CCCEECCEEeeeecccCcccccccccCCCcceEEEeCCCC
Confidence            344444444    345789999999995554444 3222 22111111             1112233468999999999


Q ss_pred             cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCCC
Q 043064          100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       100 ~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~~  172 (196)
                      .+++++|+++|+.||.|..|.++.+..++.++|||||+|.+.++|.+|+.. ++..|+|+.|.|.|+.++...
T Consensus       115 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~  186 (196)
T 1l3k_A          115 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEM  186 (196)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-----
T ss_pred             CCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHh
Confidence            999999999999999999999999988999999999999999999999976 899999999999999887754

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

Probab=99.85  E-value=1.6e-20  Score=135.56  Aligned_cols=88  Identities=26%  Similarity=0.396  Sum_probs=82.5

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||+..|.|+.|+|.
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++..+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99887654

>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=99.85  E-value=2.8e-20  Score=128.87  Aligned_cols=82  Identities=17%  Similarity=0.287  Sum_probs=74.7

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC----
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT----  158 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g----  158 (196)
                      ++.....++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.||+..|.|    
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~   81 (108)
T 1x4c_A            9 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   81 (108)
T ss_dssp             CCCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCc
Confidence            334456889999999999999999999999999999999864       799999999999999999999999999    


Q ss_pred             -cEeEEEEcccCCC
Q 043064          159 -QTLTVDWAFSNGP  171 (196)
Q Consensus       159 -~~l~v~~a~~~~~  171 (196)
                       +.|+|.++.++..
T Consensus        82 ~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           82 TAYIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEEEESSCCSC
T ss_pred             ceEEEEEeCCCCCC
Confidence             9999999988654

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

Probab=99.85  E-value=2.8e-20  Score=127.61  Aligned_cols=86  Identities=23%  Similarity=0.392  Sum_probs=80.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.+  ++.++|||||+|.+.++|.+|+..||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3456789999999999999999999999999999999987  88999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2d9p_A           89 LAQRKEER   96 (103)
T ss_dssp             ECSSCCCC
T ss_pred             EecccccC
Confidence            99887654

>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=99.85  E-value=3.9e-20  Score=127.26  Aligned_cols=87  Identities=25%  Similarity=0.413  Sum_probs=80.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC---cEe
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT---QTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g---~~l  161 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++ ++.++|||||+|.+.++|++||..||+..|.|   +.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l   89 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSL   89 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccE
Confidence            34457899999999999999999999999999999999987 89999999999999999999999999999988   999


Q ss_pred             EEEEcccCCCC
Q 043064          162 TVDWAFSNGPS  172 (196)
Q Consensus       162 ~v~~a~~~~~~  172 (196)
                      +|.|+.++..+
T Consensus        90 ~V~~a~~~~~~  100 (105)
T 2dnh_A           90 VVKFADTDKES  100 (105)
T ss_dssp             EEEESCSSCCC
T ss_pred             EEEECccCccc
Confidence            99999887654

>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=99.85  E-value=2.4e-20  Score=128.20  Aligned_cols=88  Identities=16%  Similarity=0.279  Sum_probs=80.7

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRT-GFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~-g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      +....+.++|||+|||+.+++++|+.+|++|| |..|.|+.++.+ +.++|||||+|.+.++|++|| .||+..|.|+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   86 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRI   86 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEEC
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEE
Confidence            33445678999999999999999999999999 999999999877 999999999999999999999 999999999999


Q ss_pred             EEEEcccCCCC
Q 043064          162 TVDWAFSNGPS  172 (196)
Q Consensus       162 ~v~~a~~~~~~  172 (196)
                      .|.|+.++...
T Consensus        87 ~V~~a~~~~~~   97 (104)
T 1wi8_A           87 RVDVADQAQDK   97 (104)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEccCCCCC
Confidence            99999877654

>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=99.84  E-value=1.2e-20  Score=124.80  Aligned_cols=82  Identities=32%  Similarity=0.525  Sum_probs=78.0

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|.|
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            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cc
Q 043064          166 AF  167 (196)
Q Consensus       166 a~  167 (196)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

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

Probab=99.84  E-value=4.3e-20  Score=126.74  Aligned_cols=86  Identities=21%  Similarity=0.375  Sum_probs=79.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++|| |..|.|+.++.++.++|||||+|.+.++|++|| .||+..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            445678999999999999999999999997 999999999889999999999999999999999 899999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2dng_A           89 IAEGRKQD   96 (103)
T ss_dssp             ECCCCCCC
T ss_pred             EecCCCCC
Confidence            99876643

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

Probab=99.84  E-value=2.2e-20  Score=130.27  Aligned_cols=89  Identities=28%  Similarity=0.461  Sum_probs=82.8

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  155 (196)
                      ....+.++|||+|||+.+++++|+++|++||.|.        .|.|+.++.++.++|||||+|.+.++|++||..||+..
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            3556789999999999999999999999999999        69999998899999999999999999999999999999


Q ss_pred             eCCcEeEEEEcccCCCC
Q 043064          156 LLTQTLTVDWAFSNGPS  172 (196)
Q Consensus       156 l~g~~l~v~~a~~~~~~  172 (196)
                      |.|+.|+|.|+.++...
T Consensus        90 ~~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPPM  106 (113)
T ss_dssp             ETTEECEEECSSCCCCS
T ss_pred             cCCCEEEEEECCCCCCC
Confidence            99999999999887654

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

Probab=99.84  E-value=1.4e-20  Score=128.00  Aligned_cols=86  Identities=19%  Similarity=0.329  Sum_probs=79.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCC---CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR---TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~---~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .+.++|||+|||+.+++++|+++|++||.|..|.|+.++.   ++.++|||||+|.+.++|++|+..||+..|.|+.|.|
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            4568899999999999999999999999999999998765   5689999999999999999999999999999999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876644

>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=99.84  E-value=1.4e-20  Score=127.52  Aligned_cols=84  Identities=23%  Similarity=0.455  Sum_probs=79.7

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|+|.|+.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            46789999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            7654

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

Probab=99.84  E-value=2.1e-20  Score=126.18  Aligned_cols=84  Identities=27%  Similarity=0.412  Sum_probs=79.3

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.
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            44567889999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Eccc
Q 043064          165 WAFS  168 (196)
Q Consensus       165 ~a~~  168 (196)
                      |+++
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9864

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

Probab=99.84  E-value=2.6e-20  Score=125.60  Aligned_cols=83  Identities=23%  Similarity=0.354  Sum_probs=78.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|.
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            34457889999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      ||+
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

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

Probab=99.84  E-value=1.5e-20  Score=128.04  Aligned_cols=87  Identities=23%  Similarity=0.408  Sum_probs=81.1

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCee-EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE----
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR-NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT----  160 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~-~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~----  160 (196)
                      ..+.++|||+|||+.+++++|+++|++||.|. .|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34578999999999999999999999999999 9999999889999999999999999999999999999999999    


Q ss_pred             eEEEEcccCCCC
Q 043064          161 LTVDWAFSNGPS  172 (196)
Q Consensus       161 l~v~~a~~~~~~  172 (196)
                      |+|.|+.+....
T Consensus        86 l~v~~a~~~~~~   97 (99)
T 2div_A           86 FKLNYATYSGPS   97 (99)
T ss_dssp             CCEEETTCCSSS
T ss_pred             EEEeecCCCCCC
Confidence            999999776543

>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=99.84  E-value=1.9e-20  Score=129.09  Aligned_cols=89  Identities=26%  Similarity=0.378  Sum_probs=82.1

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee---CCc
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL---LTQ  159 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l---~g~  159 (196)
                      +....+.++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..||+..+   .|+
T Consensus         7 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~   86 (106)
T 2dgp_A            7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNR   86 (106)
T ss_dssp             SCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCc
Confidence            33455678999999999999999999999999999999999988999999999999999999999999999987   899


Q ss_pred             EeEEEEcccCCC
Q 043064          160 TLTVDWAFSNGP  171 (196)
Q Consensus       160 ~l~v~~a~~~~~  171 (196)
                      .|+|.|+.++..
T Consensus        87 ~l~v~~a~~~~~   98 (106)
T 2dgp_A           87 PIQVKPADSESR   98 (106)
T ss_dssp             CCEEEECCCCSC
T ss_pred             eEEEEECCcccc
Confidence            999999987654

>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=99.84  E-value=9e-20  Score=125.06  Aligned_cols=88  Identities=19%  Similarity=0.356  Sum_probs=79.8

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|+.+..  .++|||||+|.+.++|++|+..||+..|.|+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34456679999999999999999999999999999999998753  3789999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++...
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cq3_A           87 VNNATARVMT   96 (103)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEcccCCCC
Confidence            9999887754

>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=99.84  E-value=2e-21  Score=143.62  Aligned_cols=133  Identities=15%  Similarity=0.285  Sum_probs=101.7

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhh---cccCCCCCCC--CCCCCCCCCEEEEcCCCccCcHHH
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRN---FESLGTDGGP--GPQRSIEGWIILVTGVHEEAQEDD  105 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~---~~~~~~~~~~--~~~~~~~~~~l~V~nLp~~~te~~  105 (196)
                      +...+..+++.    .+++++|||||.|.+.+.+.... ..   +++.......  ......+.++|||+|||+.+++++
T Consensus        29 ~i~~v~i~~~~----~~g~~~g~afV~f~~~~~a~~A~-~~~~~~~g~~i~v~~~~~~~~~~~~~~l~V~nlp~~~t~~~  103 (167)
T 2cjk_A           29 TVTDLKIMKDP----ATGRSRGFGFLSFEKPSSVDEVV-KTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKE  103 (167)
T ss_dssp             CEEEEECCCCT----TTSSCCSCEEEEESSTHHHHHHH-HSCCEETTEECCCEECCCHHHHHHCEEEEEEEECTTCCHHH
T ss_pred             CEEEEEEEECC----CCCCccceEEEEEccHHHHHHHH-hcccccCCeEcccccccchhhccCCCeEEECCCCCCCCHHH
Confidence            33444445554    35678999999999655554432 22   1111111111  111123467899999999999999


Q ss_pred             HHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064          106 LQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus       106 L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      |+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ +++..|+|+.|.|.||.|+
T Consensus       104 l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          104 FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             HHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            99999999999999999998899999999999999999999997 8999999999999999876

>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=99.84  E-value=2.6e-20  Score=137.63  Aligned_cols=119  Identities=28%  Similarity=0.347  Sum_probs=97.9

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-------CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEE
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDGG-------PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNL  119 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v  119 (196)
                      +++++|++|+.|.+.+. +..+...++.....+.       .......+.++|||+|||..+++++|+.+|++||.|..+
T Consensus        41 ~~~~~g~afV~f~~~~~-A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~  119 (168)
T 1b7f_A           41 TGYSYGYAFVDFTSEMD-SQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQK  119 (168)
T ss_dssp             TTEECSEEEEEESSHHH-HHHHHHHHTTCEETTEECEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEE
T ss_pred             CCccceEEEEEECCHHH-HHHHHHhcCCCEeCCcEEEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEE
Confidence            45788999999995444 4434444444433322       122334567899999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEEEEc
Q 043064          120 HLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTVDWA  166 (196)
Q Consensus       120 ~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~~a  166 (196)
                      .++.+..++.++|||||+|.+.++|.+|+..|||..+.|  ++|+|.||
T Consensus       120 ~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          120 NILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            999998899999999999999999999999999999988  99999986

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

Probab=99.84  E-value=2.1e-20  Score=128.41  Aligned_cols=87  Identities=22%  Similarity=0.366  Sum_probs=80.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhcc-CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce-eCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGE-YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE-LLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~-~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-l~g~~l~  162 (196)
                      ...+.++|||+|||+.+++++|+.+|++ ||.|..|.|+.++ ++.++|||||+|.+.++|.+||..||+.. |.|+.|.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            3456788999999999999999999999 9999999999997 99999999999999999999999999999 9999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++...
T Consensus        84 v~~a~~~~~~   93 (104)
T 2dhg_A           84 LSVAIPKASR   93 (104)
T ss_dssp             CCBCCCCCSC
T ss_pred             EEEccCCCcC
Confidence            9999776644

>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=99.84  E-value=2.9e-20  Score=138.02  Aligned_cols=116  Identities=24%  Similarity=0.397  Sum_probs=96.5

Q ss_pred             CCcCcccccCCCcHHHHHHhhhhcccCCCCCCC-------CCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEE
Q 043064           49 KTKGRGFREEADSERHSRLADRNFESLGTDGGP-------GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHL  121 (196)
Q Consensus        49 ~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i  121 (196)
                      +++|+|||.|.+.+.+.. +. .+++....+.+       ........++|||+|||+.+++++|+++|++||.|..+.+
T Consensus        49 ~~~g~afV~f~~~~~A~~-A~-~~~~~~~~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i  126 (172)
T 2g4b_A           49 QDKNFAFLEFRSVDETTQ-AM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL  126 (172)
T ss_dssp             TTTTEEEEEESSHHHHHH-HG-GGTTCEETTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEE
T ss_pred             CCCCEEEEEeCCHHHHHH-HH-HhCCcEecCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEE
Confidence            578999999995554444 43 45554333321       1122334688999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064          122 NLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus       122 ~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||
T Consensus       127 ~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          127 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             EECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            999889999999999999999999999999999999999999997

>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=99.84  E-value=1.7e-20  Score=124.86  Aligned_cols=85  Identities=26%  Similarity=0.515  Sum_probs=78.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCC-cceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF-VKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~-~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+..++. ++|||||+|.+.++|++|+..|||..|.|+.|+|.+
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            4568899999999999999999999999999999998876665 899999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      +.+..+
T Consensus        82 a~~~~~   87 (88)
T 4a8x_A           82 VLAPWP   87 (88)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            976553

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

Probab=99.84  E-value=4e-20  Score=126.00  Aligned_cols=85  Identities=26%  Similarity=0.427  Sum_probs=79.8

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN--------LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG  154 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--------v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~  154 (196)
                      +....+.++|||+|||+++++++|+++|++||.|..        |.++.++.+|.++|||||+|.+.++|++|++.|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            445566899999999999999999999999999999        999999889999999999999999999999999999


Q ss_pred             eeCCcEeEEEEcc
Q 043064          155 ELLTQTLTVDWAF  167 (196)
Q Consensus       155 ~l~g~~l~v~~a~  167 (196)
                      .|.|+.|+|.||+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999984

>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=99.84  E-value=2.3e-20  Score=129.48  Aligned_cols=86  Identities=29%  Similarity=0.453  Sum_probs=81.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|+|..|.|+.|+|.
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            44567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      |+.++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998764

>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=99.84  E-value=2.5e-20  Score=130.63  Aligned_cols=82  Identities=24%  Similarity=0.340  Sum_probs=75.3

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ..+|||+|||+.+++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|++||..|++..|.|+.|+|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            5679999999999999999999999999999999884  44789999999999999999999999999999999999987


Q ss_pred             CCCC
Q 043064          169 NGPS  172 (196)
Q Consensus       169 ~~~~  172 (196)
                      +...
T Consensus        83 ~~~~   86 (115)
T 4f25_A           83 RKER   86 (115)
T ss_dssp             CCC-
T ss_pred             cccc
Confidence            6543

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.84  E-value=2.9e-21  Score=129.53  Aligned_cols=83  Identities=17%  Similarity=0.205  Sum_probs=72.8

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      .+|||+|||+++++++|+++|++||  .|..+.++.++.+|+++|||||+|.+.++|++|++.|||..|.|+.|+|.++.
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            4699999999999999999999999  99999999998899999999999999999999999999999999999999998


Q ss_pred             cCCCC
Q 043064          168 SNGPS  172 (196)
Q Consensus       168 ~~~~~  172 (196)
                      +.++.
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            87654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.84  E-value=3.1e-21  Score=148.94  Aligned_cols=134  Identities=19%  Similarity=0.233  Sum_probs=102.6

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC---------CCCCCCCCEEEEcCCCcc
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG---------PQRSIEGWIILVTGVHEE  100 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~l~V~nLp~~  100 (196)
                      +++..+..+++.    .+++++|||||.|.+... +..+...++.....+...         ........+|||+|||+.
T Consensus        40 G~I~~v~i~~d~----~tg~~~G~afV~F~~~~~-A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~  114 (213)
T 4f02_A           40 GPILSIRVCRDM----ITRRSLGYAYVNFQQPAD-AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKS  114 (213)
T ss_dssp             SCEEEEEEEECT----TTCCEEEEEEEEESSHHH-HHHHHHHHTTCEETTEECEEEECCCCTHHHHHCTTEEEEESCCTT
T ss_pred             CCEEEEEEeccc----CCCCccccccceeCCHHH-HHHHHHHhhhhhcCCcccccccccccccccccccccceECCcccc
Confidence            344455555555    456899999999995444 443444444433322211         111224578999999999


Q ss_pred             CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064          101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       101 ~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      +++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|.+||+.|||..|+|+.|.|.||.++.
T Consensus       115 ~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~  182 (213)
T 4f02_A          115 IDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK  182 (213)
T ss_dssp             CCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHH
T ss_pred             cHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCc
Confidence            9999999999999999999999874  4479999999999999999999999999999999999998764

>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=99.83  E-value=2.9e-21  Score=135.41  Aligned_cols=82  Identities=17%  Similarity=0.300  Sum_probs=66.5

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE--
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT--  160 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~--  160 (196)
                      |+.....++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++||+.||+..|.|+.  
T Consensus        10 pp~~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           10 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             -------CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEee
Confidence            333455788999999999999999999999999999998754       89999999999999999999999999998  


Q ss_pred             ---eEEEEcccCCC
Q 043064          161 ---LTVDWAFSNGP  171 (196)
Q Consensus       161 ---l~v~~a~~~~~  171 (196)
                         |+|..+.++..
T Consensus        83 ~~~i~v~~~~~~~~   96 (115)
T 3beg_B           83 TAYIRVKVDGPRSP   96 (115)
T ss_dssp             CCBCEEEECC----
T ss_pred             eEEEEeccCCCCCC
Confidence               77777766543

>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=99.83  E-value=8.6e-20  Score=125.27  Aligned_cols=81  Identities=20%  Similarity=0.387  Sum_probs=73.9

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++        ++||||+|.+.++|++|+..||+..|.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            34557889999999999999999999999999999886        4699999999999999999999999999999999


Q ss_pred             EcccCCCCC
Q 043064          165 WAFSNGPST  173 (196)
Q Consensus       165 ~a~~~~~~~  173 (196)
                      |+.++....
T Consensus        79 ~a~~~~~~~   87 (103)
T 2dgu_A           79 FAKPPDQKR   87 (103)
T ss_dssp             ECCCCCCCC
T ss_pred             EcCCCcccc
Confidence            998876553

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.83  E-value=7.6e-21  Score=130.06  Aligned_cols=82  Identities=22%  Similarity=0.364  Sum_probs=78.3

Q ss_pred             CCCEEEEcCCCc------cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-cE
Q 043064           88 EGWIILVTGVHE------EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT-QT  160 (196)
Q Consensus        88 ~~~~l~V~nLp~------~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g-~~  160 (196)
                      ..++|||+|||.      .+++++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++|++||+.|||..|.| +.
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            357899999999      99999999999999999999999999899999999999999999999999999999999 99


Q ss_pred             eEEEEcccC
Q 043064          161 LTVDWAFSN  169 (196)
Q Consensus       161 l~v~~a~~~  169 (196)
                      |+|.++.++
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999999764

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

Probab=99.83  E-value=7.1e-21  Score=137.17  Aligned_cols=90  Identities=26%  Similarity=0.404  Sum_probs=83.2

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||..||+..|.|+.|+
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34455678899999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+++..+.
T Consensus       121 V~~a~~~~~~  130 (135)
T 2lea_A          121 VQMARYGRPP  130 (135)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999877654

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

Probab=99.83  E-value=4e-20  Score=127.26  Aligned_cols=88  Identities=15%  Similarity=0.265  Sum_probs=81.7

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||.. ++..|.|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V   89 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP   89 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEE
Confidence            3455678999999999999999999999999999999999988999999999999999999999998 999999999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.++...
T Consensus        90 ~~a~~~~~~   98 (105)
T 2dh8_A           90 KPCTPRGMQ   98 (105)
T ss_dssp             CCSCCSSCC
T ss_pred             EEccCCCCC
Confidence            999877654

>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=99.83  E-value=1.6e-19  Score=123.74  Aligned_cols=86  Identities=17%  Similarity=0.324  Sum_probs=79.3

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++||.  +++.|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            44567889999999999999999999999999999999998899999999999999999999997  5789999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99887654

>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=99.83  E-value=4.9e-20  Score=122.90  Aligned_cols=82  Identities=23%  Similarity=0.365  Sum_probs=77.6

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+ .||+..|.|+.|+|.++++
T Consensus         6 ~~~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            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            478999999999999999999999999999999999889999999999999999999999 9999999999999999977


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      ..+
T Consensus        85 ~~p   87 (89)
T 3ucg_A           85 NRP   87 (89)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            543

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

Probab=99.83  E-value=5.9e-20  Score=123.35  Aligned_cols=87  Identities=22%  Similarity=0.284  Sum_probs=79.6

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+.+++++|+.+|++||.|..|.|+.+  ++.++|||||+|.+.++|++|+..||+..|.|+.|+|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   80 (92)
T 2dgv_A            3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDV   80 (92)
T ss_dssp             CSSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34556789999999999999999999999999999999874  7889999999999999999999999999999999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.+....
T Consensus        81 ~~a~~~~~~   89 (92)
T 2dgv_A           81 RIDRNASGP   89 (92)
T ss_dssp             EECSCCSSC
T ss_pred             EEcCCCCCC
Confidence            999876643

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

Probab=99.83  E-value=5.3e-20  Score=139.55  Aligned_cols=122  Identities=21%  Similarity=0.359  Sum_probs=99.4

Q ss_pred             CCCcCcccccCCCcHHHHHHhhhhcccCCCCCC---------C------------------CCCCCCCCCEEEEcCCCcc
Q 043064           48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG---------P------------------GPQRSIEGWIILVTGVHEE  100 (196)
Q Consensus        48 ~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~---------~------------------~~~~~~~~~~l~V~nLp~~  100 (196)
                      .+++|||||.|.+.+.+...-  .+++....+.         .                  ......+.++|||+|||+.
T Consensus        48 ~~~~g~afV~F~~~~~A~~Al--~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  125 (198)
T 2yh0_A           48 NQDKNFAFLEFRSVDETTQAM--AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY  125 (198)
T ss_dssp             ETTTTEEEEEESCSHHHHHHG--GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTT
T ss_pred             cCCCCEEEEEeCCHHHHHHHH--HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCC
Confidence            367899999999655555533  3333222111         0                  0011245799999999999


Q ss_pred             CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCC
Q 043064          101 AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       101 ~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~  171 (196)
                      +++++|+.+|++||.|..|.++.++.++.++|||||+|.+.++|.+|+..||+..|+|+.|.|.|+.++..
T Consensus       126 ~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             CCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999988999999999999999999999999999999999999999988764

>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=99.83  E-value=2.7e-20  Score=133.09  Aligned_cols=87  Identities=28%  Similarity=0.486  Sum_probs=81.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++..+|||||+|.+.++|++||..||+..|.|+.|+|.
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            44567889999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.++.+
T Consensus       122 ~a~~~~p  128 (129)
T 2kxn_B          122 FSITKRP  128 (129)
T ss_dssp             CCSSSSC
T ss_pred             EecCCCC
Confidence            9987664

>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=99.83  E-value=2e-19  Score=123.36  Aligned_cols=86  Identities=19%  Similarity=0.392  Sum_probs=78.0

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+  ++|||||+|.+.++|++|+..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            34556799999999999999999999999999999999987433  5899999999999999999999999999999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .|+.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99987654

>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=99.83  E-value=7.4e-20  Score=126.28  Aligned_cols=84  Identities=23%  Similarity=0.371  Sum_probs=78.5

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++.||+..|.|+.|+
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3345668999999999999999999999999999999999997 999999999999999999999999999999999999


Q ss_pred             EEEcc
Q 043064          163 VDWAF  167 (196)
Q Consensus       163 v~~a~  167 (196)
                      |.|+.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99985

>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=99.82  E-value=2.1e-19  Score=124.51  Aligned_cols=86  Identities=22%  Similarity=0.339  Sum_probs=77.2

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.|..   ++.++|||||+|.+.++|++||+.||+..|.|+.|+
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   92 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            33455678999999999999999999999999999999864   455789999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043064          163 VDWAFSNGP  171 (196)
Q Consensus       163 v~~a~~~~~  171 (196)
                      |.|+.++..
T Consensus        93 V~~a~~~~~  101 (109)
T 1x4a_A           93 VEFPRSGRG  101 (109)
T ss_dssp             EECCCCCCC
T ss_pred             EEEcccCCC
Confidence            999977654

>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=99.82  E-value=6.3e-20  Score=135.21  Aligned_cols=119  Identities=24%  Similarity=0.403  Sum_probs=96.5

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-------CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEE
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDGG-------PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNL  119 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v  119 (196)
                      +++++|++|+.|.+.+. +..+...+++....+.       .........++|||+|||..+++++|+.+|++||.|..+
T Consensus        40 ~~~~~g~afV~f~~~~~-A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~  118 (167)
T 1fxl_A           40 TGQSLGYGFVNYIDPKD-AEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS  118 (167)
T ss_dssp             TCCEEEEEEEEESSHHH-HHHHHHHHTTCEETTEECEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEE
T ss_pred             CCcceeEEEEEECCHHH-HHHHHHHcCCCccCCceEEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEE
Confidence            45788999999995444 4434444444333322       112234457889999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc--EeEEEEc
Q 043064          120 HLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ--TLTVDWA  166 (196)
Q Consensus       120 ~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~--~l~v~~a  166 (196)
                      .++.+..+|.++|||||+|.+.++|.+|+..|||..|.|+  +|.|.||
T Consensus       119 ~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999888999999999999999999999999999999996  4888886

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

Probab=99.82  E-value=1.7e-19  Score=120.90  Aligned_cols=84  Identities=15%  Similarity=0.200  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+++|+.| .|..|.|+.+ .+|+++|||||+|.+.++|++||. ||+..|.|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            4567899999999999999999999999 9999999998 789999999999999999999999 999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.+++..
T Consensus        84 a~~~~~s   90 (91)
T 2dgw_A           84 EKSGPSS   90 (91)
T ss_dssp             ESSCCCC
T ss_pred             CCcCCCC
Confidence            9887643

>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=99.82  E-value=6.7e-20  Score=123.79  Aligned_cols=84  Identities=20%  Similarity=0.315  Sum_probs=77.5

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+..||+..|.|+.|+|
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV   89 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEE
Confidence            344567899999999999999999999999999999999987 4899999999999999999999999999999999999


Q ss_pred             EEccc
Q 043064          164 DWAFS  168 (196)
Q Consensus       164 ~~a~~  168 (196)
                      .|++.
T Consensus        90 ~~a~~   94 (95)
T 2ywk_A           90 SGPSS   94 (95)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99854

>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=99.82  E-value=9e-20  Score=126.94  Aligned_cols=88  Identities=20%  Similarity=0.300  Sum_probs=79.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHH---HhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQ---NVFGEYGEIRNLHLNLDRRTG---FVKGYALIEYENFEEAQNAITAMNGGELLT  158 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~---~~F~~~G~i~~v~i~~~~~~g---~~~g~afv~f~~~~~a~~al~~l~~~~l~g  158 (196)
                      +....++|||+|||+.+++++|+   ++|++||.|..|.|+.+..++   .++|||||+|.+.++|++||+.||+..|.|
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            45567889999999999999999   999999999999998886643   556999999999999999999999999999


Q ss_pred             cEeEEEEcccCCCC
Q 043064          159 QTLTVDWAFSNGPS  172 (196)
Q Consensus       159 ~~l~v~~a~~~~~~  172 (196)
                      +.|+|.||.++...
T Consensus        91 r~l~V~~a~~k~~~  104 (111)
T 2cpi_A           91 RTLKASLGTTKYCS  104 (111)
T ss_dssp             EEEEEESCCCCSCS
T ss_pred             EEEEEEeccccccc
Confidence            99999999888754

>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=99.82  E-value=1.3e-19  Score=120.50  Aligned_cols=81  Identities=17%  Similarity=0.373  Sum_probs=75.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++ +++..|.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPK   85 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999995 58889999999999


Q ss_pred             Ec
Q 043064          165 WA  166 (196)
Q Consensus       165 ~a  166 (196)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=9.8e-20  Score=126.08  Aligned_cols=87  Identities=17%  Similarity=0.271  Sum_probs=80.0

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCC-eeEEEEe-ecCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCcEe
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGE-IRNLHLN-LDRRTGFVKGYALIEYENFEEAQNAITAMN--GGELLTQTL  161 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~v~i~-~~~~~g~~~g~afv~f~~~~~a~~al~~l~--~~~l~g~~l  161 (196)
                      +.+.++|||+|||+.+++++|+.+|.+||. |..|.|+ .++.++.++|||||+|.+.++|..|+..|+  +..|.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            456789999999999999999999999998 9999998 787888999999999999999999999996  589999999


Q ss_pred             EEEEcccCCCC
Q 043064          162 TVDWAFSNGPS  172 (196)
Q Consensus       162 ~v~~a~~~~~~  172 (196)
                      +|.|+.++...
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999887654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.82  E-value=4.6e-20  Score=132.09  Aligned_cols=89  Identities=16%  Similarity=0.321  Sum_probs=81.4

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeE--EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc----ee
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN--LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG----EL  156 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~----~l  156 (196)
                      +......++|||+|||+.+|+++|+++|++||.|..  |.|+.++.+|+++|||||+|.+. +|.+|+..||+.    .|
T Consensus        17 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~   95 (131)
T 2m2b_A           17 PSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTI   95 (131)
T ss_dssp             CCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCG
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccC
Confidence            344566789999999999999999999999999976  99999988999999999999999 999999999999    99


Q ss_pred             CCcEeEEEEcccCCCC
Q 043064          157 LTQTLTVDWAFSNGPS  172 (196)
Q Consensus       157 ~g~~l~v~~a~~~~~~  172 (196)
                      .|+.|.|.|+.+....
T Consensus        96 ~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           96 DGKTINVEFAKGSKRD  111 (131)
T ss_dssp             GGCCCCCEECCCSCCC
T ss_pred             CCEEEEEEECCCCCCC
Confidence            9999999999876543

>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=99.82  E-value=2.4e-20  Score=128.07  Aligned_cols=85  Identities=34%  Similarity=0.490  Sum_probs=80.1

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|++|++.||+..|.|+.|+|.|+
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            34578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      .++..
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            87654

>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=99.82  E-value=1.2e-19  Score=122.99  Aligned_cols=82  Identities=17%  Similarity=0.278  Sum_probs=75.8

Q ss_pred             CCCCEEEEcCCCccCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQ----NVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|.|+.++.+   +|||||+|.+.++|++|+..||+..|.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            356889999999999999999    99999999999999988655   78999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043064          163 VDWAFSNGP  171 (196)
Q Consensus       163 v~~a~~~~~  171 (196)
                      |.|+.+.+.
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999977654

>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=99.82  E-value=1.3e-19  Score=134.64  Aligned_cols=133  Identities=18%  Similarity=0.308  Sum_probs=100.2

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC-----------CCCCCCCCCCEEEEcCCCc
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDGG-----------PGPQRSIEGWIILVTGVHE   99 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~l~V~nLp~   99 (196)
                      ++..+..+++..+  +..+++|||||.|.+.+ .+..+...++.......           .........++|||+|||+
T Consensus        29 ~i~~v~i~~~~~~--~~~~~~g~afV~f~~~~-~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~  105 (175)
T 3nmr_A           29 AVYEINVLRDRSQ--NPPQSKGCCFVTFYTRK-AALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISK  105 (175)
T ss_dssp             CEEEEEEEEECSS--SSCEEEEEEEEEESSHH-HHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCSCGGGSEEEEESCCT
T ss_pred             CEEEEEEEecCCC--CCCCcceEEEEEECCHH-HHHHHHHHhcCcEEccCCccceEEccccccccccCCCCeEEEcCCCC
Confidence            3344555555422  12378999999999544 44444444544332211           1122233578999999999


Q ss_pred             cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---CcEeEEEEcc
Q 043064          100 EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQTLTVDWAF  167 (196)
Q Consensus       100 ~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~---g~~l~v~~a~  167 (196)
                      .+|+++|+++|++||.|..+.++.+. +|.++|||||+|.+.++|.+|+..|||..+.   +++|.|.||.
T Consensus       106 ~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          106 KCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             cCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99999999999999999999999885 6899999999999999999999999998765   4999999983

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

Probab=99.82  E-value=1e-19  Score=127.84  Aligned_cols=83  Identities=27%  Similarity=0.427  Sum_probs=78.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|.
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            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            984

>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=99.82  E-value=1.1e-19  Score=123.40  Aligned_cols=84  Identities=18%  Similarity=0.186  Sum_probs=77.9

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.+
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            34468899999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8654

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

Probab=99.81  E-value=1.3e-19  Score=126.95  Aligned_cols=84  Identities=15%  Similarity=0.316  Sum_probs=79.0

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++||.. ++..|.|+.|.|.|+.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            458999999999999999999999999999999999988999999999999999999999987 9999999999999998


Q ss_pred             cCCCC
Q 043064          168 SNGPS  172 (196)
Q Consensus       168 ~~~~~  172 (196)
                      ++...
T Consensus       105 ~~~~~  109 (116)
T 1x4b_A          105 AREES  109 (116)
T ss_dssp             SCCCC
T ss_pred             CCccC
Confidence            87653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.81  E-value=1.3e-19  Score=133.69  Aligned_cols=83  Identities=18%  Similarity=0.217  Sum_probs=77.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..++|||+|||+++++++|+++|+.||  .|..|.|+.++.+|+++|||||+|.+.++|++||..|||..|.|+.|.|.+
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            457899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043064          166 AFSNG  170 (196)
Q Consensus       166 a~~~~  170 (196)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            97643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9e-20  Score=125.42  Aligned_cols=82  Identities=15%  Similarity=0.312  Sum_probs=76.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+++|+++|+++|++||.|..|.|+.++. +.++|||||+|.+.++|.+||. +++..|+|+.|.|.
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~   84 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   84 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            344568899999999999999999999999999999999976 9999999999999999999998 89999999999999


Q ss_pred             Eccc
Q 043064          165 WAFS  168 (196)
Q Consensus       165 ~a~~  168 (196)
                      |+..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            9765

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9.5e-20  Score=125.25  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCcEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~l~g~~l~v  163 (196)
                      ..+.++|||+|||+.+|+++|+++|++||.|.+|.|+.+      +|||||+|.+.++|+.|++.|++  ..|.|++|+|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345788999999999999999999999999999999865      79999999999999999998864  7899999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.++...
T Consensus        87 ~~A~~~~~~   95 (105)
T 1sjq_A           87 QFSNHKELK   95 (105)
T ss_dssp             CCCSSSSCC
T ss_pred             EEcCCCCCC
Confidence            999877654

>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=99.81  E-value=3.3e-19  Score=120.96  Aligned_cols=82  Identities=28%  Similarity=0.378  Sum_probs=74.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC--CcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL--TQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~--g~~l~  162 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.+..+      +|||||+|.+.++|++|+..||+..|.  |+.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            4456788999999999999999999999999999988754      689999999999999999999999999  99999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.+++.+
T Consensus        87 V~~a~~~~~~   96 (97)
T 1why_A           87 VDFAKSGPSS   96 (97)
T ss_dssp             EEECCCCCCC
T ss_pred             EEECCCCCCC
Confidence            9999887653

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

Probab=99.81  E-value=5.8e-19  Score=120.74  Aligned_cols=86  Identities=30%  Similarity=0.526  Sum_probs=77.3

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+.+++++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3456678999999999999999999999874   6777788789999999999999999999999999999999999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|++++...
T Consensus        87 ~~a~~~~~~   95 (102)
T 2fc8_A           87 DWAKPKGEG   95 (102)
T ss_dssp             EECCCCCSS
T ss_pred             EEecCCCCC
Confidence            999877653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.81  E-value=2.1e-19  Score=127.21  Aligned_cols=82  Identities=27%  Similarity=0.367  Sum_probs=77.8

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|+ .||+..|.|+.|+|.|+.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            578999999999999999999999999999999999889999999999999999999999 7999999999999999976


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      ..+
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            554

>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=99.81  E-value=7.7e-19  Score=120.26  Aligned_cols=82  Identities=13%  Similarity=0.175  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM--NGGELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~l~g~~l~  162 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.+      +|||||+|.+.++|..|+..|  ++..|.|++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456789999999999999999999999999999988754      799999999999999999976  46789999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++...
T Consensus        85 V~~a~~~~~~   94 (101)
T 2cq1_A           85 IQYSNHKELK   94 (101)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEcCcccCc
Confidence            9999877654

>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=99.81  E-value=1.6e-19  Score=134.63  Aligned_cols=117  Identities=21%  Similarity=0.325  Sum_probs=93.4

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC---------CCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCee
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDGG---------PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR  117 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~  117 (196)
                      .++++|||||.|.+.+.+.. +. .++.....+.         .......+.++|||+|||+.+++++|+.+|++||.|.
T Consensus        50 ~~~~~g~afV~f~~~~~a~~-A~-~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~  127 (175)
T 1fje_B           50 TGTNRKFGYVDFESAEDLEK-AL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR  127 (175)
T ss_dssp             EETTTTEEEEEESSHHHHHH-HH-HGGGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEE
T ss_pred             CCccccEEEEEECCHHHHHH-HH-hcCCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEE
Confidence            34689999999995555444 33 2554433321         1122334578999999999999999999999999887


Q ss_pred             EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064          118 NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       118 ~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      .+     ..++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.+++
T Consensus       128 ~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          128 LV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             EE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             Ee-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCCC
Confidence            66     3588899999999999999999999999999999999999998764

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

Probab=99.81  E-value=6.8e-19  Score=124.69  Aligned_cols=87  Identities=22%  Similarity=0.340  Sum_probs=81.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|++|+..||+..|.|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999987 99999999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      ||.+....
T Consensus       110 ~a~~~~~~  117 (124)
T 2kt5_A          110 LVASQIDL  117 (124)
T ss_dssp             EECCTTCC
T ss_pred             EeCCCCCC
Confidence            99876654

>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=99.81  E-value=6.2e-19  Score=123.03  Aligned_cols=84  Identities=17%  Similarity=0.310  Sum_probs=78.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--------
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL--------  156 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l--------  156 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+..|||..|        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            44567899999999999999999999999999999999997 999999999999999999999999999999        


Q ss_pred             CCcEeEEEEcccC
Q 043064          157 LTQTLTVDWAFSN  169 (196)
Q Consensus       157 ~g~~l~v~~a~~~  169 (196)
                      .+++|.|.|+.|.
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999754

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

Probab=99.81  E-value=6.3e-19  Score=118.44  Aligned_cols=80  Identities=21%  Similarity=0.333  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.++        ++||||+|.+.++|++|+..||+..|.|+.|+|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            45567899999999999999999999999999999987        4499999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        78 ~a~~~~~~   85 (92)
T 2dgt_A           78 LSTSRLRT   85 (92)
T ss_dssp             ESSCCCSC
T ss_pred             EccCCCCC
Confidence            99877654

>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=99.81  E-value=2.3e-19  Score=122.96  Aligned_cols=80  Identities=16%  Similarity=0.168  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCcEe
Q 043064           85 RSIEGWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG--ELLTQTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~--~l~g~~l  161 (196)
                      ...+.++|||+|||+ .+|+++|+.+|++||.|.+|.|+.+      +|||||+|.+.++|..|+..||+.  .|.|++|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   84 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   84 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEE
Confidence            445788999999999 9999999999999999999999865      589999999999999999998864  5999999


Q ss_pred             EEEEcccCC
Q 043064          162 TVDWAFSNG  170 (196)
Q Consensus       162 ~v~~a~~~~  170 (196)
                      .|.||.+..
T Consensus        85 ~V~~a~~~~   93 (102)
T 1x4d_A           85 RVHLSQKYK   93 (102)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCCC
Confidence            999998654

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=4.1e-19  Score=121.89  Aligned_cols=84  Identities=23%  Similarity=0.360  Sum_probs=76.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .....++|||+|||+.+|+++|+++|++|| +..|.|+.++ +++++|||||+|.+.++|++|| .+|+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEE
Confidence            445678999999999999999999999999 4599999997 9999999999999999999999 479999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      ++.+...
T Consensus        88 ~~~~~~~   94 (102)
T 1wez_A           88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             ECCCCCC
Confidence            9876553

>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=99.80  E-value=3.3e-19  Score=151.31  Aligned_cols=89  Identities=25%  Similarity=0.377  Sum_probs=82.4

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.|
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            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCCCCC
Q 043064          166 AFSNGPSTG  174 (196)
Q Consensus       166 a~~~~~~~~  174 (196)
                      +.++....+
T Consensus       179 a~~~~~~~~  187 (437)
T 3pgw_S          179 ERGRTVKGW  187 (437)
T ss_pred             eCCCCCCCC
Confidence            988765433

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

Probab=99.80  E-value=5.7e-19  Score=118.18  Aligned_cols=79  Identities=19%  Similarity=0.345  Sum_probs=73.4

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+++++++|+++|++||.|..|.++        ++||||+|.+.++|++|+..||+..|.|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            4567899999999999999999999999999999987        57999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.++...
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9877654

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

Probab=99.80  E-value=7.8e-19  Score=119.94  Aligned_cols=83  Identities=28%  Similarity=0.436  Sum_probs=75.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|   .++.+ .+++++|||||+|.+.++|++||..||+..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45568999999999999999999999999987   45555 588899999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.++..
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9987654

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

Probab=99.80  E-value=3.3e-20  Score=122.83  Aligned_cols=81  Identities=22%  Similarity=0.354  Sum_probs=75.9

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.++.++|||||+|.+.++|++|+..||+..|.|+.|+|.|+
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            45789999999999999999999999999999999999889999999999999999999999999999999999988765


Q ss_pred             c
Q 043064          167 F  167 (196)
Q Consensus       167 ~  167 (196)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.80  E-value=1.1e-19  Score=122.68  Aligned_cols=81  Identities=19%  Similarity=0.210  Sum_probs=75.6

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++||+.||+..|.|+.|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            35889999999999999999999999999988888888899999999999999999999999999999999999999985


Q ss_pred             c
Q 043064          168 S  168 (196)
Q Consensus       168 ~  168 (196)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.80  E-value=8.3e-20  Score=124.77  Aligned_cols=84  Identities=17%  Similarity=0.304  Sum_probs=75.4

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .....++|||+|||+.+++++|+.+|++|| |..|.|+.++ .+|+++|||||+|.+.++|.+|+ .|++..|.|+.|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            445679999999999999999999999999 9999999887 58999999999999999999999 89999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .++.++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9997754

>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=99.80  E-value=1.8e-19  Score=125.84  Aligned_cols=83  Identities=20%  Similarity=0.375  Sum_probs=78.4

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|| .||+..|.|+.|.|.|+.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecC
Confidence            3579999999999999999999999999999999999888999999999999999999999 999999999999999998


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      ++..
T Consensus       103 ~~~~  106 (114)
T 2cq4_A          103 AEKN  106 (114)
T ss_dssp             HHHH
T ss_pred             CCcc
Confidence            7643

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

Probab=99.80  E-value=7.9e-20  Score=118.17  Aligned_cols=75  Identities=17%  Similarity=0.379  Sum_probs=71.9

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +|||+|||+.+++++|+.+|++||.|..|.++.++.++.++|||||+|.+.++|++|++ |++..|+|+.|.|.||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998899999999999999999999997 9999999999999986

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.80  E-value=3.3e-19  Score=121.45  Aligned_cols=79  Identities=22%  Similarity=0.330  Sum_probs=71.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE--LLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~--l~g~~l~  162 (196)
                      ...++++|||+|||..+|+++|+.+|++||.|.+|.++..      +|||||+|.+.++|.+|+..|++..  |.|++|.
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            3446789999999999999999999999999999998753      7899999999999999999999875  8899999


Q ss_pred             EEEcccC
Q 043064          163 VDWAFSN  169 (196)
Q Consensus       163 v~~a~~~  169 (196)
                      |+|++++
T Consensus        91 V~~S~~k   97 (100)
T 3r27_A           91 VNYSTSQ   97 (100)
T ss_dssp             EEECSCS
T ss_pred             EEecccc
Confidence            9999765

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.80  E-value=3.2e-19  Score=123.81  Aligned_cols=86  Identities=17%  Similarity=0.365  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..+ +..|+|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3445788999999999999999999999999999999999888999999999999999999999876 589999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9987664

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

Probab=99.80  E-value=5.9e-19  Score=127.22  Aligned_cols=82  Identities=32%  Similarity=0.538  Sum_probs=77.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34467899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             Ec
Q 043064          165 WA  166 (196)
Q Consensus       165 ~a  166 (196)
                      ||
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>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=99.79  E-value=1.3e-19  Score=141.54  Aligned_cols=81  Identities=17%  Similarity=0.227  Sum_probs=76.6

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCC--CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYG--EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G--~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..++|||+||++.+|+++|+++|++||  .|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.|
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  999999999999999999999999999999999999999999999999999


Q ss_pred             ccc
Q 043064          166 AFS  168 (196)
Q Consensus       166 a~~  168 (196)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            864

>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=99.79  E-value=9.5e-19  Score=123.00  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=73.8

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCcEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~l~g~~l~v  163 (196)
                      ..++++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|++  ..|.|++|+|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            446789999999999999999999999999999999865      79999999999999999998874  6799999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.++...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999887655

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

Probab=99.79  E-value=5e-19  Score=122.78  Aligned_cols=85  Identities=19%  Similarity=0.357  Sum_probs=77.6

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||..+++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|++|+..|||..|.|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345567899999999999999999999999999999998874  347899999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .|+.++.
T Consensus       102 ~~a~~~~  108 (109)
T 2err_A          102 NNATARV  108 (109)
T ss_dssp             EECCCSC
T ss_pred             EECCCCc
Confidence            9997753

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.79  E-value=2.7e-19  Score=118.30  Aligned_cols=73  Identities=23%  Similarity=0.304  Sum_probs=69.2

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +..|||+||++.+|+++|+++|.+||+|.++.++.+      +|||||+|.+.++|.+|++.||+..|.|++|+|.+|.
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            567999999999999999999999999999998763      8999999999999999999999999999999999983

>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=99.79  E-value=4.6e-20  Score=123.45  Aligned_cols=82  Identities=22%  Similarity=0.375  Sum_probs=73.9

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.+ |..|+..||+..|.|+.|+|.+|.+.
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            57999999999999999999999999999999999888999999999999999 99999999999999999999999877


Q ss_pred             CCC
Q 043064          170 GPS  172 (196)
Q Consensus       170 ~~~  172 (196)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            654

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

Probab=99.79  E-value=3.9e-19  Score=121.44  Aligned_cols=77  Identities=19%  Similarity=0.421  Sum_probs=72.3

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ++|||+|||+.+++++|+++|++||.|..|.++.+     ++|||||+|.+.++|++|+..||+..|.|+.|+|.|+.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999866     5899999999999999999999999999999999999887


Q ss_pred             CC
Q 043064          170 GP  171 (196)
Q Consensus       170 ~~  171 (196)
                      ..
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.79  E-value=1.2e-19  Score=126.85  Aligned_cols=87  Identities=21%  Similarity=0.344  Sum_probs=74.9

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+.+|+++|+++|++||.|..+.+..+..++.++|||||+|.+.++|++|+..||+..|.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34678999999999999999999999999984432222223788899999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9877654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.79  E-value=5.3e-19  Score=121.85  Aligned_cols=83  Identities=24%  Similarity=0.361  Sum_probs=75.7

Q ss_pred             CCCCCEEEEcCCCccC------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           86 SIEGWIILVTGVHEEA------QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      ....++|||+|||+.+      |+++|+.+|++||.|..|.|+  +.+|.++|||||+|.+.++|.+|+..|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3447899999999999      889999999999999999988  36889999999999999999999999999999998


Q ss_pred             -EeEEEEcccCC
Q 043064          160 -TLTVDWAFSNG  170 (196)
Q Consensus       160 -~l~v~~a~~~~  170 (196)
                       .|+|.|+....
T Consensus        90 ~~l~V~~a~~~~  101 (105)
T 2nlw_A           90 HTFRVNLFTDFD  101 (105)
T ss_dssp             CEEEEECSCCCC
T ss_pred             ceEEEEEcchHh
Confidence             99999996543

>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=99.79  E-value=1.4e-18  Score=118.28  Aligned_cols=83  Identities=19%  Similarity=0.344  Sum_probs=75.4

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+.+++++|+.+|++||.|..|.++.+      +|||||+|.+.++|++|+..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   83 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   83 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEE
Confidence            34456789999999999999999999999999999998754      789999999999999999999999999999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.++...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpj_A           84 RFACHSASL   92 (99)
T ss_dssp             EESSCCSCC
T ss_pred             EEcCCCCCC
Confidence            999876643

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

Probab=99.79  E-value=1e-18  Score=116.90  Aligned_cols=80  Identities=24%  Similarity=0.419  Sum_probs=72.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.++        ++||||+|.+.++|++|+..||+..|.|+.|+|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567889999999999999999999999999999987        3499999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.+....
T Consensus        77 ~a~~~~~~   84 (90)
T 2dnp_A           77 LSTKGQKK   84 (90)
T ss_dssp             ESCCCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>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=99.79  E-value=1.8e-18  Score=119.09  Aligned_cols=82  Identities=22%  Similarity=0.279  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc--eeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG--ELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~--~l~g~~l~  162 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|++.  .|.|++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4456789999999999999999999999999999988754      789999999999999999988654  59999999


Q ss_pred             EEEcccCCCC
Q 043064          163 VDWAFSNGPS  172 (196)
Q Consensus       163 v~~a~~~~~~  172 (196)
                      |.|+.++...
T Consensus        85 V~~a~~~~~~   94 (104)
T 1wex_A           85 FNYSTSKRIT   94 (104)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCcccc
Confidence            9999876543

>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=99.79  E-value=6.7e-19  Score=141.03  Aligned_cols=124  Identities=20%  Similarity=0.225  Sum_probs=100.5

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhcccCCCCCC----------CCCCCCCCCCEEEEcCCCccC-cHHHHHHhhccCC
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFESLGTDGG----------PGPQRSIEGWIILVTGVHEEA-QEDDLQNVFGEYG  114 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~l~V~nLp~~~-te~~L~~~F~~~G  114 (196)
                      .+++++|+|||.|.+...+ ..+...+++....+.          ..+....+.++|||+|||+.+ ++++|+.+|+.||
T Consensus       132 ~~g~~~g~afV~f~~~~~a-~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G  210 (284)
T 3smz_A          132 RTGQSKGYGFAEYMKKDSA-ARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVH  210 (284)
T ss_dssp             TTCCEEEEEEEEESSHHHH-HHHHHHHTTCEETTEECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSS
T ss_pred             CCCccceEEEEEECCHHHH-HHHHHHhCCCEeCCcEEEEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCC
Confidence            3557899999999954444 334334444333221          112334567899999999995 9999999999999


Q ss_pred             CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCC
Q 043064          115 EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       115 ~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~  171 (196)
                      .|..+.|+.+. +|.++|+|||+|.+.++|.+|+..|||..|+|+.|.|.|+.++..
T Consensus       211 ~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          211 SPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             CCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             CeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            99999999885 899999999999999999999999999999999999999987764

>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=99.79  E-value=1.1e-18  Score=120.82  Aligned_cols=81  Identities=19%  Similarity=0.424  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.+      +|||||+|.+.++|.+|+..|++..|.|+.|+|.|
T Consensus        22 ~~~~~~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           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            345689999999999999999999999999999999865      78999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.+++..
T Consensus        96 a~~~~~~  102 (109)
T 1x4g_A           96 GKESPDM  102 (109)
T ss_dssp             CCCCCSS
T ss_pred             cCCCCCC
Confidence            9887654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.79  E-value=7.4e-19  Score=125.19  Aligned_cols=84  Identities=19%  Similarity=0.304  Sum_probs=75.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQ----NVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      ...+.++|||+|||+.+++++|+    .+|++||.|..|.+.   .+++++|||||+|.+.++|..|+..|||..|.|++
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34567899999999999998876    699999999998775   36788999999999999999999999999999999


Q ss_pred             eEEEEcccCCC
Q 043064          161 LTVDWAFSNGP  171 (196)
Q Consensus       161 l~v~~a~~~~~  171 (196)
                      |+|.||.++..
T Consensus       102 l~V~~a~~~~~  112 (127)
T 2a3j_A          102 LVITFSETPQS  112 (127)
T ss_dssp             CEEEECCCCCH
T ss_pred             EEEEEccCcch
Confidence            99999987653

>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=99.78  E-value=2e-18  Score=118.74  Aligned_cols=84  Identities=13%  Similarity=0.211  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeE-EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN-LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .....++|||+|||+.+++++|+++|++||.|.. |.|+.+ .+|+++|||||+|.+.++|++||.. ++..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v   88 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEI   88 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEE
Confidence            3456789999999999999999999999999987 888888 6999999999999999999999987 999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .++.+..
T Consensus        89 ~~~~~~~   95 (104)
T 1wg5_A           89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9986544

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.6e-19  Score=117.12  Aligned_cols=77  Identities=18%  Similarity=0.396  Sum_probs=73.2

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ++|||+|||+.+++++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|++|+..++ ..|+|+.|.|.+|.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a~   77 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEecC
Confidence            469999999999999999999999999999999998889999999999999999999999999 99999999999873

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.5e-19  Score=123.14  Aligned_cols=83  Identities=14%  Similarity=0.121  Sum_probs=77.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCe-eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEI-RNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i-~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ..+.++|||+|||+.+|+++|+++|+.||.| ..|.|+.++ +|+++|||||+|.+.++|++||.. |+..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            3457889999999999999999999999999 889999997 999999999999999999999986 9999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      ++.++.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            998765

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

Probab=99.78  E-value=4.1e-18  Score=115.94  Aligned_cols=79  Identities=22%  Similarity=0.309  Sum_probs=72.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccC--CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEY--GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~--G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ...+.++|||+|||+.+++++|+.+|++|  |.|..|.+.        +|||||+|.+.++|++|+..||+..|.|+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            34567899999999999999999999999  899988765        67999999999999999999999999999999


Q ss_pred             EEEcccCCC
Q 043064          163 VDWAFSNGP  171 (196)
Q Consensus       163 v~~a~~~~~  171 (196)
                      |.|+.++..
T Consensus        83 v~~a~~~~~   91 (99)
T 2cpd_A           83 VTLAKPVDK   91 (99)
T ss_dssp             EECCCCCCC
T ss_pred             EEECCCCCC
Confidence            999987654

>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=99.78  E-value=1.3e-18  Score=114.99  Aligned_cols=79  Identities=24%  Similarity=0.333  Sum_probs=72.3

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCcEe
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM-NGGELLTQTL  161 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l-~~~~l~g~~l  161 (196)
                      +....+.++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|.+.++|..|+..| ++..+.|+.|
T Consensus         6 ~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l   79 (85)
T 2ytc_A            6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL   79 (85)
T ss_dssp             CCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEEC
T ss_pred             CCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEE
Confidence            334556788999999999999999999999999999999864      789999999999999999988 9999999999


Q ss_pred             EEEEcc
Q 043064          162 TVDWAF  167 (196)
Q Consensus       162 ~v~~a~  167 (196)
                      +|.||+
T Consensus        80 ~v~~ak   85 (85)
T 2ytc_A           80 NVKWGR   85 (85)
T ss_dssp             CEEECC
T ss_pred             EEEecC
Confidence            999984

>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=99.78  E-value=6.1e-19  Score=141.81  Aligned_cols=121  Identities=21%  Similarity=0.364  Sum_probs=93.5

Q ss_pred             CCCcCcccccCCCcHHHHHHhhhhcccCCCCCC--------CCC------CCCCCCCEEEEcCCCcc-CcHHHHHHhhcc
Q 043064           48 KKTKGRGFREEADSERHSRLADRNFESLGTDGG--------PGP------QRSIEGWIILVTGVHEE-AQEDDLQNVFGE  112 (196)
Q Consensus        48 ~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~------~~~~~~~~l~V~nLp~~-~te~~L~~~F~~  112 (196)
                      ++++|||||.|.+... +..+...+++....+.        +..      ....+.++|||+|||+. +++++|+.+|++
T Consensus       156 ~~~~g~afV~f~~~~~-a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~  234 (292)
T 2ghp_A          156 NTSRRFAYIDVTSKED-ARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG  234 (292)
T ss_dssp             ---CCEEEEECSSHHH-HHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGG
T ss_pred             CCcceEEEEEECCHHH-HHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhc
Confidence            4688999999995444 4434444444333221        110      22345789999999999 999999999999


Q ss_pred             CCCeeEEEEeecCC-CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064          113 YGEIRNLHLNLDRR-TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       113 ~G~i~~v~i~~~~~-~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      ||.|..|.|+.+.. +|.++|||||+|.+.++|.+|+ .|||..|.|+.|.|.|+.+++
T Consensus       235 ~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          235 FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             GSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             cCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            99999999998765 4899999999999999999999 999999999999999998864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.78  E-value=1.2e-19  Score=124.03  Aligned_cols=85  Identities=13%  Similarity=0.270  Sum_probs=76.6

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+.+++++|+.+|++||.|.. .++.+..++.++|||||+|.+.++|++||+ ||+..|.|+.|+|.|
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345789999999999999999999999999887 566666688899999999999999999998 999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.++...
T Consensus        92 a~~~~~~   98 (101)
T 1fj7_A           92 PKGRDGT   98 (101)
T ss_dssp             CSCCCCS
T ss_pred             cCCCCCC
Confidence            9876654

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

Probab=99.78  E-value=2e-18  Score=117.08  Aligned_cols=82  Identities=24%  Similarity=0.279  Sum_probs=72.9

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      .....++|||+|||+.+++++|+.+|++||.|. +.++.    +.++|||||+|.+.++|++|+..||+..|.|+.|+|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            344578999999999999999999999999996 66654    3568999999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.++.+
T Consensus        90 ~a~~~~~   96 (97)
T 2e5j_A           90 LARQQRD   96 (97)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9987654

>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=99.78  E-value=2e-18  Score=126.21  Aligned_cols=81  Identities=20%  Similarity=0.418  Sum_probs=74.9

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.|+.+     ++|||||+|.+.++|..|+..||+..|.|++|+|.
T Consensus        69 ~~~~~~~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           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            4456799999999999999999999999999999999876     38999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      |+.++.
T Consensus       144 ~a~~~~  149 (150)
T 2i2y_A          144 LSNGEK  149 (150)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997764

>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=99.78  E-value=1.8e-18  Score=138.50  Aligned_cols=123  Identities=21%  Similarity=0.289  Sum_probs=100.8

Q ss_pred             CCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC-CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCC
Q 043064           48 KKTKGRGFREEADSERHSRLADRNFESLGTDGGPGP-QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR  126 (196)
Q Consensus        48 ~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~  126 (196)
                      .+++|+|||.|.+. ..+..+...+++....+.+.. ......++|||+|||+.+++++|+.+|+.||.|..+.++.+..
T Consensus        54 ~~~~g~afV~f~~~-~~A~~A~~~l~~~~~~g~~i~v~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~  132 (284)
T 3smz_A           54 DKYKGTAFVTLLNG-EQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER  132 (284)
T ss_dssp             ETTTTEEEEEESSH-HHHHHHHHHHTTCEETTEECEEEECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT
T ss_pred             ecCCCEEEEEeCCH-HHHHHHHHHcCCCeeCCeEEEEEecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCC
Confidence            36789999999954 444444445555444332221 1233567899999999999999999999999999999999988


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCC
Q 043064          127 TGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       127 ~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~  171 (196)
                      +|.++|||||+|.+.++|.+|+..|++..|.|+.|.|.|+.+...
T Consensus       133 ~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          133 TGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            999999999999999999999999999999999999999987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=1.5e-20  Score=131.83  Aligned_cols=87  Identities=25%  Similarity=0.411  Sum_probs=80.8

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeE--------EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRN--------LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL  157 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~--------v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~  157 (196)
                      ..+.++|||+|||+.+++++|+++|++||.|..        |.|+.++.++.++|||||+|.+.++|++|+..||+..|.
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            345788999999999999999999999999998        889988888999999999999999999999999999999


Q ss_pred             CcEeEEEEcccCCCC
Q 043064          158 TQTLTVDWAFSNGPS  172 (196)
Q Consensus       158 g~~l~v~~a~~~~~~  172 (196)
                      |+.|+|.|+.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999887653

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=1.4e-18  Score=122.28  Aligned_cols=84  Identities=18%  Similarity=0.285  Sum_probs=77.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGE---IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      .....++|||+|||+++|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|++||+ +|+..|+|+.|
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i   90 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYI   90 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEE
Confidence            3456789999999999999999999999999   89999999875 9999999999999999999998 99999999999


Q ss_pred             EEEEcccCC
Q 043064          162 TVDWAFSNG  170 (196)
Q Consensus       162 ~v~~a~~~~  170 (196)
                      .|.++.++.
T Consensus        91 ~V~~a~~~~   99 (118)
T 2db1_A           91 EVFKSHRTE   99 (118)
T ss_dssp             EEEEECHHH
T ss_pred             EEEECCHHH
Confidence            999986553

>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=99.78  E-value=5.7e-19  Score=119.62  Aligned_cols=84  Identities=18%  Similarity=0.432  Sum_probs=75.6

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQ----NVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      ...++++|||+|||+.+++++|+    .+|++||.|..|.++.   ++.++|||||+|.+.++|..|+..|||..|.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            34567899999999999999999    9999999999998863   5677899999999999999999999999999999


Q ss_pred             eEEEEcccCCC
Q 043064          161 LTVDWAFSNGP  171 (196)
Q Consensus       161 l~v~~a~~~~~  171 (196)
                      |+|.|+.++..
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999987653

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

Probab=99.77  E-value=1e-18  Score=118.37  Aligned_cols=79  Identities=16%  Similarity=0.336  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           86 SIEGWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        86 ~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ..+.++|||+|||+ .+++++|+.+|++||.|..|.|.        +|||||+|.+.++|+.|+..||+..+.|+.|+|.
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            45678999999998 99999999999999999999884        6899999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876643

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

Probab=99.77  E-value=1.2e-18  Score=117.80  Aligned_cols=83  Identities=23%  Similarity=0.375  Sum_probs=74.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..+     ..++.++|||||+|.+.++|.+|+..|++..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34467899999999999999999999999988766     2478889999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        87 ~a~~~~~~   94 (96)
T 1fjc_A           87 YTGEKGGT   94 (96)
T ss_dssp             ECSSSCCC
T ss_pred             EcCCCCCC
Confidence            99877654

>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=99.77  E-value=1.3e-18  Score=117.07  Aligned_cols=79  Identities=25%  Similarity=0.369  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCC-eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC-ceeCCcEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGE-IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG-GELLTQTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~-i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~-~~l~g~~l~v  163 (196)
                      ..+.++|||+|||+++++++|+.+|++||. |..+.+.       ++|||||+|.+.++|++|+..||+ ..|.|+.|+|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            345688999999999999999999999999 6555553       378999999999999999999999 9999999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .|+.++..
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99987654

>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=99.77  E-value=5.4e-19  Score=125.32  Aligned_cols=84  Identities=14%  Similarity=0.206  Sum_probs=76.1

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+|+++|+.+|+.||.|..+.++.+..+|+++|||||+|.+.++|++||. ||+..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456899999999999999999999999999886666666799999999999999999999999 999999999999999


Q ss_pred             cccCC
Q 043064          166 AFSNG  170 (196)
Q Consensus       166 a~~~~  170 (196)
                      +.++.
T Consensus       101 a~~~~  105 (124)
T 1wel_A          101 ITKKG  105 (124)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87643

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

Probab=99.77  E-value=1.1e-18  Score=121.39  Aligned_cols=80  Identities=20%  Similarity=0.208  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYG-EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..++|||+|||+.+++++|+++|++|| .|..+.+..    ..++|||||+|.+.++|++||+.|||..|.|+.|+|.++
T Consensus        27 ~~~~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           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            468999999999999999999999999 899998853    246899999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      ...++
T Consensus       103 ~~~p~  107 (111)
T 2jvr_A          103 DNPPP  107 (111)
T ss_dssp             CC---
T ss_pred             CCCCC
Confidence            75543

>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=99.77  E-value=1.9e-18  Score=120.15  Aligned_cols=81  Identities=20%  Similarity=0.201  Sum_probs=72.1

Q ss_pred             CCCCCCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC--CceeCCcEe
Q 043064           85 RSIEGWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN--GGELLTQTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~--~~~l~g~~l  161 (196)
                      ...++++|||+|||++ +++++|+.+|++||.|..|.|+..      +|||||+|.+.++|+.|+..|+  +..|.|++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3556889999999998 999999999999999999998743      7999999999999999999886  456999999


Q ss_pred             EEEEcccCCC
Q 043064          162 TVDWAFSNGP  171 (196)
Q Consensus       162 ~v~~a~~~~~  171 (196)
                      +|.|+.++..
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999977654

>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=99.77  E-value=1.2e-18  Score=125.60  Aligned_cols=83  Identities=17%  Similarity=0.263  Sum_probs=76.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGE---IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      .....++|||+|||+++|+++|+++|++||.   |..|.|+.++. |+++|||||+|.+.++|++||+ ||+..|+|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3456789999999999999999999999999   88999999975 9999999999999999999998 99999999999


Q ss_pred             EEEEcccC
Q 043064          162 TVDWAFSN  169 (196)
Q Consensus       162 ~v~~a~~~  169 (196)
                      .|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99998654

>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=99.77  E-value=3.6e-19  Score=129.19  Aligned_cols=86  Identities=29%  Similarity=0.429  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEE------EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNL------HLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v------~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      ..+.++|||+|||+.+|+++|+.+|++||.|..+      .+.. ..++.++|||||+|.+.++|.+||..|||..|.|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            4457899999999999999999999999998764      1111 14788899999999999999999999999999999


Q ss_pred             EeEEEEcccCCCC
Q 043064          160 TLTVDWAFSNGPS  172 (196)
Q Consensus       160 ~l~v~~a~~~~~~  172 (196)
                      .|.|.||.+..++
T Consensus       121 ~l~V~~a~~~~~~  133 (143)
T 3egn_A          121 PMVVQFARSARPK  133 (143)
T ss_dssp             ECEEEECCCSCC-
T ss_pred             EEEEEECCCCCCc
Confidence            9999999876544

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=4.7e-18  Score=114.63  Aligned_cols=80  Identities=16%  Similarity=0.252  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+.+|++||.|..|  +.++.++.   ||||+|.+.++|++||. ||+..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEE
Confidence            3456799999999999999999999999999987  55555655   99999999999999999 999999999999998


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      +.++..
T Consensus        79 a~~~~~   84 (94)
T 2e5g_A           79 REQKEF   84 (94)
T ss_dssp             SCCSCC
T ss_pred             CCcCCC
Confidence            866554

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

Probab=99.76  E-value=3.2e-18  Score=118.59  Aligned_cols=79  Identities=24%  Similarity=0.476  Sum_probs=72.7

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|.++        +|||||+|.+.++|++|+..|||..|.|+.|.|.
T Consensus        27 ~~~~~~~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           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            45567999999999999999999999999999999987        6899999999999999999999999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      |+.+...
T Consensus        99 ~a~~~~~  105 (108)
T 2jvo_A           99 YSKLPAK  105 (108)
T ss_dssp             SCSCCC-
T ss_pred             EecCCCC
Confidence            9987664

>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=99.76  E-value=8.4e-18  Score=116.59  Aligned_cols=77  Identities=26%  Similarity=0.467  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ...++|||+|||+. +++++|+.+|++||.|..|.|        .+|||||+|.+.++|+.|+..||+..|.|+.|+|.|
T Consensus        25 ~~~~~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           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34589999999999 999999999999999999988        378999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      +.+...
T Consensus        97 a~~~~~  102 (110)
T 1wf1_A           97 AGEPKP  102 (110)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            975443

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

Probab=99.76  E-value=1.6e-18  Score=118.37  Aligned_cols=77  Identities=22%  Similarity=0.314  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ...++|||+|||..+++++|+.+|++||.|..|.+..      .+|||||+|.+.++|.+|+..||+..|.|+.|+|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            3468999999999999999999999999999999873      3799999999999999999999999999999999999


Q ss_pred             ccC
Q 043064          167 FSN  169 (196)
Q Consensus       167 ~~~  169 (196)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.76  E-value=6.1e-18  Score=114.88  Aligned_cols=78  Identities=18%  Similarity=0.346  Sum_probs=71.5

Q ss_pred             CCCCCCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           85 RSIEGWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ...+.++|||+|||+ .+++++|+.+|++||.|..|.+.        +|||||+|.+.++|.+|+..||+..|.|+.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999998 99999999999999999999883        789999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .|++++.
T Consensus        90 ~~a~~~~   96 (97)
T 2xnq_A           90 EVSSSNA   96 (97)
T ss_dssp             EECCCCC
T ss_pred             EecCCCC
Confidence            9997654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.6e-17  Score=112.64  Aligned_cols=81  Identities=23%  Similarity=0.387  Sum_probs=72.6

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+||  .+++++|+.+|++||.|..|.|.      .++|||||+|.+.++|++||..||+..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            34456789999996  89999999999999999999885      34789999999999999999999999999999999


Q ss_pred             EEcccCCCC
Q 043064          164 DWAFSNGPS  172 (196)
Q Consensus       164 ~~a~~~~~~  172 (196)
                      .|+.++...
T Consensus        82 ~~a~~~~~~   90 (97)
T 1x5p_A           82 NIARKQPML   90 (97)
T ss_dssp             ECCSSCCCC
T ss_pred             EECCCCCCC
Confidence            999887654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.76  E-value=9.8e-19  Score=114.80  Aligned_cols=73  Identities=27%  Similarity=0.466  Sum_probs=67.9

Q ss_pred             CCEEEEcCCCccC------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc-Ee
Q 043064           89 GWIILVTGVHEEA------QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ-TL  161 (196)
Q Consensus        89 ~~~l~V~nLp~~~------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~-~l  161 (196)
                      +++|||+|||..+      ++++|+.+|++||.|..|.|+  +.+|+++|||||+|.+.++|++|+..|||..|.|+ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3689999999999      789999999999999999987  35889999999999999999999999999999999 88


Q ss_pred             EE
Q 043064          162 TV  163 (196)
Q Consensus       162 ~v  163 (196)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.76  E-value=6.5e-18  Score=130.26  Aligned_cols=85  Identities=21%  Similarity=0.293  Sum_probs=78.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|.+||..+++..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043064          166 AFSNG  170 (196)
Q Consensus       166 a~~~~  170 (196)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            86543

>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=99.76  E-value=4.4e-18  Score=118.83  Aligned_cols=81  Identities=22%  Similarity=0.406  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .++++|||+|||+.+++++|+.+|++||.|..|.|+.+   +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45689999999999999999999999999999999854   445899999999999999999999999999999999999


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      .+..
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            8654

>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=99.76  E-value=5.3e-19  Score=114.17  Aligned_cols=75  Identities=20%  Similarity=0.441  Sum_probs=71.3

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +|||+|||+.+++++|+.+|++||.|..|.++.++.++.++|||||+|.+.++|++|+. +++..|.|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999998889999999999999999999997 4889999999999886

>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=99.76  E-value=3.9e-19  Score=128.53  Aligned_cols=84  Identities=24%  Similarity=0.370  Sum_probs=75.1

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+++|+++|+++|++|| |..|.|+.++. ++++|||||+|.+.++|++|| .+|+..|+|+.|.|.+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999 77999999974 999999999999999999999 7899999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      +.+....
T Consensus       120 a~~~~~~  126 (139)
T 2hgn_A          120 NSTTGAS  126 (139)
T ss_dssp             CCCSCC-
T ss_pred             CCCCCCC
Confidence            9776543

>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=99.75  E-value=1e-18  Score=120.84  Aligned_cols=84  Identities=21%  Similarity=0.243  Sum_probs=77.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCC---eeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGE---IRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~---i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      .....++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|++||. +|+..|+|+.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYV   84 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEE
Confidence            3456789999999999999999999999988   89999999875 9999999999999999999998 99999999999


Q ss_pred             EEEEcccCC
Q 043064          162 TVDWAFSNG  170 (196)
Q Consensus       162 ~v~~a~~~~  170 (196)
                      .|.++.++.
T Consensus        85 ~V~~a~~~~   93 (107)
T 2lmi_A           85 EVYEINNED   93 (107)
T ss_dssp             CCEECCHHH
T ss_pred             EEEECCHHH
Confidence            999987643

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

Probab=99.75  E-value=3.8e-18  Score=128.23  Aligned_cols=85  Identities=22%  Similarity=0.359  Sum_probs=79.5

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34557899999999999999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      ||.+..
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            997654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.75  E-value=1.5e-18  Score=118.64  Aligned_cols=83  Identities=22%  Similarity=0.418  Sum_probs=76.9

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.++ ++.++|||||+|.+.++|++|+.  ++..|+|+.|.|.+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEE
Confidence            3456889999999999999999999999999999999997 99999999999999999999997  99999999999999


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      +.++..
T Consensus        83 a~~~~~   88 (102)
T 2xs2_A           83 AIRKQN   88 (102)
T ss_dssp             EEECC-
T ss_pred             CCcCcc
Confidence            987654

>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=99.75  E-value=5.4e-18  Score=117.97  Aligned_cols=78  Identities=18%  Similarity=0.236  Sum_probs=71.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+++++|+.+|++||.|..|.|+.      .+|||||+|.+.++|+.|+..||+..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467899999999999999999999999999998874      37899999999999999999999999999999999997


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      ....
T Consensus        83 ~~~~   86 (111)
T 1whx_A           83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            6543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=5.3e-18  Score=117.66  Aligned_cols=79  Identities=20%  Similarity=0.301  Sum_probs=73.2

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+|+++|+++|+.| .|..|.|+.++ .|+++|||||+|.+.++|++|| .+|+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            45789999999999999999999999 89999999986 5999999999999999999999 699999999999998886


Q ss_pred             cC
Q 043064          168 SN  169 (196)
Q Consensus       168 ~~  169 (196)
                      ++
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            53

>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=99.75  E-value=1.3e-17  Score=122.64  Aligned_cols=83  Identities=28%  Similarity=0.485  Sum_probs=78.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||+.+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|++..+.|+.|.|.|+.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            35789999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.75  E-value=1.1e-17  Score=133.82  Aligned_cols=75  Identities=23%  Similarity=0.383  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CcEeEEEEc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL-TQTLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~-g~~l~v~~a  166 (196)
                      +.++|||+|||..+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|.+|+..|||..|. |+.|+|.|+
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            46889999999999999999999999999999998654     689999999999999999999999999 999999998


Q ss_pred             c
Q 043064          167 F  167 (196)
Q Consensus       167 ~  167 (196)
                      +
T Consensus       281 k  281 (282)
T 3pgw_A          281 K  281 (282)
T ss_pred             c
Confidence            5

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

Probab=99.74  E-value=7.2e-18  Score=113.96  Aligned_cols=81  Identities=20%  Similarity=0.268  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNL-HLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ....++|||+|||+.+++++|+.+|++||.|..| .|+.++.++    .|||+|.+.++|..|+..||+..|.|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456889999999999999999999999999999 577765443    39999999999999999999999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      |+.++.
T Consensus        88 ~a~~~~   93 (96)
T 2e44_A           88 YIPDEM   93 (96)
T ss_dssp             ECCCCC
T ss_pred             EcCccc
Confidence            998773

>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=99.74  E-value=1.1e-17  Score=123.34  Aligned_cols=84  Identities=24%  Similarity=0.436  Sum_probs=79.4

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||+.+++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+..|++..+.|+.|.|.|+.
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            46889999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      +...
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            6653

>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=99.73  E-value=1.4e-17  Score=132.23  Aligned_cols=121  Identities=16%  Similarity=0.251  Sum_probs=96.0

Q ss_pred             CCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCC-CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCC
Q 043064           49 KTKGRGFREEADSERHSRLADRNFESLGTDGGPGP-QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRT  127 (196)
Q Consensus        49 ~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~  127 (196)
                      +++|||||.|.+ ...+..+...+++....+.... ....+..+|||+|||..+|+++|+++|+.||.|..|.|+.+ .+
T Consensus        56 ~~kg~afV~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           56 RDRGFGFIRLES-RTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DR  133 (261)
T ss_dssp             TTTTEEEEECSS-HHHHHHHHHHHTTCEETTEECEEEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TT
T ss_pred             CCCcEEEEEECC-HHHHHHHHHHcCCcEECCceeEeeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CC
Confidence            468999999995 4444444445555444432221 12345789999999999999999999999999999999999 58


Q ss_pred             CCcceEEEEEecCHHHHHHHHHHhCC-ceeC---CcEeEEEEcccCCC
Q 043064          128 GFVKGYALIEYENFEEAQNAITAMNG-GELL---TQTLTVDWAFSNGP  171 (196)
Q Consensus       128 g~~~g~afv~f~~~~~a~~al~~l~~-~~l~---g~~l~v~~a~~~~~  171 (196)
                      |.++|||||+|.+.++|.+|+..||+ ..+.   +++|.|.++.+...
T Consensus       134 g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          134 GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence            99999999999999999999999954 4444   99999999987643

>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=99.73  E-value=6.9e-18  Score=135.60  Aligned_cols=119  Identities=12%  Similarity=0.032  Sum_probs=92.4

Q ss_pred             CcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCC-CeeEEEEeecCCCC
Q 043064           50 TKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYG-EIRNLHLNLDRRTG  128 (196)
Q Consensus        50 ~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g  128 (196)
                      ++|+|||.|.+.+.+.. +. .++.....+.+........++|||+|||+.+++++|+.+|+.|| .|..|.++.++ .+
T Consensus        80 ~~g~afV~f~~~~~A~~-A~-~~~~~~~~g~~i~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~  156 (292)
T 2ghp_A           80 NFRFARIEFARYDGALA-AI-TKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FN  156 (292)
T ss_dssp             SSEEEEEEESSHHHHHH-HH-TTTTCEETTEECEEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC------
T ss_pred             CcEEEEEEECCHHHHHH-HH-HhCCcEeCCcEEEEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CC
Confidence            57999999995555444 33 24554444444333445688999999999999999999999999 99999998875 47


Q ss_pred             CcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCCC
Q 043064          129 FVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       129 ~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~~  171 (196)
                      .++|||||+|.+.++|..|+..|++..|.|+.|.|.|+.+...
T Consensus       157 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          157 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             --CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC--
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            8899999999999999999999999999999999999987654

>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=99.73  E-value=2e-17  Score=110.16  Aligned_cols=76  Identities=20%  Similarity=0.265  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+++++|+++|++| .|..+.+.      +++|||||+|.+.++|++|+..||+..+.|+.|+|.|+.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 99999885      458999999999999999999999999999999999996


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            554

>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=99.73  E-value=1.8e-17  Score=115.39  Aligned_cols=80  Identities=23%  Similarity=0.319  Sum_probs=71.2

Q ss_pred             CCCCCEEEE--cCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-----CC
Q 043064           86 SIEGWIILV--TGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL-----LT  158 (196)
Q Consensus        86 ~~~~~~l~V--~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l-----~g  158 (196)
                      ..+.++|||  +||++.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++|++.|||..|     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            445788999  779999999999999999999999987642      78999999999999999999999988     68


Q ss_pred             cEeEEEEcccCCC
Q 043064          159 QTLTVDWAFSNGP  171 (196)
Q Consensus       159 ~~l~v~~a~~~~~  171 (196)
                      ++|.|.|+...+-
T Consensus        96 ~~l~v~~a~~~p~  108 (114)
T 2cq2_A           96 ITLYLNFVEKVQW  108 (114)
T ss_dssp             EECEEEEESCCCC
T ss_pred             cEEEEEecccCcc
Confidence            9999999976543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.1e-17  Score=117.79  Aligned_cols=77  Identities=22%  Similarity=0.291  Sum_probs=70.4

Q ss_pred             CEEEEcCC----CccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecC----HHH----HHHHHH--HhCCce
Q 043064           90 WIILVTGV----HEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN----FEE----AQNAIT--AMNGGE  155 (196)
Q Consensus        90 ~~l~V~nL----p~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~----~~~----a~~al~--~l~~~~  155 (196)
                      +.|||+||    |+.+++.+|+.+|+.||+|.+|.++.|+.||.++|||||+|.+    ...    |.+|+.  .|++..
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            57999999    9999999999999999999999999999999999999999995    322    888988  789999


Q ss_pred             eCCcEeEEEEc
Q 043064          156 LLTQTLTVDWA  166 (196)
Q Consensus       156 l~g~~l~v~~a  166 (196)
                      |+|+.|+|.+-
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999975

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=110.00  Aligned_cols=76  Identities=16%  Similarity=0.268  Sum_probs=67.3

Q ss_pred             CCCCE-EEEcCCCccCcHHH----HHHhhccC-CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           87 IEGWI-ILVTGVHEEAQEDD----LQNVFGEY-GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        87 ~~~~~-l~V~nLp~~~te~~----L~~~F~~~-G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      .++.+ |||+|||+.+++++    |..+|++| |+|.+|       ++   |+|||.|.+.++|++|++.|||..|.|++
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            34566 99999999999987    55899999 599887       33   89999999999999999999999999999


Q ss_pred             eEEEEcccCCCC
Q 043064          161 LTVDWAFSNGPS  172 (196)
Q Consensus       161 l~v~~a~~~~~~  172 (196)
                      |+|.||+.++.-
T Consensus        76 i~v~~A~~~sd~   87 (96)
T 2diu_A           76 IIVSFTPKNREL   87 (96)
T ss_dssp             CEEESSCCSCCC
T ss_pred             EEEEecCCCcce
Confidence            999999887653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.72  E-value=1.9e-17  Score=125.73  Aligned_cols=77  Identities=21%  Similarity=0.351  Sum_probs=71.3

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CcEeEEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYG-EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL-TQTLTVDW  165 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~-g~~l~v~~  165 (196)
                      +.++|||+|||..+++++|+++|++|| .|..|.++.+.     +|+|||+|.+.++|.+|+..|||..|+ |+.|+|.|
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            478999999999999999999999999 99999986542     789999999999999999999999999 99999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      +++.
T Consensus       194 a~~~  197 (198)
T 1qm9_A          194 SKST  197 (198)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            9764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.72  E-value=5.2e-17  Score=115.59  Aligned_cols=80  Identities=20%  Similarity=0.323  Sum_probs=71.5

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--cEeEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY-ALIEYENFEEAQNAITAMNGGELLT--QTLTV  163 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~-afv~f~~~~~a~~al~~l~~~~l~g--~~l~v  163 (196)
                      .....|||+||+..+|+++|..+|++||.|.+|.|....     +|| |||+|.+.++|+.|++.|||..|.|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            345678899999999999999999999999999887542     677 9999999999999999999999988  89999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .|+++..-
T Consensus       101 ~~ak~~~l  108 (130)
T 3zzy_A          101 DFSKLTSL  108 (130)
T ss_dssp             EECSCSSC
T ss_pred             EecCCCce
Confidence            99987643

>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=99.72  E-value=1.3e-17  Score=128.09  Aligned_cols=78  Identities=13%  Similarity=0.203  Sum_probs=69.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCe--eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc----Ee
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEI--RNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ----TL  161 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i--~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~----~l  161 (196)
                      ++++|||+|||+.+|+++|+++|++||.|  ..+.++.+.  +..+|+|||+|.+.++|.+||..|||..|.|.    ++
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~  199 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY  199 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCE
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcce
Confidence            46789999999999999999999999999  888887664  55579999999999999999999999999876    67


Q ss_pred             EEEEcc
Q 043064          162 TVDWAF  167 (196)
Q Consensus       162 ~v~~a~  167 (196)
                      .|.|++
T Consensus       200 ~vk~~f  205 (205)
T 3tyt_A          200 TLKLCF  205 (205)
T ss_dssp             ECEEEC
T ss_pred             EEEecC
Confidence            777763

>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=99.72  E-value=3.6e-17  Score=127.40  Aligned_cols=77  Identities=21%  Similarity=0.339  Sum_probs=70.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCC-CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC-CcEeEEEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYG-EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL-TQTLTVDW  165 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G-~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~-g~~l~v~~  165 (196)
                      +.++|||+|||+.+++++|+++|++|| .|..|.++..     .+|||||+|.+.++|.+|+..|||..|. |+.|+|.|
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            368999999999999999999999999 9999998643     2689999999999999999999999999 99999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      +++.
T Consensus       225 a~~~  228 (229)
T 2adc_A          225 SKST  228 (229)
T ss_dssp             CSSC
T ss_pred             ecCC
Confidence            9764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.2e-17  Score=118.22  Aligned_cols=81  Identities=19%  Similarity=0.175  Sum_probs=73.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCe----eEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEI----RNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i----~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ...++|||+|||+++|+++|+++|++||.|    ..|.|+.+ .+|+++|||||+|.+.++|++||+. |+..|+|+.|.
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~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            346789999999999999999999999875    68999988 4899999999999999999999985 99999999999


Q ss_pred             EEEcccC
Q 043064          163 VDWAFSN  169 (196)
Q Consensus       163 v~~a~~~  169 (196)
                      |..+.++
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9987544

>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=99.71  E-value=1.2e-17  Score=118.66  Aligned_cols=82  Identities=17%  Similarity=0.261  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCee--EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR--NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .....++|||+|||+.+|+++|+++|++| .|.  .|.|+.++. |+++|||||+|.+.++|++||+ +++..|+|+.|.
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~  114 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIE  114 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            34457889999999999999999999999 677  899999875 9999999999999999999997 477999999999


Q ss_pred             EEEcccC
Q 043064          163 VDWAFSN  169 (196)
Q Consensus       163 v~~a~~~  169 (196)
                      |.++.++
T Consensus       115 V~~a~~~  121 (126)
T 2hgm_A          115 VFKSSQE  121 (126)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9988543

>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=99.71  E-value=7.7e-17  Score=118.89  Aligned_cols=81  Identities=20%  Similarity=0.264  Sum_probs=72.0

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v  163 (196)
                      .....+|||+||++.+|+++|+++|++||.|.+|.|...    ..+|||||+|.+.++|+.|++.|||..|.|  +.|+|
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V  118 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  118 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEE
Confidence            344577999999999999999999999999999998643    247899999999999999999999999965  99999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .|++++.
T Consensus       119 ~~Ak~~~  125 (164)
T 1sjr_A          119 DFSKLTS  125 (164)
T ss_dssp             EECSSSS
T ss_pred             EEecCCc
Confidence            9998864

>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=99.71  E-value=5.6e-17  Score=122.61  Aligned_cols=87  Identities=17%  Similarity=0.309  Sum_probs=78.3

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+++|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.. ++..|.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v   86 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   86 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeee
Confidence            3445678999999999999999999999999999999999988999999999999999999999975 899999999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .++.+...
T Consensus        87 ~~~~~~~~   94 (196)
T 1l3k_A           87 KRAVSRED   94 (196)
T ss_dssp             EECCC---
T ss_pred             ecccCccc
Confidence            99876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.70  E-value=1.7e-16  Score=112.23  Aligned_cols=77  Identities=23%  Similarity=0.337  Sum_probs=68.5

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceE-EEEEecCHHHHHHHHHHhCCceeCC--cEeEEEE
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY-ALIEYENFEEAQNAITAMNGGELLT--QTLTVDW  165 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~-afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~~  165 (196)
                      ...|||+||++.+++++|..+|++||.|..|.|.. +     .|| |||+|.+.++|..|++.|||..|.|  +.|+|.|
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            34578999999999999999999999999998864 2     376 9999999999999999999999987  6999999


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      |+++.-
T Consensus        99 Ak~~~l  104 (124)
T 2e5i_A           99 ARPTRL  104 (124)
T ss_dssp             CSCSCC
T ss_pred             ecCCcc
Confidence            987753

>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=99.70  E-value=9.6e-17  Score=107.26  Aligned_cols=77  Identities=18%  Similarity=0.365  Sum_probs=62.8

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce--eCCcEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE--LLTQTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~--l~g~~l~v  163 (196)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|.|+.+     ++|||||+|.+.++|++    +++..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            446789999999999999999999999999999999864     58999999999999984    45554  56999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .+|.++..
T Consensus        79 ~~a~~k~~   86 (89)
T 3d2w_A           79 SNAEPKHN   86 (89)
T ss_dssp             EECC----
T ss_pred             EEcCCCCc
Confidence            99987653

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

Probab=99.69  E-value=1.4e-16  Score=116.95  Aligned_cols=81  Identities=25%  Similarity=0.496  Sum_probs=75.0

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ++|||+|||+.+|+++|+++|++||.|..|.++.++ +++++|||||+|.+.++|..|+..|++..+.|+.|.|.|+.+.
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 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999885 6778999999999999999999999999999999999999766


Q ss_pred             CC
Q 043064          170 GP  171 (196)
Q Consensus       170 ~~  171 (196)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.69  E-value=1e-16  Score=123.13  Aligned_cols=77  Identities=22%  Similarity=0.342  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCC-ccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           88 EGWIILVTGVH-EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp-~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ++++|||+||| +.+++++|+.+|++||.|.+|.|+.++     +|||||+|.+.++|+.||+.|||..|.|+.|+|.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46899999999 799999999999999999999998653     799999999999999999999999999999999999


Q ss_pred             ccC
Q 043064          167 FSN  169 (196)
Q Consensus       167 ~~~  169 (196)
                      +..
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=5.6e-17  Score=113.21  Aligned_cols=79  Identities=19%  Similarity=0.211  Sum_probs=67.6

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCC---CCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRT---GFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~---g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ....++|||+|||+.+++++|+++|++||.|. +.++.+..+   |+++|||||+|.+.++|++||+.|+  .++|+.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~   81 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYL   81 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEE
Confidence            34568899999999999999999999999999 888877666   7999999999999999999999883  36677666


Q ss_pred             EEEcc
Q 043064          163 VDWAF  167 (196)
Q Consensus       163 v~~a~  167 (196)
                      +..+.
T Consensus        82 ~~~~~   86 (114)
T 2dnl_A           82 CVSSP   86 (114)
T ss_dssp             EECCS
T ss_pred             eccCC
Confidence            65443

>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=99.69  E-value=4.6e-17  Score=108.33  Aligned_cols=79  Identities=15%  Similarity=0.254  Sum_probs=67.0

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||+.+++++|+.+|++||.|..|.|+.+     ++|||||+|.+.++|++++.  ....+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEec
Confidence            45689999999999999999999999999999998764     48999999999999986532  134568999999999


Q ss_pred             ccCCCC
Q 043064          167 FSNGPS  172 (196)
Q Consensus       167 ~~~~~~  172 (196)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876643

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

Probab=99.68  E-value=1.6e-16  Score=121.86  Aligned_cols=83  Identities=29%  Similarity=0.354  Sum_probs=74.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||+++|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|++..|.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            35789999999999999999999999999999999988899999999999999999999999999999999999998876


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      ...
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=5.3e-16  Score=106.83  Aligned_cols=83  Identities=14%  Similarity=0.136  Sum_probs=73.2

Q ss_pred             CCCCCEEEEcCCCc-----cCcHHHHHHhhccCCCeeEEEEeecCCC-CCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           86 SIEGWIILVTGVHE-----EAQEDDLQNVFGEYGEIRNLHLNLDRRT-GFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        86 ~~~~~~l~V~nLp~-----~~te~~L~~~F~~~G~i~~v~i~~~~~~-g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      ..++++|+|.||..     +-++++|+++|++||.|.+|.|+.++.+ +.++||+||+|.+.++|.+|+..|||..+.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34678999999963     2368999999999999999999987644 67899999999999999999999999999999


Q ss_pred             EeEEEEccc
Q 043064          160 TLTVDWAFS  168 (196)
Q Consensus       160 ~l~v~~a~~  168 (196)
                      .|.|.|+.+
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999965

>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=99.67  E-value=1.8e-16  Score=104.99  Aligned_cols=72  Identities=21%  Similarity=0.382  Sum_probs=66.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEY----G-------EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  155 (196)
                      .+.++|||+|||+.+++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|++|+ .||+..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            356889999999999999999999999    8       8999988755      799999999999999999 999999


Q ss_pred             eCCcEeEEEE
Q 043064          156 LLTQTLTVDW  165 (196)
Q Consensus       156 l~g~~l~v~~  165 (196)
                      |.|+.|+|..
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999974

>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=99.65  E-value=6.5e-16  Score=114.47  Aligned_cols=84  Identities=21%  Similarity=0.323  Sum_probs=75.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCceeC---CcEeE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTG--FVKGYALIEYENFEEAQNAITAMNGGELL---TQTLT  162 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~~l~---g~~l~  162 (196)
                      +.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++  .++|||||+|.+.++|++|++.|++..+.   ++.+.
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            46789999999999999999999999999999999998776  89999999999999999999999998865   67888


Q ss_pred             EEEcccCCC
Q 043064          163 VDWAFSNGP  171 (196)
Q Consensus       163 v~~a~~~~~  171 (196)
                      +.++.+...
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            888876543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.65  E-value=3.9e-16  Score=122.09  Aligned_cols=81  Identities=21%  Similarity=0.313  Sum_probs=71.3

Q ss_pred             CCCCCEEEEcCCCccC---------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 043064           86 SIEGWIILVTGVHEEA---------QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL  156 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~---------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l  156 (196)
                      ....++|||+||+..+         ++++|+.+|++||.|..|.|+.+      +|||||+|.+.++|+.|++.|++..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4567899999999998         79999999999999999999854      79999999999999999999999999


Q ss_pred             ------------CCcEeEEEEcccCCCC
Q 043064          157 ------------LTQTLTVDWAFSNGPS  172 (196)
Q Consensus       157 ------------~g~~l~v~~a~~~~~~  172 (196)
                                  .|+.|.|.||...+..
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             eccccccccccCCCCEEEEEEccCCCCH
Confidence                        8999999999876643

>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=99.65  E-value=3.2e-16  Score=115.46  Aligned_cols=80  Identities=21%  Similarity=0.452  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.++|||+|||+.+|+++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|..|+.  ++..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            46789999999999999999999999999999999998899999999999999999999998  4678999999999886


Q ss_pred             cC
Q 043064          168 SN  169 (196)
Q Consensus       168 ~~  169 (196)
                      +.
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            53

>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=99.65  E-value=1e-15  Score=122.33  Aligned_cols=83  Identities=18%  Similarity=0.445  Sum_probs=76.0

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHH----HhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQ----NVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~----~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      ...+.++|||+|||+.+++++|+    .+|++||.|..|.++.   +++++|||||+|.+.++|.+||..||+..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            44568899999999999999976    8999999999998874   7788999999999999999999999999999999


Q ss_pred             eEEEEcccCC
Q 043064          161 LTVDWAFSNG  170 (196)
Q Consensus       161 l~v~~a~~~~  170 (196)
                      |+|.|+.+..
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997655

>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=99.63  E-value=1.6e-15  Score=115.44  Aligned_cols=79  Identities=15%  Similarity=0.291  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+.+|+++|+.+|++||.|..|.|+.+. ++.++|||||+|.+.++|++|+..+ +..|+|+.|.|.|+..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            5789999999999999999999999999999999885 6889999999999999999999765 5699999999998764


Q ss_pred             C
Q 043064          169 N  169 (196)
Q Consensus       169 ~  169 (196)
                      -
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.62  E-value=9.7e-15  Score=101.48  Aligned_cols=83  Identities=22%  Similarity=0.341  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEcCCCccC-----------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 043064           85 RSIEGWIILVTGVHEEA-----------QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG  153 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~-----------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~  153 (196)
                      ...++++|+|.||....           ++++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            44568899999994433           25899999999999999965 443   2689999999999999999999999


Q ss_pred             ceeCCcEeEEEEcccCCC
Q 043064          154 GELLTQTLTVDWAFSNGP  171 (196)
Q Consensus       154 ~~l~g~~l~v~~a~~~~~  171 (196)
                      ..|.|+.|+|.|+.++..
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999987654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.62  E-value=1.3e-15  Score=118.52  Aligned_cols=81  Identities=20%  Similarity=0.397  Sum_probs=74.7

Q ss_pred             CCCCCCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           85 RSIEGWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ...+.++|||+|||+ .+++++|+++|++||.|..|.|+.++     +|||||+|.+.++|++|+..|++..|.|+.|.|
T Consensus        30 ~~~~~~~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           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345678999999999 99999999999999999999998775     789999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .|+.+..
T Consensus       105 ~~a~~~~  111 (229)
T 2adc_A          105 TLSKHQN  111 (229)
T ss_dssp             ECCSCCC
T ss_pred             EEecCcc
Confidence            9998653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.60  E-value=1.5e-15  Score=115.17  Aligned_cols=78  Identities=21%  Similarity=0.416  Sum_probs=72.8

Q ss_pred             CCCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           88 EGWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+++|||+|||+ .+++++|+++|++||.|..|.++.++     +|||||+|.+.++|.+|+..||+..|.|+.|.|.|+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            468899999999 99999999999999999999998765     789999999999999999999999999999999999


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      .+..
T Consensus        77 ~~~~   80 (198)
T 1qm9_A           77 KHQN   80 (198)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8653

>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=99.59  E-value=6.7e-15  Score=116.71  Aligned_cols=80  Identities=23%  Similarity=0.420  Sum_probs=72.9

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      .....+.++|||+|||+++|+++|+.+|+.||.|..|.|..+      +|||||+|.+.++|..|+..|++..|.|+.|.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            334456789999999999999999999999999999998654      78999999999999999999999999999999


Q ss_pred             EEEccc
Q 043064          163 VDWAFS  168 (196)
Q Consensus       163 v~~a~~  168 (196)
                      |.|+.+
T Consensus        90 v~~a~~   95 (261)
T 3sde_A           90 IRFATH   95 (261)
T ss_dssp             EEECCC
T ss_pred             eeeccc
Confidence            999865

>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=99.57  E-value=8.5e-16  Score=114.23  Aligned_cols=85  Identities=14%  Similarity=0.297  Sum_probs=73.1

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+.+++++|+++|..||.+..+ ++.+..++.++|||||+|.+.++|.+|+ .||+..|.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEe
Confidence            44567899999999999999999999999887662 3334457888999999999999999999 599999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      ++.++..
T Consensus        87 ~~~~~~~   93 (175)
T 1fje_B           87 KPKGRDS   93 (175)
T ss_dssp             CCCCSSC
T ss_pred             cCCCccc
Confidence            9976543

>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=99.57  E-value=1.2e-14  Score=100.07  Aligned_cols=83  Identities=12%  Similarity=0.247  Sum_probs=71.4

Q ss_pred             CCCCEEEEcCC--CccCc--------HHHHHHhhccCCCeeEEEEeecCCC--CCcceEEEEEecCHHHHHHHHHHhCCc
Q 043064           87 IEGWIILVTGV--HEEAQ--------EDDLQNVFGEYGEIRNLHLNLDRRT--GFVKGYALIEYENFEEAQNAITAMNGG  154 (196)
Q Consensus        87 ~~~~~l~V~nL--p~~~t--------e~~L~~~F~~~G~i~~v~i~~~~~~--g~~~g~afv~f~~~~~a~~al~~l~~~  154 (196)
                      .+++.|.|.|+  |..+.        +++|++.|++||.|.+|.|+.++.+  +.++|++||+|.+.++|.+|+..|||.
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            35788999998  43443        4799999999999999999887644  367899999999999999999999999


Q ss_pred             eeCCcEeEEEEcccC
Q 043064          155 ELLTQTLTVDWAFSN  169 (196)
Q Consensus       155 ~l~g~~l~v~~a~~~  169 (196)
                      .++|+.|+|.|+...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998543

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

Probab=99.53  E-value=1e-13  Score=104.71  Aligned_cols=77  Identities=19%  Similarity=0.356  Sum_probs=67.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEY----G-------EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL  156 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l  156 (196)
                      ..++|||+|||+.+++++|+++|++|    |       .|..+.+.      ..+|||||+|.+.++|++|+ .||+..|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46789999999999999999999999    5       56666553      34899999999999999999 8999999


Q ss_pred             CCcEeEEEEcccCCC
Q 043064          157 LTQTLTVDWAFSNGP  171 (196)
Q Consensus       157 ~g~~l~v~~a~~~~~  171 (196)
                      .|+.|.|.++.+...
T Consensus        76 ~g~~i~v~~~~~~~~   90 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQP   90 (198)
T ss_dssp             TTEEEEEECCCCCCC
T ss_pred             cCceEEEeCCCCCCC
Confidence            999999999877643

>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=99.53  E-value=8e-15  Score=100.70  Aligned_cols=72  Identities=15%  Similarity=0.366  Sum_probs=64.1

Q ss_pred             EcCCCccCcHHHHHHhh------------ccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           94 VTGVHEEAQEDDLQNVF------------GEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        94 V~nLp~~~te~~L~~~F------------~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      +.||++.+++++|++.|            ++||.|.+|.|+.+. ++.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777778887777666            999999999999875 57889999999999999999999999999999999


Q ss_pred             EEEEc
Q 043064          162 TVDWA  166 (196)
Q Consensus       162 ~v~~a  166 (196)
                      +|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99987

>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=99.53  E-value=3.1e-14  Score=105.21  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=67.6

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccC----C-------CeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEY----G-------EIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL  156 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~----G-------~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l  156 (196)
                      +.++|||+|||+.+|+++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|.+|+ .||+..|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~------~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT------TTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC------CCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            45789999999999999999999999    6       6777766543      799999999999999999 8999999


Q ss_pred             CCcEeEEEEcccCC
Q 043064          157 LTQTLTVDWAFSNG  170 (196)
Q Consensus       157 ~g~~l~v~~a~~~~  170 (196)
                      .|+.|.|.++.+..
T Consensus        76 ~g~~i~v~~~~~~~   89 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQ   89 (172)
T ss_dssp             TTEECEEECCSSCC
T ss_pred             cCceeeecCCcccC
Confidence            99999999986554

>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=99.52  E-value=7e-14  Score=98.07  Aligned_cols=81  Identities=14%  Similarity=0.284  Sum_probs=70.8

Q ss_pred             CCCEEEEcCCCc--cC---cHHHHHHhhccCCCeeEEEEeecCC----CCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 043064           88 EGWIILVTGVHE--EA---QEDDLQNVFGEYGEIRNLHLNLDRR----TGFVKGYALIEYENFEEAQNAITAMNGGELLT  158 (196)
Q Consensus        88 ~~~~l~V~nLp~--~~---te~~L~~~F~~~G~i~~v~i~~~~~----~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g  158 (196)
                      ++++|+|.|+-.  .+   .+++|++.|++||.|.+|.|+.++.    ++..+|++||+|.+.++|.+|+..|||..++|
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            578899999832  22   3689999999999999999998754    35678999999999999999999999999999


Q ss_pred             cEeEEEEccc
Q 043064          159 QTLTVDWAFS  168 (196)
Q Consensus       159 ~~l~v~~a~~  168 (196)
                      +.|+|.|+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999854

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=3.4e-13  Score=91.82  Aligned_cols=76  Identities=22%  Similarity=0.316  Sum_probs=63.5

Q ss_pred             CCEEEEcCCC-------ccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           89 GWIILVTGVH-------EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        89 ~~~l~V~nLp-------~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      .++|-|....       ..+++++|+++|++||.|..|.|+     ++++|||||+|.+.++|+.|+..+++  +.|++|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            4556666544       468999999999999999999987     35689999999999999999987544  679999


Q ss_pred             EEEEcccCCC
Q 043064          162 TVDWAFSNGP  171 (196)
Q Consensus       162 ~v~~a~~~~~  171 (196)
                      +|.|+.+++.
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999987764

>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=99.43  E-value=3.3e-13  Score=110.71  Aligned_cols=77  Identities=23%  Similarity=0.348  Sum_probs=66.4

Q ss_pred             CCCCCCEEEEcC--CCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeC---Cc
Q 043064           85 RSIEGWIILVTG--VHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQ  159 (196)
Q Consensus        85 ~~~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~---g~  159 (196)
                      .+.++.+|||+|  |+..+|+++|+++|++||.|..|.+..      .+|||||+|.+.++|++|++.|||..+.   |+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            356788999999  578899999999999999999987753      3799999999999999999999999873   44


Q ss_pred             --EeEEEEcc
Q 043064          160 --TLTVDWAF  167 (196)
Q Consensus       160 --~l~v~~a~  167 (196)
                        .|.|.|+.
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence              68888874

>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=99.37  E-value=3.4e-12  Score=88.86  Aligned_cols=79  Identities=11%  Similarity=0.219  Sum_probs=66.4

Q ss_pred             CCCCCEEEEcCCCccC----------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCce
Q 043064           86 SIEGWIILVTGVHEEA----------QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~----------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  155 (196)
                      ..+++.|.|.|+=..-          .+++|++.|++||.|.+|.|..+.    .+|++||+|.+.++|.+|+..|||..
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3467789999883211          236889999999999999886542    48999999999999999999999999


Q ss_pred             eCCcEeEEEEccc
Q 043064          156 LLTQTLTVDWAFS  168 (196)
Q Consensus       156 l~g~~l~v~~a~~  168 (196)
                      ++|+.|+|.|+..
T Consensus        80 f~GR~i~v~~~~~   92 (114)
T 3s6e_A           80 FAGKMITAAYVPL   92 (114)
T ss_dssp             ETTEECEEEEECH
T ss_pred             ECCEEEEEEEEcH
Confidence            9999999999854

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.26  E-value=2.5e-11  Score=80.19  Aligned_cols=76  Identities=28%  Similarity=0.454  Sum_probs=64.3

Q ss_pred             CCCEEEEcCCCc----cCcH----HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           88 EGWIILVTGVHE----EAQE----DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        88 ~~~~l~V~nLp~----~~te----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      +..+|+|.-++.    ++..    .+|...|++||.|..++++.++        +||+|.+.++|.+||. |||..++|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            345788877662    2323    6789999999999999998763        8999999999999998 999999999


Q ss_pred             EeEEEEcccCCCC
Q 043064          160 TLTVDWAFSNGPS  172 (196)
Q Consensus       160 ~l~v~~a~~~~~~  172 (196)
                      .|+|.++.|.+..
T Consensus        77 ~LkV~lkt~dW~~   89 (91)
T 2dnr_A           77 TITIALKSPSGPS   89 (91)
T ss_dssp             EEEEEECCCSSCS
T ss_pred             EEEEEeCCCCccc
Confidence            9999999988764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.23  E-value=7.7e-11  Score=82.47  Aligned_cols=79  Identities=19%  Similarity=0.273  Sum_probs=68.2

Q ss_pred             CCCCCCCCCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecC-HHHHHHHHHHhC--CceeC
Q 043064           82 GPQRSIEGWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN-FEEAQNAITAMN--GGELL  157 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~-~~~a~~al~~l~--~~~l~  157 (196)
                      +...-.+++.|||+||+.. ++.++|+++|++||.|..|.+..+.      ..|||.|.+ ..+|..|+..|+  +..|.
T Consensus        11 ~~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~------~tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           11 GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             CCCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC------SEEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             CcccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC------CEEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            3445667899999999999 9999999999999999999998764      259999999 899999999985  67799


Q ss_pred             CcEeEEEEc
Q 043064          158 TQTLTVDWA  166 (196)
Q Consensus       158 g~~l~v~~a  166 (196)
                      |..+++...
T Consensus        85 g~~~~~evL   93 (121)
T 1owx_A           85 NKEVTWEVL   93 (121)
T ss_dssp             SSSEEEEEC
T ss_pred             CcEEEEEEC
Confidence            988888643

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.98  E-value=7.4e-10  Score=73.49  Aligned_cols=72  Identities=15%  Similarity=0.259  Sum_probs=60.6

Q ss_pred             CCCEEEEcCCCcc-----CcH----HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC
Q 043064           88 EGWIILVTGVHEE-----AQE----DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT  158 (196)
Q Consensus        88 ~~~~l~V~nLp~~-----~te----~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g  158 (196)
                      +..+|+|.-++..     +..    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+||. |+|..++|
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            4567999887632     222    5689999999999999999773        9999999999999998 99999999


Q ss_pred             cEeEEEEccc
Q 043064          159 QTLTVDWAFS  168 (196)
Q Consensus       159 ~~l~v~~a~~  168 (196)
                      +.|+|.+..+
T Consensus        85 r~L~V~~k~~   94 (95)
T 1ufw_A           85 RAVKISGPSS   94 (95)
T ss_dssp             EEEEEECCCC
T ss_pred             eEEEEeccCC
Confidence            9999997643

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.96  E-value=2.6e-09  Score=82.35  Aligned_cols=80  Identities=13%  Similarity=0.270  Sum_probs=65.7

Q ss_pred             CCEEEEcCCCc-----cCcHHHHHHhhccCCCeeEEEEeecC----CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCc
Q 043064           89 GWIILVTGVHE-----EAQEDDLQNVFGEYGEIRNLHLNLDR----RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQ  159 (196)
Q Consensus        89 ~~~l~V~nLp~-----~~te~~L~~~F~~~G~i~~v~i~~~~----~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~  159 (196)
                      ...+.+.|+-.     .-.+++|...|++||.|.++.|+.+.    .++..+|++||+|.+.++|.+|+..|||..++|+
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            34455555422     33568999999999999999998554    3458899999999999999999999999999999


Q ss_pred             EeEEEEccc
Q 043064          160 TLTVDWAFS  168 (196)
Q Consensus       160 ~l~v~~a~~  168 (196)
                      .|.|.|...
T Consensus       204 ~i~~~~~~~  212 (222)
T 3dxb_A          204 KVVAEVYDQ  212 (222)
T ss_dssp             BCEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.65  E-value=1.4e-07  Score=63.91  Aligned_cols=71  Identities=15%  Similarity=0.193  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccC-----CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEY-----GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~-----G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      ..++|-|-|||..++...|+.++..+     |.|..+.+..+      .+-|+|+|.+...|-+|.-.|+|..|.|++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD------H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD------FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT------TTEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC------CCceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35779999999999999999999999     99999999877      45699999999999999999999999999999


Q ss_pred             EE
Q 043064          163 VD  164 (196)
Q Consensus       163 v~  164 (196)
                      +.
T Consensus        94 ~g   95 (117)
T 2l9w_A           94 SG   95 (117)
T ss_dssp             EE
T ss_pred             ec
Confidence            86

>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=98.19  E-value=5.2e-06  Score=55.87  Aligned_cols=76  Identities=12%  Similarity=0.153  Sum_probs=63.2

Q ss_pred             CCEEEEcCCCccC-c----HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           89 GWIILVTGVHEEA-Q----EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        89 ~~~l~V~nLp~~~-t----e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      .++|+|.||+..+ .    ...++.+|..|+++....+...-      .-..|.|.+.++|.+|-..||+..+.|+.|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3569999998865 2    25789999999998887766542      23689999999999999999999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      -|+.+..
T Consensus        79 YFgq~~~   85 (104)
T 1wey_A           79 YFAQTLH   85 (104)
T ss_dssp             ECCCCSS
T ss_pred             EecCCCC
Confidence            9998543

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.83  E-value=0.00038  Score=46.63  Aligned_cols=76  Identities=16%  Similarity=0.146  Sum_probs=60.5

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhcc-----CCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGE-----YGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~-----~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      +.-..+|.|.|||+.+.++.|.-+|..     -|+|..+....        +-|+|+|.+...|++.|+. ..+.|.+..
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~   75 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQ   75 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSB
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeE
Confidence            344678999999999999999999976     36788876642        3589999999999999853 478899999


Q ss_pred             eEEEEcccCC
Q 043064          161 LTVDWAFSNG  170 (196)
Q Consensus       161 l~v~~a~~~~  170 (196)
                      |.|.-..++.
T Consensus        76 LsV~P~~~~~   85 (104)
T 2dhx_A           76 LSLRPAPPRA   85 (104)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEcCCCCC
Confidence            9996544443

>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=97.77  E-value=0.00022  Score=46.99  Aligned_cols=77  Identities=14%  Similarity=0.151  Sum_probs=59.2

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCceeCC-----cEeE
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTG--FVKGYALIEYENFEEAQNAITAMNGGELLT-----QTLT  162 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~~l~g-----~~l~  162 (196)
                      ++|.|++||+.+|++++.+.++.+..+....++....+.  ...+-|||.|.+.+++..-...++|+.+..     .+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            478999999999999999999998776655555443332  234569999999999999999999998632     2345


Q ss_pred             EEEc
Q 043064          163 VDWA  166 (196)
Q Consensus       163 v~~a  166 (196)
                      |++|
T Consensus        82 VE~A   85 (91)
T 1uw4_A           82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6666

>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=97.42  E-value=0.00065  Score=44.99  Aligned_cols=56  Identities=21%  Similarity=0.335  Sum_probs=46.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN  152 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  152 (196)
                      ..+.++| +.|+.+...+|..+|+.||.| .|.|+-+-       .|||.|.+++.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3566777 999999999999999999954 56666552       69999999999999998663

>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=97.32  E-value=0.0016  Score=44.90  Aligned_cols=72  Identities=17%  Similarity=0.255  Sum_probs=56.5

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC-cEeEEEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT-QTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g-~~l~v~~  165 (196)
                      ...+.|.|-+.|+.. -..+...|++||.|.+....    .+  ..+.+|.|.+..+|++||. .||..|+| ..|-|..
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKP   93 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEE
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEE
Confidence            346778999999985 56677899999999987652    12  3589999999999999995 59999975 5666655


Q ss_pred             c
Q 043064          166 A  166 (196)
Q Consensus       166 a  166 (196)
                      -
T Consensus        94 ~   94 (119)
T 1wwh_A           94 C   94 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=97.26  E-value=0.00058  Score=45.36  Aligned_cols=54  Identities=19%  Similarity=0.275  Sum_probs=45.5

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN  152 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  152 (196)
                      +.++| +.|+.+...+|..+|+.|| -..|.|+-+-       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999998 4467776552       69999999999999998764

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

Probab=97.04  E-value=8.4e-05  Score=50.97  Aligned_cols=56  Identities=14%  Similarity=0.086  Sum_probs=18.0

Q ss_pred             CCcCcccccCCCcHHHHHHhhhhcccCCCCCCC---------------CCCCCCCCCEEEEcCCCccCcHHH
Q 043064           49 KTKGRGFREEADSERHSRLADRNFESLGTDGGP---------------GPQRSIEGWIILVTGVHEEAQEDD  105 (196)
Q Consensus        49 ~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~l~V~nLp~~~te~~  105 (196)
                      +++|||||.|.+.+. +..+...++.....+..               ........++|||+|||+.+|++.
T Consensus        43 ~~kg~afV~f~~~~~-A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           43 GSKGYGFVHFETQEA-AERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             EEEEEEEEEESCHHH-HHHHHHHHTTCEETTEECEEEESSCCCC----------------------------
T ss_pred             CCCceEEEEECCHHH-HHHHHHHcCCCEECCEEEEEEECCCccccccccccccCCCCceEeCCCCCCccccc
Confidence            478999999995444 44344444443332211               011223356799999999998764

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

Probab=96.98  E-value=0.0023  Score=42.43  Aligned_cols=78  Identities=10%  Similarity=0.135  Sum_probs=53.8

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCceeCC-----cEe
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTG--FVKGYALIEYENFEEAQNAITAMNGGELLT-----QTL  161 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~~l~g-----~~l  161 (196)
                      +-+|.|+.||+.+|++++.+.++.+-.+....++....+.  ..-.-|||.|.+.++...-.+.++|+.+..     .+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            4569999999999999998888775443222222211111  122458999999999999999999998632     245


Q ss_pred             EEEEc
Q 043064          162 TVDWA  166 (196)
Q Consensus       162 ~v~~a  166 (196)
                      .|+||
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            56666

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.19  E-value=0.013  Score=40.91  Aligned_cols=75  Identities=24%  Similarity=0.210  Sum_probs=53.4

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeE-EEEeec------------CCCC-CcceEEEEEecCHHHHHHHHHHhCCce
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRN-LHLNLD------------RRTG-FVKGYALIEYENFEEAQNAITAMNGGE  155 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~-v~i~~~------------~~~g-~~~g~afv~f~~~~~a~~al~~l~~~~  155 (196)
                      ..|.|-+.|+..+ ..+...|++||.|.+ +.+...            +-.. ....+..|.|.+..+|.+||. .||..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            4577888988755 556778999999866 211110            0000 124588999999999999995 69999


Q ss_pred             eCCcEeEEEEc
Q 043064          156 LLTQTLTVDWA  166 (196)
Q Consensus       156 l~g~~l~v~~a  166 (196)
                      |+|..|-|...
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99988777654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.02  E-value=0.0035  Score=53.10  Aligned_cols=55  Identities=18%  Similarity=0.279  Sum_probs=41.2

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT  149 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~  149 (196)
                      .+.|+|. .|..+++.+|.++|++||+|.++.+..+.     .-|+.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            4679997 79999999999999999999998776543     3699999999988887753

>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=95.31  E-value=0.007  Score=43.02  Aligned_cols=42  Identities=19%  Similarity=0.076  Sum_probs=37.7

Q ss_pred             CCCcceEEEEEecCHHHHHHHHHHh-CCceeCCcEeEEEEcccC
Q 043064          127 TGFVKGYALIEYENFEEAQNAITAM-NGGELLTQTLTVDWAFSN  169 (196)
Q Consensus       127 ~g~~~g~afv~f~~~~~a~~al~~l-~~~~l~g~~l~v~~a~~~  169 (196)
                      ..+.+|+++|+|.+.+.|++|++.+ |+..|+| .|.+.++.++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            4467899999999999999999999 9999999 9999988654

>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=95.22  E-value=0.025  Score=40.29  Aligned_cols=34  Identities=18%  Similarity=0.164  Sum_probs=27.4

Q ss_pred             EEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc
Q 043064          119 LHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG  154 (196)
Q Consensus       119 v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~  154 (196)
                      +.|..+.  .+.+||+||+|.+.++|++|+..+++.
T Consensus         3 ~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            3 YKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             EEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            4555553  367999999999999999999887754

>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=94.02  E-value=0.0048  Score=41.74  Aligned_cols=65  Identities=12%  Similarity=0.101  Sum_probs=38.5

Q ss_pred             CCcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCC
Q 043064           49 KTKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGE  115 (196)
Q Consensus        49 ~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~  115 (196)
                      .++|+|||.|.+ ..++..+...+++....+......-.... --..+++...++++|..+|++||.
T Consensus        45 ~~~g~afV~f~~-~~~A~~A~~~l~g~~~~g~~l~v~~a~~~-~~~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           45 ETRGTAYVVYED-IFDAKNAVDHLSGFNVSNRYLVVLYYNAN-RAFQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             TTTTCEEEEESS-HHHHHHHHHHHTTCBSSSCBCEEEECCHH-HHTTTSCHHHHHHHHHHHHHHHCC
T ss_pred             CCCcEEEEEECC-HHHHHHHHHHcCCCEECCeEEEEEEecCC-hhhhhhhHhHhHHHHHHHHHHhCC
Confidence            468999999994 44444454556655443322110000000 001567788899999999999974

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

Probab=93.44  E-value=0.053  Score=35.46  Aligned_cols=48  Identities=19%  Similarity=0.123  Sum_probs=27.1

Q ss_pred             CcCcccccCCCcHHHHHHhhhhcccCCCCCCC-----------------CCCCCCCCCEEEEcCCC
Q 043064           50 TKGRGFREEADSERHSRLADRNFESLGTDGGP-----------------GPQRSIEGWIILVTGVH   98 (196)
Q Consensus        50 ~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~l~V~nLp   98 (196)
                      ++|||||.|.+.+.+ ..+...++.....+..                 .+.......+|||+||+
T Consensus        36 ~~g~afV~f~~~~~a-~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDA-EDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SSSEEEEECSSHHHH-HHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCCEEEEEECCHHHH-HHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCccccCCCceecCCCC
Confidence            689999999954444 3333334433222211                 11122236789999986

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=91.74  E-value=0.16  Score=32.97  Aligned_cols=47  Identities=11%  Similarity=0.224  Sum_probs=32.2

Q ss_pred             CcCcccccCCCcHHHHHHhhhhcccCCCCCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhc
Q 043064           50 TKGRGFREEADSERHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFG  111 (196)
Q Consensus        50 ~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~  111 (196)
                      +||||||+|. +...+.++...++...          ..+++|.|.    ..++.++..+|.
T Consensus        42 ~kGfaFVey~-~~~eA~~Ai~~Ln~~~----------l~gr~I~V~----~A~e~~~~~~~~   88 (89)
T 2wbr_A           42 NQGIALCKYT-TREEANKAQMALNNCV----------LANTTIFAE----SPSENEVQSIMQ   88 (89)
T ss_dssp             TTTEEEEEES-SHHHHHHHHHHHTTEE----------ETTEEEEEE----CCCHHHHHHHHC
T ss_pred             CCcEEEEEEC-CHHHHHHHHHHhcCCE----------ECCcEEEEE----ECCHHHHHHHhh
Confidence            7999999999 5556666666666533          345667774    237788887775

>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=90.25  E-value=0.93  Score=38.79  Aligned_cols=56  Identities=21%  Similarity=0.287  Sum_probs=45.2

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCC
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG  153 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~  153 (196)
                      .+.++|+ +|..+...+|.++|+.||. ..|.++-+       ..|||.|.+.+.|..++..+..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            4667776 8888999999999999995 45666543       3599999999999999988753

>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=90.00  E-value=0.27  Score=31.24  Aligned_cols=44  Identities=14%  Similarity=0.033  Sum_probs=27.1

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCC
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDG   79 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~   79 (196)
                      .+..+..+++.    .+++++|||||.|.+ ..++..+...+++....+
T Consensus        29 ~v~~v~i~~~~----~~g~~kG~afV~f~~-~~~a~~Ai~~l~g~~~~g   72 (90)
T 3p5t_L           29 DILEIKFFENR----ANGQSKGFALVGVGS-EASSKKLMDLLPKRELHG   72 (90)
T ss_dssp             CCCCEEEEECT----TTCCEEEEEEECC-C-HHHHHHHHHHGGGSCSSS
T ss_pred             ceEEEEEEecC----CCCccCcEEEEEECC-HHHHHHHHHHcCCCeeCC
Confidence            34556666665    355889999999994 444444555666654443

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

Probab=87.92  E-value=0.22  Score=32.50  Aligned_cols=37  Identities=14%  Similarity=0.152  Sum_probs=24.0

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhccc
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFES   74 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~   74 (196)
                      ..+..+++.    .++++||||||.|.+.+.+.+ +...++.
T Consensus        39 ~~v~i~~d~----~tg~srG~aFV~f~~~~~A~~-Ai~~lng   75 (95)
T 2lkz_A           39 NNIRLIKDK----QTQQNRGFAFVQLSSAMDASQ-LLQILQS   75 (95)
T ss_dssp             GGEECCCCS----SSSSCSSEEEEECSSSHHHHH-HHHHHHS
T ss_pred             EEEEEEecC----CCCCCceEeEEEECCHHHHHH-HHHHhcC
Confidence            355666665    456899999999996555444 3344443

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

Probab=87.81  E-value=0.29  Score=31.40  Aligned_cols=31  Identities=13%  Similarity=0.224  Sum_probs=21.6

Q ss_pred             CCCcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           32 RAPQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        32 ~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      +..+..+++.    .+++++|||||.|.+.+.+.+
T Consensus        29 v~~v~i~~d~----~t~~~rg~aFV~F~~~~~A~~   59 (91)
T 2lxi_A           29 AREVRLMRNK----SSGQSRGFAFVEFSHLQDATR   59 (91)
T ss_dssp             CSBCCSSSCS----SSCCCSSEEEEECSSHHHHHH
T ss_pred             eEEEEEEecC----CCCCcCceEEEEecCHHHHHH
Confidence            4456666665    456899999999995555444

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=86.21  E-value=0.24  Score=32.35  Aligned_cols=40  Identities=20%  Similarity=0.073  Sum_probs=24.7

Q ss_pred             CCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCC
Q 043064           32 RAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLG   76 (196)
Q Consensus        32 ~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~   76 (196)
                      +..+..+++.    .+++++|||||.|.+ ...+..+...+++..
T Consensus        39 i~~v~i~~d~----~tg~~kG~afV~f~~-~~~A~~Ai~~lng~~   78 (100)
T 3ns6_A           39 VVNMEFPIDE----ATGKTKGFLFVECGS-MNDAKKIIKSFHGKR   78 (100)
T ss_dssp             EEEEECCEET----TTTEECSEEEEEESS-HHHHHHHHHHHTTCB
T ss_pred             EeEEEEEEcC----CCCccceEEEEEECC-HHHHHHHHHHhCCcc
Confidence            3445555554    446899999999994 444444444555543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=85.35  E-value=0.63  Score=28.76  Aligned_cols=32  Identities=34%  Similarity=0.252  Sum_probs=21.2

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCC
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDG   79 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~   79 (196)
                      +++++||||+.|.+ ..++..+...+++....+
T Consensus        43 ~g~~~g~afV~f~~-~~~A~~Ai~~lng~~~~g   74 (81)
T 2krb_A           43 DGKTKGYIFLEYAS-PAHAVDAVKNADGYKLDK   74 (81)
T ss_dssp             TTBCCCEEEEEESS-HHHHHHHHTTSSSCCCSS
T ss_pred             CCcEeEEEEEEECC-HHHHHHHHHHhcCcccCC
Confidence            45789999999994 444554555566554443

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

Probab=83.90  E-value=0.26  Score=32.91  Aligned_cols=41  Identities=12%  Similarity=0.001  Sum_probs=26.0

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      +++..+..+++.    .+++++|||||.|.+ ..++..+...++..
T Consensus        31 G~i~~v~i~~d~----~tg~~rG~aFV~f~~-~~~A~~Ai~~lng~   71 (110)
T 3s8s_A           31 GEVEEVEILLHP----RTRKHLGLARVLFTS-TRGAKETVKNLHLT   71 (110)
T ss_dssp             SCEEEEEEEECT----TTCCEEEEEEEEESS-HHHHHHHHHHHTTC
T ss_pred             CCeeEEEEEECC----CCCceeeEEEEEECC-HHHHHHHHHHhCCC
Confidence            444455555555    456899999999995 44444454555554

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=83.48  E-value=0.88  Score=31.07  Aligned_cols=35  Identities=11%  Similarity=0.124  Sum_probs=23.0

Q ss_pred             cccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           35 QPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        35 ~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      +..+++.    .+++++|||||.|.+.  .+..+...++..
T Consensus        55 v~i~~d~----~tg~~rG~aFV~f~~~--~a~~Ai~~l~g~   89 (131)
T 2m2b_A           55 VRVIKDK----QTQLNRGFAFIQLSTI--EAAQLLQILQAL   89 (131)
T ss_dssp             EECCBCS----SSSSBCSCEEEECCHH--HHHHHHHHHTTC
T ss_pred             EEEEEcC----CCCCcceEEEEEECCH--HHHHHHHHhcCC
Confidence            5555555    3568999999999944  444444555554

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=83.00  E-value=1.4  Score=26.61  Aligned_cols=33  Identities=15%  Similarity=0.217  Sum_probs=21.4

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      ++...+..+++.    .+++++|+||+.|.+.+.+..
T Consensus        25 G~v~~v~i~~~~----~~~~~~g~afV~f~~~~~a~~   57 (77)
T 1uaw_A           25 GEVKECLVMRDP----LTKRSRGFGFVTFMDQAGVDK   57 (77)
T ss_dssp             SCCCCEEEECCC----CSSSCSSEEEECCCCTTHHHH
T ss_pred             CCEEEEEEecCC----CCCCcCceEEEEEcCHHHHHH
Confidence            344455555554    356789999999995555444

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

Probab=82.41  E-value=1.5  Score=26.32  Aligned_cols=30  Identities=10%  Similarity=0.099  Sum_probs=18.9

Q ss_pred             CCCcccccccccCCCCCCCcCcccccCCCcHHHH
Q 043064           32 RAPQPKLKSAITGGAPKKTKGRGFREEADSERHS   65 (196)
Q Consensus        32 ~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~   65 (196)
                      ...+..+++.    .+++++|++|+.|.+...+.
T Consensus        26 i~~v~i~~~~----~~~~~~g~afV~f~~~~~a~   55 (75)
T 2mss_A           26 VDDAMLMFDK----TTNRHRGFGFVTFESEDIVE   55 (75)
T ss_dssp             CSEECCCBCS----SSTTSCBEEEEECSCHHHHH
T ss_pred             EEEEEEEecC----CCCCcCcEEEEEECCHHHHH
Confidence            3344444443    34578999999999554443

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

Probab=82.28  E-value=1.5  Score=28.21  Aligned_cols=31  Identities=13%  Similarity=0.190  Sum_probs=19.9

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhcccCCC
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFESLGT   77 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~   77 (196)
                      .+.+++||+||.|.+ ...+..+...++....
T Consensus        49 ~~~~~~g~afV~f~~-~~~A~~A~~~l~g~~~   79 (102)
T 1x5s_A           49 ETQRSRGFGFVTFEN-IDDAKDAMMAMNGKSV   79 (102)
T ss_dssp             SSCSCCSEEEEECSS-HHHHHHHHHHHTTCCT
T ss_pred             CCCCcccEEEEEECC-HHHHHHHHHHhCCCEE
Confidence            345789999999994 4444444445555443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=81.60  E-value=1.1  Score=30.67  Aligned_cols=31  Identities=10%  Similarity=0.169  Sum_probs=20.6

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCC
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTD   78 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~   78 (196)
                      +.+++|||||.|.+ ..++..+...+++....
T Consensus        68 ~~~~rG~aFV~F~~-~~~A~~Ai~~lng~~l~   98 (127)
T 2a3j_A           68 SDDNSGKAYIVFAT-QESAQAFVEAFQGYPFQ   98 (127)
T ss_dssp             CCSSCCCEEEEESS-HHHHHHHHHHSTTCCCT
T ss_pred             CCCcCCEEEEEECC-HHHHHHHHHHHCCCEeC
Confidence            34789999999994 44455455566665443

>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=81.53  E-value=0.31  Score=31.84  Aligned_cols=41  Identities=12%  Similarity=0.207  Sum_probs=24.8

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      +++..+..+++.    .+++++|||||.|.+. .++..+...+++.
T Consensus        44 G~I~~v~i~~d~----~tg~~kG~afV~f~~~-~~A~~Ai~~lng~   84 (99)
T 4fxv_A           44 GEVESAKLIRDK----VAGHSLGYGFVNYVTA-KDAERAINTLNGL   84 (99)
T ss_dssp             SCEEEEEEEECS----SSCCEEEEEEEEESSH-HHHHHHHHHHTTC
T ss_pred             CCEEEeEeeecC----CCCcccccEEEEECCH-HHHHHHHHHhCCC
Confidence            334445555554    4568899999999954 4444444455443

>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=80.84  E-value=1.2  Score=27.99  Aligned_cols=41  Identities=22%  Similarity=0.190  Sum_probs=24.9

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCC
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDG   79 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~   79 (196)
                      ..+..+++.    .+++++|||||.|.+.+  +..+...+++....+
T Consensus        29 ~~v~i~~~~----~~~~~~g~afV~f~~~~--a~~a~~~l~g~~~~g   69 (90)
T 2ki2_A           29 FNVKLIYDR----ETKKPKGFGFVEMQEES--VSEAIAKLDNTDFMG   69 (90)
T ss_dssp             SEEEECCCS----SSCCCCEEEEEEECTTH--HHHHHHTSCSSCCSS
T ss_pred             EEEEEEEcC----CCCCcceEEEEEECCHH--HHHHHHHhCCCEECC
Confidence            344444444    34578999999999655  444445555554433

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=80.72  E-value=0.92  Score=29.79  Aligned_cols=31  Identities=16%  Similarity=0.009  Sum_probs=19.9

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      ++..+..+++.     .++++|||||.|.+.+.+..
T Consensus        37 ~v~~v~i~~d~-----~g~~rG~aFV~F~~~e~a~~   67 (103)
T 1s79_A           37 QVLNIQMRRTL-----HKAFKGSIFVVFDSIESAKK   67 (103)
T ss_dssp             CEEEEEEECCC-----TTSCCCEEEEEESSHHHHHH
T ss_pred             CEEEEEEEECC-----CCCCccEEEEEECCHHHHHH
Confidence            33445555543     26799999999995444444

---

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	196
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	8e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	8e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	4e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	9e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-10
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	6e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	6e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	7e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	8e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	4e-09
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:) 5e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	7e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	4e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	9e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	1e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	1e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.003

>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 = 80.1 bits (197), Expect = 8e-21
 Identities = 55/88 (62%), Positives = 70/88 (79%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           PQRS+EGWI+ VT +HEEAQED++Q  F +YGEI+N+HLNLDRRTGF KGYAL+EYE  +
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 143 EAQNAITAMNGGELLTQTLTVDWAFSNG 170
           +A  A  A+NG E++ QT+ VDW F  G
Sbjct: 61  QALAAKEALNGAEIMGQTIQVDWCFVKG 88

>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 = 64.6 bits (157), Expect = 7e-15
 Identities = 17/75 (22%), Positives = 34/75 (45%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +H +  E  L   F   G I ++ +  D  T    GYA + ++   +A+ A+  M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 152 NGGELLTQTLTVDWA 166
           N   +  + + + W+
Sbjct: 63  NFDVIKGKPVRIMWS 77

>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 = 64.6 bits (157), Expect = 9e-15
 Identities = 29/83 (34%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 86  SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           SI+   + VT +     +D L  +FG+YG I   ++  D+ TG  +G A + Y   EEAQ
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 146 NAITAMNGGELL--TQTLTVDWA 166
            AI+A+N       +Q L+V  A
Sbjct: 63  EAISALNNVIPEGGSQPLSVRLA 85

>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 = 62.7 bits (152), Expect = 4e-14
 Identities = 15/76 (19%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  +  ++ L+  FG++GE++   +  D  T   +G+  + + +       + A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 152 NGGELLTQTLTVDWAF 167
           +  EL ++T+    AF
Sbjct: 62  SRHELDSKTIDPKVAF 77

>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 = 62.6 bits (152), Expect = 5e-14
 Identities = 18/77 (23%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR-TGFVKGYALIEYENFEEAQNAITA 150
           ILV  +  +A + +++ +F  +GE++ + L      TG  +G+  +++   ++A+ A  A
Sbjct: 11  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 70

Query: 151 M-NGGELLTQTLTVDWA 166
           + +   L  + L ++WA
Sbjct: 71  LCHSTHLYGRRLVLEWA 87

>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 = 62.0 bits (150), Expect = 8e-14
 Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 86  SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQ 145
           SI    + V+G+ +   + +L+ +F +YG I    + +D+ TG  +G   I ++   EA+
Sbjct: 3   SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 62

Query: 146 NAITAMNGGELL--TQTLTVDWA 166
            AI  +NG +    T+ +TV +A
Sbjct: 63  EAIKGLNGQKPSGATEPITVKFA 85

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (150), Expect = 1e-13
 Identities = 18/75 (24%), Positives = 38/75 (50%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +     E+ +  +F + G+I+ + + LD+      G+  +EY +  +A+NA+  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 152 NGGELLTQTLTVDWA 166
           NG  L  + +  DW 
Sbjct: 70  NGTRLDDRIIRTDWD 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 2e-13
 Identities = 23/75 (30%), Positives = 44/75 (58%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + +   +++ +++FG  GEI +  L  D+ TG   GY  + Y + ++A+ AI  +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 152 NGGELLTQTLTVDWA 166
           NG  L T+T+ V +A
Sbjct: 65  NGLRLQTKTIKVSYA 79

>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 = 60.8 bits (147), Expect = 4e-13
 Identities = 20/100 (20%), Positives = 46/100 (46%), Gaps = 3/100 (3%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I+ +  +  +   +++ ++FG+YG IR +       T   +G A + YE+  +A+NA   
Sbjct: 9   ILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 151 MNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSR 190
           ++G  +  + L V +  +N        +K     +  + +
Sbjct: 66  LSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEK 105

>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 = 60.0 bits (145), Expect = 4e-13
 Identities = 19/75 (25%), Positives = 40/75 (53%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  + ++  + +L  +F   G I    +  D +TG+  GYA +++ +  ++Q AI  +
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 152 NGGELLTQTLTVDWA 166
           NG  +  + L V +A
Sbjct: 65  NGITVRNKRLKVSYA 79

>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 = 58.9 bits (142), Expect = 1e-12
 Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRR---TGFVKGYALIEYENFEEAQNAI 148
           + +  ++    E+ L+ VF + G I++  ++  +         G+  +EY+  E+AQ A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 149 TAMNGGELLTQTLTVDWA 166
             + G  +    L V  +
Sbjct: 61  KQLQGHTVDGHKLEVRIS 78

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-12
 Identities = 29/102 (28%), Positives = 51/102 (50%), Gaps = 9/102 (8%)

Query: 80  GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYE 139
           GP  +R+ +   + V G+ E+  E  L  +F + G + N H+  DR TG  +GY  +E+ 
Sbjct: 1   GPISERN-QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 59

Query: 140 NFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNM 181
           + E+A  AI  M+  +L  + + V+ A +          KN+
Sbjct: 60  SEEDADYAIKIMDMIKLYGKPIRVNKASA--------HNKNL 93

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 2e-12
 Identities = 26/76 (34%), Positives = 43/76 (56%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           ++ V G+ EE  +  L   F  +G+I ++ + LD  T   +G+A +E+E  E+A  AI  
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 151 MNGGELLTQTLTVDWA 166
           MN  EL  +T+ V+ A
Sbjct: 67  MNESELFGRTIRVNLA 82

>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 = 58.1 bits (140), Expect = 3e-12
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     +D ++ +   +G ++  +L  D  TG  KGYA  EY +      AI  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L V  A
Sbjct: 64  NGMQLGDKKLLVQRA 78

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 3e-12
 Identities = 29/83 (34%), Positives = 46/83 (55%)

Query: 84  QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEE 143
           +R+ +   I VT + E+ +E DLQ +F  +G I  ++L  D+ TG  KG+A I +   E+
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 144 AQNAITAMNGGELLTQTLTVDWA 166
           A  AI  ++G       L V+WA
Sbjct: 63  AARAIAGVSGFGYDHLILNVEWA 85

>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 = 58.1 bits (140), Expect = 4e-12
 Identities = 15/90 (16%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 84  QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEE 143
           Q S +   +   G+     +  ++  F  +G+I  + +  ++       Y+ + +   E 
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHES 66

Query: 144 AQNAITAMNGGELLTQTLTVDWAFSNGPST 173
           A +AI ++NG  +    +   W   +   T
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWGKESPDMT 96

>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 = 56.5 bits (136), Expect = 9e-12
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           +LV+ +     + D+Q +F E+G ++   ++   R+G   G A + +E   +A  A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQY 61

Query: 152 NGGELLTQTLTVDWAFS 168
           NG  L  + + +    S
Sbjct: 62  NGVPLDGRPMNIQLVTS 78

>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 = 56.6 bits (136), Expect = 1e-11
 Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 5/92 (5%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
            ++      +L   +     ED+L+ VF +        + L  + G  KG A IE+++  
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEA 64

Query: 143 EAQNAITAMNGGELLTQTLTVDWAFSNGPSTG 174
           +A+  +    G E+  +++++ +    G + G
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 55.9 bits (134), Expect = 2e-11
 Identities = 27/81 (33%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLH-LNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I +  +  E  E  L + F  +G I     +  D  TG  KGYA I + +F+ +  AI A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 151 MNGGELLTQTLTVDWAFSNGP 171
           MNG  L  + +TV +AF    
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 55.1 bits (132), Expect = 3e-11
 Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 5/88 (5%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G    P P   +      V G+     E DL+ VF +YG I ++ +  D+++   +G+A 
Sbjct: 1   GNRANPDPNCCL-----GVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 55

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTV 163
           + +EN ++A+ A    NG EL  + + V
Sbjct: 56  VYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 55.3 bits (133), Expect = 4e-11
 Identities = 24/107 (22%), Positives = 50/107 (46%), Gaps = 16/107 (14%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVH-EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKG 132
           S G+ G   P+       + +  ++    ++ D++ +F +YG+I    ++        KG
Sbjct: 2   SSGSSGKTDPRS--MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KG 51

Query: 133 YALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS-----NGPSTG 174
           +A ++Y N   A+ A+   +G  +  Q L ++ A       +GPS+G
Sbjct: 52  FAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPSSG 98

>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 = 55.2 bits (132), Expect = 4e-11
 Identities = 25/98 (25%), Positives = 40/98 (40%), Gaps = 8/98 (8%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHL--------NLDRRTGFVKGYA 134
           P    +   I V G+++    DDL + F + G ++             LD+ TG  KG A
Sbjct: 2   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 61

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS 172
            + YE+   A+ A+   +G +     L V  A    P 
Sbjct: 62  TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 56.9 bits (136), Expect = 5e-11
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+ E+ +E  L++ F +YG+I  + +  DR +G  +G+A + +++ +     +   
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 158

Query: 152 NGGELLTQTLTVDWAFS 168
               +      V  A S
Sbjct: 159 KYHTVNGHNCEVRKALS 175

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (108), Expect = 3e-07
 Identities = 13/62 (20%), Positives = 29/62 (46%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  E  ++ L++ F ++G + +  +  D  T   +G+  + Y   EE   A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 152 NG 153
             
Sbjct: 69  PH 70

>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 = 55.1 bits (132), Expect = 5e-11
 Identities = 28/105 (26%), Positives = 46/105 (43%), Gaps = 12/105 (11%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  G  R      + V  +   + E+DL+ +F  YG +  LH  +D  T   KG+A 
Sbjct: 1   GSSGSSGSGR------LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAF 54

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWAFS------NGPSTG 174
           + +   E A  A   ++G     + L V  +        +GPS+G
Sbjct: 55  VTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 54.3 bits (130), Expect = 9e-11
 Identities = 26/95 (27%), Positives = 47/95 (49%), Gaps = 1/95 (1%)

Query: 79  GGPGPQRS-IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
           G  G Q+   EG  + +  + +E  + DL  +F  +G + +  + +D++T   K +  + 
Sbjct: 7   GAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVS 66

Query: 138 YENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS 172
           Y+N   AQ AI +MNG ++  + L V    S   S
Sbjct: 67  YDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 53.8 bits (129), Expect = 9e-11
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 6/82 (7%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  E++++ +F +YG+   + ++        KG+  I  E    A+ A   +
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAKVEL 64

Query: 152 NGGELLTQTLTVDWAFSNGPST 173
           +   L  + L V +A  +   T
Sbjct: 65  DNMPLRGKQLRVRFACHSASLT 86

>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 = 53.9 bits (129), Expect = 9e-11
 Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 77  TDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALI 136
           + G PGP       II V  +      D++ + F  Y  I           G   G A++
Sbjct: 3   SSGKPGP------TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 56

Query: 137 EYENFEEAQNAITAMNGGELLTQTLTVDWA 166
            +E+ +EA  A+  +N   + ++ + +   
Sbjct: 57  AFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>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 = 54.3 bits (130), Expect = 9e-11
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNL--HLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           + + G+ +  + +++     +  E                 +G+A +EYE+   A  A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 150 AMNGG--ELLTQTLTVDWA 166
            +  G  +L    + VDWA
Sbjct: 64  KLMPGRIQLWGHQIAVDWA 82

>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 = 53.4 bits (128), Expect = 2e-10
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V G+  +  E DL+  F  +GE+  + +  D +TG  KG+  + +  +E     ++  
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 152 NGGELLTQTLTVDWAFS 168
           +   +  +        S
Sbjct: 71  H--MIDGRWCDCKLPNS 85

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 2e-10
 Identities = 14/77 (18%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  E  ++ L++ F ++G + +  +  D  T   +G+  + Y   EE   A+   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 67

Query: 152 NGGELLTQTLTVDWAFS 168
              ++  + +    A S
Sbjct: 68  RPHKVDGRVVEPKRAVS 84

>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 = 52.3 bits (125), Expect = 3e-10
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 81  PGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYEN 140
           P  ++S  G I  +  + +      L + F  +G I +  +  D       G+  + +E 
Sbjct: 1   PSLRKSGVGNIF-IKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGF--VHFET 57

Query: 141 FEEAQNAITAMNGGELLTQTLTVDWA 166
            E A+ AI  MNG  L  + + V   
Sbjct: 58  QEAAERAIEKMNGMLLNDRKVFVGRF 83

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 4e-10
 Identities = 19/108 (17%), Positives = 40/108 (37%), Gaps = 17/108 (15%)

Query: 63  RHSRLADRNFESLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN 122
           +H+ L     E+           + +  ++   G+      + L  V  + G +  L + 
Sbjct: 2   KHTLLRHEGIET--------VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 53

Query: 123 LDRRTGFVKGYALIEYENFEEAQNAITAMNGGELL---TQTLTVDWAF 167
            ++   F        Y   EE++ A   +NG E++    Q +T+   F
Sbjct: 54  PNKPYSFA------RYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNF 95

>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 = 52.4 bits (125), Expect = 6e-10
 Identities = 12/77 (15%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  E  E+ L+N + ++G++ +  +  D  +   +G+  + + +  E   A+ A 
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AA 81

Query: 152 NGGELLTQTLTVDWAFS 168
               +  + +    A +
Sbjct: 82  RPHSIDGRVVEPKRAVA 98

>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 = 52.0 bits (124), Expect = 6e-10
 Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V+ +    ++ DL+ +FG++G+I ++ +  + R    KG+  + +EN  +A  A   +
Sbjct: 14  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKL 71

Query: 152 NGGELLTQTLTVDWA 166
           +G  +  + + V+ A
Sbjct: 72  HGTVVEGRKIEVNNA 86

>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 = 52.3 bits (125), Expect = 6e-10
 Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 5/89 (5%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I+V  +      D L  +F ++G +  +           +  AL++Y +   AQ+A  ++
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLSL 65

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKN 180
           +G  +     T+   FS   ++   K  N
Sbjct: 66  DGQNIYNACCTLRIDFSK-LTSLNVKYNN 93

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 7e-10
 Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  +  E  +  +F + G  ++  +  +  +     +  +E+    +A  A+ AM
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF--VEFYEHRDAAAALAAM 68

Query: 152 NGGELLTQTLTVDWA 166
           NG ++L + + V+WA
Sbjct: 69  NGRKILGKEVKVNWA 83

>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 = 51.7 bits (123), Expect = 7e-10
 Identities = 24/75 (32%), Positives = 44/75 (58%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V G+  +  E  L+ VF +YG+I  + +  DR T   +G+  + +EN ++A++A+ AM
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 152 NGGELLTQTLTVDWA 166
           NG  +  + + VD A
Sbjct: 68  NGKSVDGRQIRVDQA 82

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 8e-10
 Identities = 21/97 (21%), Positives = 44/97 (45%), Gaps = 6/97 (6%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G   GP          I V  +  + +  D+++VF +YG IR++     +       +A 
Sbjct: 4   GVIRGPAGNNDCR---IYVGNLPPDIRTKDIEDVFYKYGAIRDID---LKNRRGGPPFAF 57

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPS 172
           +E+E+  +A++A+   +G +     L V++  S   +
Sbjct: 58  VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 94

>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 = 50.9 bits (121), Expect = 9e-10
 Identities = 10/75 (13%), Positives = 31/75 (41%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + +T       + +++++  +   +         R    + +A I+  + E+A+  +  +
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 152 NGGELLTQTLTVDWA 166
           NG ++   TL    +
Sbjct: 64  NGLKIEGYTLVTKVS 78

>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 = 51.7 bits (123), Expect = 1e-09
 Identities = 22/103 (21%), Positives = 42/103 (40%), Gaps = 7/103 (6%)

Query: 82  GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF 141
           G Q+      I V G+     +  L+  F  +G+I    +  DR+TG  +GY  +   + 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 142 EEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPG 184
             A+ A    N   +  +   V+ A+         K ++++ G
Sbjct: 63  AAAERACKDPN-PIIDGRKANVNLAYLGA------KPRSLQTG 98

>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 = 50.8 bits (121), Expect = 1e-09
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I+ V  +     E+ ++  F               R   ++ YA + + N E+A  A+ A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 151 MNGGELLTQTLTVDWA 166
           +NG  L    + V  A
Sbjct: 64  LNGKVLDGSPIEVTLA 79

>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 = 50.0 bits (119), Expect = 2e-09
 Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+  +  E+ ++  FG +GE+ ++ L +D +T   +G+  I ++  E  +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60

Query: 152 NGGELLTQTLTVDWA 166
               +      +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>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 = 50.4 bits (120), Expect = 2e-09
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           +    +    +  DL++ F   G++R++ +  DR +   KG A +E+   +    AI  +
Sbjct: 21  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 79

Query: 152 NGGELLTQTLTVDWA 166
            G  LL   + V  +
Sbjct: 80  TGQRLLGVPIIVQAS 94

>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 = 49.6 bits (118), Expect = 3e-09
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+  +  + DL++ F ++GE+ +  L LD  TG  +G+  + ++  E     +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQ 60

Query: 152 NGGELLTQTLTV 163
              +L  + +  
Sbjct: 61  KEHKLNGKVIDP 72

>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 = 49.3 bits (117), Expect = 4e-09
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + +  +      DDL+ +FG+             +     GYA ++Y +   A  AI  +
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 152 NGG-ELLTQTLTVDWA 166
           +G  EL  + + VD++
Sbjct: 58  SGKVELHGKIMEVDYS 73

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 5e-09
 Identities = 12/72 (16%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 94  VTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNG 153
           +   ++E  E+    +  +YGE+  +++  D     + G   +++   E+A+ A+  +N 
Sbjct: 32  MQEHYDEFFEEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

Query: 154 GELLTQTLTVDW 165
                Q +  + 
Sbjct: 91  RWFNGQPIHAEL 102

>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 = 49.8 bits (118), Expect = 5e-09
 Identities = 32/101 (31%), Positives = 50/101 (49%), Gaps = 9/101 (8%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V  +  EA E+ L+++F E G + +  L  DR TG  KGY   EY++ E A +A+  +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSP 192
           NG E   + L VD A S          KN    ++  + +P
Sbjct: 71  NGREFSGRALRVDNAAS---------EKNKEELKSLGTGAP 102

>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 = 49.0 bits (116), Expect = 5e-09
 Identities = 13/75 (17%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+      +D+++ F ++G++ +  L  D+ T   +G+  + +E+ +  +     +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 152 NGGELLTQTLTVDWA 166
           +  E+  + +    A
Sbjct: 61  HFHEINNKMVECKKA 75

>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 = 48.9 bits (116), Expect = 7e-09
 Identities = 29/103 (28%), Positives = 44/103 (42%), Gaps = 9/103 (8%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           S G+ G  G  ++     + V G+        L   F  +G IR +             +
Sbjct: 2   SSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSF 55

Query: 134 ALIEYENFEEAQNAITAMNGGEL--LTQTLTVDWAFSNGPSTG 174
           A I+YE+ + AQ A   M G  L    + L VD+A  +GPS+G
Sbjct: 56  AYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA-KSGPSSG 97

>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 = 49.0 bits (116), Expect = 8e-09
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 6/96 (6%)

Query: 83  PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFE 142
           P    EG  + +  +  +++E+ L  V  ++G+++ + + L   T   KG A  ++   E
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 143 EAQNAITAMN------GGELLTQTLTVDWAFSNGPS 172
            AQ  + A +      G +L  + L VD A +   +
Sbjct: 62  AAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 86  SIEGWIILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRR-TGFVKGYALIEYENFEE 143
           ++EG  I++  +  E   E+ L+  F  +G I  +++   ++   F    A + +EN + 
Sbjct: 1   TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 60

Query: 144 AQNAITAMNGGELLTQTLTVDWA 166
           A+ A+  MN   L  + ++V  A
Sbjct: 61  AERAL-QMNRSLLGNREISVSLA 82

>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 = 48.5 bits (115), Expect = 1e-08
 Identities = 14/76 (18%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEY-GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I +  ++E+ ++D+L+            +   L  R+  ++G A + ++    A NA+ +
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 151 MNGGELLTQTLTVDWA 166
           M G     + + + +A
Sbjct: 66  MQGFPFYDKPMRIQYA 81

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 7/105 (6%)

Query: 76  GTDGGPGPQRSIEG-WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G +      +   +  +  +  E+ ++  F                   +KG+ 
Sbjct: 1   GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN-----GPSTG 174
             E+E+ +    +  ++N   L  + + VD A        GPS+G
Sbjct: 61  YAEFEDLDSLL-SALSLNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 49.5 bits (117), Expect = 1e-08
 Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 10/100 (10%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V  +     E  L+ +F  YG I ++ +  DR T   +GY  +++++   AQ AI  +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRS 191
           NG  +L + L V  A             + RPG       
Sbjct: 105 NGFNILNKRLKVALA----------ASGHQRPGIAGAVGD 134

>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 = 47.1 bits (111), Expect = 4e-08
 Identities = 14/104 (13%), Positives = 34/104 (32%), Gaps = 11/104 (10%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
              +T +     + D+           N    L    G   G AL++++N ++A+ +   
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-R 68

Query: 151 MNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRR 194
           ++  +L  +   V               ++MR    +     + 
Sbjct: 69  LHRKKLNGREAFVHVV----------TLEDMREIEKNPPAQGKS 102

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 9e-08
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 8/79 (10%)

Query: 88  EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNA 147
           +G  + V G   +     L+  F  +G I +L ++  R        A + YE  E A  A
Sbjct: 4   KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQA 55

Query: 148 ITAMNGGELLTQTLTVDWA 166
           +  +NG ++ +  L V+ A
Sbjct: 56  VAELNGTQVESVQLKVNIA 74

>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 = 46.0 bits (108), Expect = 1e-07
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 6/85 (7%)

Query: 85  RSIEGWIILVTGVHEEAQEDDLQNVF---GEYGEIRNLHLNLDRRTG---FVKGYALIEY 138
           R ++  ++ V G+ +   + ++       G++G+I  + +N              A + Y
Sbjct: 4   RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTY 63

Query: 139 ENFEEAQNAITAMNGGELLTQTLTV 163
              E+A  AI  +N   +  +TL  
Sbjct: 64  IRSEDALRAIQCVNNVVVDGRTLKA 88

>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 = 45.9 bits (108), Expect = 1e-07
 Identities = 18/75 (24%), Positives = 36/75 (48%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + +  +     E DL ++F  + E +   +     TG ++G A I + N E A  A+  +
Sbjct: 21  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 80

Query: 152 NGGELLTQTLTVDWA 166
           NG +L  + L +++ 
Sbjct: 81  NGYKLYGKILVIEFG 95

>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 = 46.1 bits (109), Expect = 1e-07
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 4/64 (6%)

Query: 103 EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT 162
            +DL+    ++G+IR L L          G A + + + EEA   I  ++G     + +T
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 163 VDWA 166
               
Sbjct: 89  AQAW 92

>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 = 45.1 bits (106), Expect = 2e-07
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           I V G+ E+ +E  L++ F +YG+I  + +  DR +G  +G+A + +++  ++ + I   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIVIQ 63

Query: 152 NGGELLTQTLTVDWA 166
               +      V  A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 2e-07
 Identities = 18/70 (25%), Positives = 34/70 (48%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + + G+     + DL  +   YG+I +    LD+ T   KGY  +++++   AQ A+TA+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 152 NGGELLTQTL 161
               +  Q  
Sbjct: 61  KASGVQAQMA 70

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 3e-07
 Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 12/88 (13%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ILV  + +++   ++ ++  +Y                 K  A +   N E+AQNAI   
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKY-------CYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 152 NGGELLTQTLTVDWA-----FSNGPSTG 174
           +      + L V          +GPS+G
Sbjct: 61  HQYSFRGKDLIVQLQPTDALLCSGPSSG 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 = 44.4 bits (104), Expect = 4e-07
 Identities = 23/110 (20%), Positives = 44/110 (40%), Gaps = 17/110 (15%)

Query: 76  GTDGGPGPQRSIE-GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G  G    +    ++ V G+ E   E DL     ++G I  + +   +R        
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQAL----- 55

Query: 135 LIEYENFEEAQNAITAMNGG--ELLTQTLTVDWAFS--------NGPSTG 174
            +E+EN + A+  +T        +  Q    +++ S        +GPS+G
Sbjct: 56  -VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 43.3 bits (101), Expect = 1e-06
 Identities = 15/102 (14%), Positives = 39/102 (38%), Gaps = 7/102 (6%)

Query: 78  DGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIE 137
             G  P  +     + + G+     ++++   F     + N         G   G A ++
Sbjct: 5   SSGNSPDTA-NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 138 YENFEEAQNAITAMNGGELLTQTLTVDWAF-----SNGPSTG 174
           + + E A+ A+   +   +  + + +  +      ++GPS+G
Sbjct: 64  FASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 6/88 (6%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN-----LDRRTGFVKGYALIEYENFEEAQN 146
           + V  +     E+ + + F     +  L        L  +    K +A +E+ + +E   
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 147 AITAMNGGELLTQTLTVDWAFSNGPSTG 174
           A+   +G     Q+L +       P  G
Sbjct: 64  AMA-FDGIIFQGQSLKIRRPHDYQPLPG 90

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 14/106 (13%)

Query: 74  SLGTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           S G+ GGP  +RS   + +LV+G+       DL++   E G++               G 
Sbjct: 2   SSGSSGGPPTRRS--DFRVLVSGLPPSGSWQDLKDHMREAGDVCYAD-------VQKDGM 52

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF-----SNGPSTG 174
            ++EY   E+ + A+  ++  +  +      +       S+GPS+G
Sbjct: 53  GMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSSG 98

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 1e-06
 Identities = 11/76 (14%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 93  LVTGVHEEAQEDDLQNVFGEYGEIRNLHL--NLDRRTGFVKGYALIEYENFEEAQNAITA 150
           L+     E   +D+++   +YG ++++ +   +D       G   +E+ +  + Q A+  
Sbjct: 18  LLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG 77

Query: 151 MNGGELLTQTLTVDWA 166
           + G +   + +   + 
Sbjct: 78  LTGRKFANRVVVTKYC 93

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 12/116 (10%), Positives = 36/116 (31%), Gaps = 22/116 (18%)

Query: 79  GGPGPQRSIEGWIILVTGVHEEAQED-----DLQNVFGEYGEIRNLHLNLDRRTGFVKGY 133
           G  G         ++    +++   +       +++F  Y +          +   +   
Sbjct: 1   GSSGSSG------LIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRI--- 51

Query: 134 ALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRS 189
               + N   A +A   ++  E L + + + +A +           ++ P    +S
Sbjct: 52  ---NFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL-----HIGSSHLAPPNPDKS 99

>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 = 43.3 bits (101), Expect = 1e-06
 Identities = 17/89 (19%), Positives = 31/89 (34%), Gaps = 5/89 (5%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           +     + ++   +DL  +F  +GEI+ +      + G +        E  +EA      
Sbjct: 13  LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEKAKEALGKAKD 67

Query: 151 MNGGELLTQTLTVDWAFSNGPSTGPFKRK 179
            N G L  +   V W    G       +K
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKK 96

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 2e-06
 Identities = 15/88 (17%), Positives = 37/88 (42%), Gaps = 12/88 (13%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + V     +  ED+L+  F +YG++ +            + +A + + + + AQ+     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQIAQSLC--G 60

Query: 152 NGGELLTQTLTVDWAF-----SNGPSTG 174
               +   ++ +  A      ++GPS+G
Sbjct: 61  EDLIIKGISVHISNAEPKHNSNSGPSSG 88

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 3e-06
 Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 9/105 (8%)

Query: 76  GTDG-GPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYA 134
           G+ G      +S  G  + + G+   A E+D+ N F     +R          G V G A
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEA 58

Query: 135 LIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS-----NGPSTG 174
            +E+   E+A  A  A +   +  + + +    +     +GPS+G
Sbjct: 59  DVEFATHEDAVAA-MAKDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 6e-06
 Identities = 20/107 (18%), Positives = 50/107 (46%), Gaps = 7/107 (6%)

Query: 91  IILVTGVHEEA-QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT 149
           ++LV+ ++ E      L  +FG YG+++ + +  +++       AL++  +  +AQ A++
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 58

Query: 150 AMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRSPRRRY 196
            +NG +L  + + +  +        P + +  +        SP  R+
Sbjct: 59  HLNGHKLHGKPIRITLSKHQNVQL-PREGQEDQGLTKDYGNSPLHRF 104

>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 = 40.1 bits (93), Expect = 1e-05
 Identities = 12/83 (14%), Positives = 32/83 (38%), Gaps = 2/83 (2%)

Query: 84  QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEE 143
           +  ++   + + G   +A  DD++    + G++ N            KG   + +++ E 
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIES 59

Query: 144 AQNAITAMNGGELLTQTLTVDWA 166
           A+  +    G +     L + + 
Sbjct: 60  AKKFV-ETPGQKYKETDLLILFK 81

>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 = 40.3 bits (93), Expect = 1e-05
 Identities = 19/116 (16%), Positives = 40/116 (34%), Gaps = 10/116 (8%)

Query: 76  GTDGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYAL 135
           G+ G  G  +++    IL   +       ++Q  F  +G +                 A+
Sbjct: 1   GSSGSSGRSKTV----ILAKNLPAGTLAAEIQETFSRFGSLG------RVLLPEGGITAI 50

Query: 136 IEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRS 191
           +E+    EA+ A   +   +     L ++WA        P K+ +       ++ S
Sbjct: 51  VEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAES 106

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (85), Expect = 1e-04
 Identities = 16/100 (16%), Positives = 33/100 (33%), Gaps = 15/100 (15%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           ++V+G+       DL++   E G++    +  D            E+   E+   A+  +
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVV-------EFVRKEDMTYAVRKL 55

Query: 152 NGGELLTQTLTVDWAFSNGPSTGPFKRKNMRPGRTHRSRS 191
           +  +  +      +           K    R     RSRS
Sbjct: 56  DNTKFRSHEGETAYIRV--------KVDGPRSPSYGRSRS 87

>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 = 36.3 bits (83), Expect = 4e-04
 Identities = 11/75 (14%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 92  ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM 151
           + ++ +     E +L+N+   +G++ +  +  D              E+ E+ +  I   
Sbjct: 21  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF-ARMESTEKCEAVIGHF 79

Query: 152 NGGELLTQTLTVDWA 166
           NG  + T        
Sbjct: 80  NGKFIKTPPGVSAPT 94

>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 = 33.3 bits (75), Expect = 0.003
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 91  IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITA 150
           I+ +T + EE  E  L  +F ++   + +              A +E+    ++  A  A
Sbjct: 10  ILFLTNLPEETNEMMLSMLFNQFPGFKEVR-----LVPNRHDIAFVEFTTELQSNAAKEA 64

Query: 151 MNGGELL-TQTLTVDWA 166
           + G ++  T  + + +A
Sbjct: 65  LQGFKITPTHAMKITFA 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	196
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.91
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.89
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.89
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.88
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.85
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.82
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.81
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.81
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.81
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.81
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.8
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.8
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.8
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.8
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.8
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.79
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.79
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.78
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.77
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.76
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.76
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.71
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
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	99.59
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.58
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.56
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.52
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.48
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.42
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.74
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.74
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.38
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.05
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	90.16
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	88.78
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	88.69
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	88.22
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	87.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	87.76
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	86.72
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	86.23
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	85.78
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	84.57
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	84.31
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	84.24
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	82.89
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	82.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	82.51
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	82.19
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	81.88
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	81.32
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	80.98
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	80.7
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	80.57
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	80.52
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	80.44

>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=99.91  E-value=6.2e-24  Score=140.68  Aligned_cols=88  Identities=63%  Similarity=1.125  Sum_probs=82.5

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      |+++.++++|||+|||+.+++++|.++|++||.|..|.++.++.+|+++|||||+|.+.++|+.|+..|||..|.|+.|+
T Consensus         1 P~~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~   80 (88)
T d1rk8a_           1 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   80 (88)
T ss_dssp             CCCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            45677889999999999999999999999999999999999988999999999999999999999999999999999999


Q ss_pred             EEEcccCC
Q 043064          163 VDWAFSNG  170 (196)
Q Consensus       163 v~~a~~~~  170 (196)
                      |.||.++.
T Consensus        81 V~~a~~kG   88 (88)
T d1rk8a_          81 VDWCFVKG   88 (88)
T ss_dssp             EEESEECC
T ss_pred             EEEecCCC
Confidence            99998763

>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=99.89  E-value=2.7e-23  Score=135.73  Aligned_cols=80  Identities=24%  Similarity=0.430  Sum_probs=77.3

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++||+.|||..|.|+.|+|.||+|
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            56899999999999999999999999999999999988999999999999999999999999999999999999999976

>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=99.89  E-value=8.9e-23  Score=137.90  Aligned_cols=86  Identities=24%  Similarity=0.332  Sum_probs=80.8

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      +...++|||+|||+.+++++|+++|.+||.|..|.|+.++.+++++|||||+|.+.++|+.||+.||+..|.|+.|+|.+
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      +.++..
T Consensus        85 a~~~~~   90 (99)
T d1whwa_          85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             CCCCCc
Confidence            987654

>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=99.89  E-value=6.1e-23  Score=136.38  Aligned_cols=85  Identities=33%  Similarity=0.516  Sum_probs=80.4

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cccCC
Q 043064          166 AFSNG  170 (196)
Q Consensus       166 a~~~~  170 (196)
                      |+|+.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98764

>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=1.1e-22  Score=138.17  Aligned_cols=85  Identities=26%  Similarity=0.405  Sum_probs=80.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .++++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.||..|||..|.|+.|+|.||
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      .++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            88765

>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=3.7e-23  Score=137.13  Aligned_cols=84  Identities=31%  Similarity=0.489  Sum_probs=79.5

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+++++++|+++|++||+|..|.|+.++.+|.++|||||+|.+.++|+.|+..||+..|+|+.|+|.||.
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            45789999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      |+..
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=99.89  E-value=1e-22  Score=132.93  Aligned_cols=80  Identities=29%  Similarity=0.497  Sum_probs=76.9

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+++++++|+++|++||.|..|.++.+..++.++|||||+|.+.++|+.|++.|||..|.|+.|+|.||+|
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            35799999999999999999999999999999999988999999999999999999999999999999999999999976

>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=99.89  E-value=1.7e-22  Score=135.01  Aligned_cols=84  Identities=21%  Similarity=0.422  Sum_probs=79.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.++.++.++.++|||||+|.+.++|..|++.|||..|+|++|+|.|+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      .+..
T Consensus        85 ~~~~   88 (93)
T d1h2vz_          85 AGFK   88 (93)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            6443

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=9.1e-23  Score=136.31  Aligned_cols=85  Identities=28%  Similarity=0.375  Sum_probs=80.2

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ...++|||+|||..+|+++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|+.|++.||+..|.|+.|+|.||
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            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      .++..
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            87653

>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=99.88  E-value=1.1e-22  Score=133.62  Aligned_cols=82  Identities=26%  Similarity=0.476  Sum_probs=78.2

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ++|||+|||+.+|+++|+++|++||+|..|.|+.++.+|.++|||||+|.+.++|..|+..||+..|.|++|.|.||.+.
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            57999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             CC
Q 043064          170 GP  171 (196)
Q Consensus       170 ~~  171 (196)
                      ..
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.3e-22  Score=130.64  Aligned_cols=78  Identities=22%  Similarity=0.342  Sum_probs=75.4

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .|||+|||+.+|+++|..+|++||+|.+|.|+.++.+|+++|||||+|.+.++|..|++.|||..|.|++|+|.||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999999953

>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=99.87  E-value=1.1e-21  Score=140.40  Aligned_cols=86  Identities=27%  Similarity=0.402  Sum_probs=80.5

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|..||+.||+..|+|+.|+|.||
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            34578999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 043064          167 FSNGPS  172 (196)
Q Consensus       167 ~~~~~~  172 (196)
                      .++..+
T Consensus       120 ~~~~~~  125 (139)
T d1u6fa1         120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.87  E-value=6.9e-22  Score=134.41  Aligned_cols=87  Identities=22%  Similarity=0.327  Sum_probs=79.1

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      +.....++|||+|||+.+++++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|++||+.+|+ .|.|+.|.|
T Consensus         5 ~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V   83 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   83 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEE
Confidence            3445567899999999999999999999999999999999998999999999999999999999998775 799999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .||.++..
T Consensus        84 ~~a~~~~~   91 (103)
T d2cqda1          84 NLAYLGAK   91 (103)
T ss_dssp             EESTTTCC
T ss_pred             EEcCCCCC
Confidence            99976543

>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=99.87  E-value=6.8e-22  Score=129.85  Aligned_cols=81  Identities=36%  Similarity=0.491  Sum_probs=76.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v  163 (196)
                      ....++|||+|||+++++++|+++|++||.|..+.|+.++.+|+++|||||+|.+.++|.+|++.||+..+.|  ++|+|
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            3456789999999999999999999999999999999998899999999999999999999999999999876  88999


Q ss_pred             EEc
Q 043064          164 DWA  166 (196)
Q Consensus       164 ~~a  166 (196)
                      .||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            997

>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=99.87  E-value=7.3e-22  Score=132.11  Aligned_cols=86  Identities=22%  Similarity=0.458  Sum_probs=78.5

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHh-CCceeCCcEeEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAM-NGGELLTQTLTV  163 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afv~f~~~~~a~~al~~l-~~~~l~g~~l~v  163 (196)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.+. .+|.++|||||+|.+.++|.+||..| |+..|.|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3456779999999999999999999999999999998775 37899999999999999999999998 899999999999


Q ss_pred             EEcccCCC
Q 043064          164 DWAFSNGP  171 (196)
Q Consensus       164 ~~a~~~~~  171 (196)
                      .||.++..
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987653

>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=99.87  E-value=4.6e-22  Score=132.00  Aligned_cols=86  Identities=28%  Similarity=0.499  Sum_probs=80.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ....+|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|+.|+..||+..|.|+.|+|.||
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            34677999999999999999999999999999999988889999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 043064          167 FSNGPS  172 (196)
Q Consensus       167 ~~~~~~  172 (196)
                      .++...
T Consensus        83 ~~~~~~   88 (90)
T d1x5sa1          83 GKSSDN   88 (90)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            877643

>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=99.87  E-value=7.3e-22  Score=129.71  Aligned_cols=80  Identities=28%  Similarity=0.515  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeEEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLTVD  164 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~v~  164 (196)
                      ...++|||+|||+.+|+++|+++|++||+|.++.|+.++.+|.++|||||+|.+.++|..|++.|||..+.|  ++|+|.
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            446789999999999999999999999999999999998899999999999999999999999999999987  569999


Q ss_pred             Ec
Q 043064          165 WA  166 (196)
Q Consensus       165 ~a  166 (196)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            87

>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=3.8e-22  Score=130.46  Aligned_cols=81  Identities=33%  Similarity=0.565  Sum_probs=75.7

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEE-EEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNL-HLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v-~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      |||+|||+++|+++|+++|++||.|..+ .++.++.+|+++|||||+|.+.++|+.||+.|++..|.|++|+|.||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999999764 788888899999999999999999999999999999999999999998876


Q ss_pred             CC
Q 043064          171 PS  172 (196)
Q Consensus       171 ~~  172 (196)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.86  E-value=2.1e-21  Score=128.73  Aligned_cols=83  Identities=18%  Similarity=0.341  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+  +++.|+|+.|.|.+|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~--~~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeC
Confidence            456789999999999999999999999999999999999899999999999999999999997  456899999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87653

>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=99.86  E-value=6.8e-22  Score=128.66  Aligned_cols=79  Identities=13%  Similarity=0.149  Sum_probs=69.4

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|.+|++.|||..+.|++|+|.|+.|
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            6899999999999999999999999999888887778899999999999999999999999999999999999999977

>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=99.86  E-value=3.4e-22  Score=136.17  Aligned_cols=82  Identities=35%  Similarity=0.521  Sum_probs=78.2

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+++++++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++|+.|++.||+..|.|+.|+|.||.+
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            46799999999999999999999999999999999998999999999999999999999999999999999999999976


Q ss_pred             CC
Q 043064          169 NG  170 (196)
Q Consensus       169 ~~  170 (196)
                      ..
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.9e-21  Score=127.04  Aligned_cols=76  Identities=29%  Similarity=0.485  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      +.++|||+|||+.+|+++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|..|+..||+..|+|++|+|
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            4678999999999999999999999999999999999889999999999999999999999999999999999987

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=1.6e-21  Score=125.93  Aligned_cols=77  Identities=25%  Similarity=0.431  Sum_probs=73.6

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      +|||+|||+.+++++|+++|++||.|..+.|+.++ +++++|||||+|.+.++|+.|++.|||..|+|++|+|.+|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            59999999999999999999999999999999885 899999999999999999999999999999999999999853

>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=99.85  E-value=3.9e-21  Score=127.49  Aligned_cols=83  Identities=19%  Similarity=0.409  Sum_probs=75.5

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+.++|||+|||+++|+++|+++|++||.|..|.|+.++.++  +|||||+|.+.++|+.|+..||+..|.|+.|+|.||
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            346789999999999999999999999999999998886444  789999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      .+...
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            76543

>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=99.85  E-value=7.7e-21  Score=126.78  Aligned_cols=85  Identities=19%  Similarity=0.339  Sum_probs=77.3

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+++|++||+|..|.++.+.  +.++|||||+|.+.++|.+|+..||+..|.|+.|+|.|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4456789999999999999999999999999999998875  33689999999999999999999999999999999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      |+++...
T Consensus        86 A~~r~~t   92 (93)
T d2cq3a1          86 ATARVMT   92 (93)
T ss_dssp             CCSSCCC
T ss_pred             cCcCCCC
Confidence            9987653

>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=3.8e-21  Score=129.40  Aligned_cols=89  Identities=25%  Similarity=0.431  Sum_probs=80.5

Q ss_pred             CCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC------Ccee
Q 043064           83 PQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN------GGEL  156 (196)
Q Consensus        83 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~------~~~l  156 (196)
                      |.....+++|||+|||+++|+++|+.+|++||.|..+.++.+..++.++|||||+|.+.++|..||+.||      +..|
T Consensus         2 P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~   81 (98)
T d1x4ha1           2 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL   81 (98)
T ss_dssp             CCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES
T ss_pred             ccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE
Confidence            3345567889999999999999999999999999999999998899999999999999999999999886      5678


Q ss_pred             CCcEeEEEEcccCCC
Q 043064          157 LTQTLTVDWAFSNGP  171 (196)
Q Consensus       157 ~g~~l~v~~a~~~~~  171 (196)
                      .|+.|+|.||.++..
T Consensus        82 ~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          82 DGRQLKVDLAVTRDE   96 (98)
T ss_dssp             SSCEEEEECCCCCCC
T ss_pred             CCEEEEEEECCCCCc
Confidence            999999999987654

>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=99.85  E-value=3.6e-21  Score=126.04  Aligned_cols=79  Identities=16%  Similarity=0.325  Sum_probs=74.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+++|+++|.++|++||.|..+.|+.++.+|+++|||||+|.+.++|++||+ ++++.|.|+.|+|..|.
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 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            35689999999999999999999999999999999999999999999999999999999996 69999999999999885

>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=99.85  E-value=2.2e-21  Score=131.83  Aligned_cols=83  Identities=14%  Similarity=0.301  Sum_probs=78.0

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+||+ +++..|.|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            4789999999999999999999999999999999998899999999999999999999995 799999999999999988


Q ss_pred             CCCC
Q 043064          169 NGPS  172 (196)
Q Consensus       169 ~~~~  172 (196)
                      +..+
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            7654

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.2e-21  Score=130.46  Aligned_cols=88  Identities=28%  Similarity=0.462  Sum_probs=79.8

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCee--------EEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIR--------NLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL  156 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~--------~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l  156 (196)
                      .....++|||+|||+.+|+++|+++|++||.|.        .+.+..++.+|+++|||||+|.+.++|..||+.|||..|
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            445678999999999999999999999999874        466677778899999999999999999999999999999


Q ss_pred             CCcEeEEEEcccCCCC
Q 043064          157 LTQTLTVDWAFSNGPS  172 (196)
Q Consensus       157 ~g~~l~v~~a~~~~~~  172 (196)
                      .|+.|+|.||+++++.
T Consensus        84 ~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          84 QGSKLKVSLARKKPPM   99 (101)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCEEEEEEEcCCCCCC
Confidence            9999999999987764

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=3e-21  Score=126.67  Aligned_cols=79  Identities=20%  Similarity=0.422  Sum_probs=73.0

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCC---CcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTG---FVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g---~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      |||+|||+++|+++|+++|++||.|.+|.|+.++.++   .++|||||+|.+.++|..|++.||+..|+|+.|.|.|+.+
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            7999999999999999999999999999998876554   4689999999999999999999999999999999999865


Q ss_pred             CC
Q 043064          169 NG  170 (196)
Q Consensus       169 ~~  170 (196)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.85  E-value=6.6e-22  Score=127.47  Aligned_cols=77  Identities=18%  Similarity=0.397  Sum_probs=73.5

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ++|||+|||+++|+++|+++|++||.|.++.|+.++.+|+++|||||+|.+.++|++||. ++++.|+|+.|.|.+|.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~Af   77 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEECC
Confidence            579999999999999999999999999999999999999999999999999999999996 79999999999999873

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=2e-21  Score=127.82  Aligned_cols=83  Identities=24%  Similarity=0.401  Sum_probs=72.3

Q ss_pred             CCCCEEEEcCCCccCc-HHHHHHhhccCCCeeEEEEeec-CCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           87 IEGWIILVTGVHEEAQ-EDDLQNVFGEYGEIRNLHLNLD-RRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~t-e~~L~~~F~~~G~i~~v~i~~~-~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...++|||+|||++++ ++.|+++|++||.|..|.|+.+ ..++.++|||||+|.+.++|+.||+ ||+..|+|+.|+|.
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVS   80 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEE
Confidence            4578999999999876 5679999999999999998754 4688999999999999999999995 99999999999999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      ||.++|
T Consensus        81 ~a~~kP   86 (86)
T d2ghpa3          81 LADKKP   86 (86)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998765

>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=99.84  E-value=4.5e-21  Score=126.94  Aligned_cols=81  Identities=25%  Similarity=0.330  Sum_probs=74.4

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ..+|||+|||+++++++|+++|++||.|..+.|+.+.  +.++|||||+|.+.++|++||+.|||..|+|+.|.|.+|.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4579999999999999999999999999999998875  34679999999999999999999999999999999999987


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      +..
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            653

>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=99.84  E-value=3.6e-21  Score=123.39  Aligned_cols=75  Identities=20%  Similarity=0.434  Sum_probs=71.1

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +|||+|||+++|+++|.++|++||+|..|.|+.++.+++++|||||+|.+.++|++||+ +++..|.|+.|.|..|
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 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            49999999999999999999999999999999999999999999999999999999996 7999999999998654

>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=99.84  E-value=3.6e-21  Score=130.26  Aligned_cols=80  Identities=21%  Similarity=0.379  Sum_probs=76.0

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+.+++++|+++|+.||.|..|.|+.+..+|+++|||||+|.+.++|.+|+. |||..|.|+.|.|.++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            5789999999999999999999999999999999998899999999999999999999995 999999999999999865


Q ss_pred             C
Q 043064          169 N  169 (196)
Q Consensus       169 ~  169 (196)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.83  E-value=3.3e-20  Score=124.15  Aligned_cols=81  Identities=23%  Similarity=0.380  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ..+.++|||+|||+++|+++|+++|++||.|..+.+..   ++..++||||+|.+.++|+.||+.||++.|.|++|+|.|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~---~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45567899999999999999999999999999988754   345689999999999999999999999999999999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      |++.
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            9654

>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=99.83  E-value=2.5e-20  Score=120.54  Aligned_cols=77  Identities=22%  Similarity=0.439  Sum_probs=73.2

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++ +++..|+|+.|+|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4689999999999999999999999999999999999999999999999999999999995 8999999999999876

>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=99.82  E-value=2.6e-21  Score=131.17  Aligned_cols=85  Identities=21%  Similarity=0.351  Sum_probs=79.3

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .++++|||+|||..+++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|..|++.|||..|.|++|+|.||
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            35789999999999999999999999999999888887778999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      +++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.82  E-value=2.2e-20  Score=125.23  Aligned_cols=77  Identities=18%  Similarity=0.456  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||..+++++|+.+|++||.|.+|.|+.+      +|||||+|.+.++|..|+..|||..|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3578999999999999999999999999999999866      7899999999999999999999999999999999997


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      +++
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            765

>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=99.82  E-value=2.6e-20  Score=126.00  Aligned_cols=84  Identities=17%  Similarity=0.245  Sum_probs=76.7

Q ss_pred             CCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           84 QRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        84 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      ....+.++|||+|||+++++++|+.+|++||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..|.|+++.|
T Consensus        13 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v   91 (101)
T d1x5oa1          13 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   91 (101)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCcc
Confidence            34455688999999999999999999999999999998887 48899999999999999999999999999999999998


Q ss_pred             EEccc
Q 043064          164 DWAFS  168 (196)
Q Consensus       164 ~~a~~  168 (196)
                      .++.|
T Consensus        92 ~~~~P   96 (101)
T d1x5oa1          92 APTEP   96 (101)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87765

>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=99.82  E-value=5.6e-21  Score=122.42  Aligned_cols=75  Identities=20%  Similarity=0.441  Sum_probs=70.9

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +|||+|||+++|+++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++||+ .+++.|+|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999996 4778899999999865

>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=99.82  E-value=1.3e-20  Score=120.66  Aligned_cols=75  Identities=17%  Similarity=0.379  Sum_probs=71.9

Q ss_pred             EEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           91 IILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        91 ~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.+++||||+|.+.++|++|++ +|+..|+|++|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            49999999999999999999999999999999998899999999999999999999996 9999999999999986

>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=6.6e-20  Score=122.88  Aligned_cols=83  Identities=23%  Similarity=0.375  Sum_probs=74.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ...+.++|||+|||+++|+++|+++|++||.|..+.     .++.+++||||+|.+.++|+.|++.||+..|.|++|+|.
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~   86 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            344578999999999999999999999999886654     267789999999999999999999999999999999999


Q ss_pred             EcccCCCC
Q 043064          165 WAFSNGPS  172 (196)
Q Consensus       165 ~a~~~~~~  172 (196)
                      |+.++...
T Consensus        87 ~a~~k~~~   94 (96)
T d1fjca_          87 YTGEKGGT   94 (96)
T ss_dssp             ECSSSCCC
T ss_pred             EeCCCCCC
Confidence            99887654

>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=99.81  E-value=8.6e-20  Score=126.01  Aligned_cols=79  Identities=24%  Similarity=0.427  Sum_probs=73.0

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      .+++|||+|||..+++++|.++|++||.|..|.+..   ++.++|||||+|.+.++|..||+.|||..|.|+.|.|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            467899999999999999999999999999998874   45668999999999999999999999999999999999986


Q ss_pred             cC
Q 043064          168 SN  169 (196)
Q Consensus       168 ~~  169 (196)
                      +.
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.81  E-value=7.1e-20  Score=120.29  Aligned_cols=77  Identities=21%  Similarity=0.387  Sum_probs=71.6

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+++++|+.+|++||.|.+|.+..+      ++||||+|.+.++|..|+..|||..|.|+.|+|.||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3467999999999999999999999999999998765      6899999999999999999999999999999999997


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      +..
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            654

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.2e-19  Score=121.97  Aligned_cols=83  Identities=17%  Similarity=0.308  Sum_probs=72.9

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      .+.++|||+|||+.+|+++|+++|++|| |..+.++.+. .++.++|||||+|.+.++|++|+ .||+..|.|+.|+|.|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            3568999999999999999999999998 7777776554 46889999999999999998777 5999999999999999


Q ss_pred             cccCCC
Q 043064          166 AFSNGP  171 (196)
Q Consensus       166 a~~~~~  171 (196)
                      |.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            977654

>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=99.81  E-value=9.2e-20  Score=118.95  Aligned_cols=77  Identities=21%  Similarity=0.345  Sum_probs=70.1

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCcEeEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL-LTQTLTVD  164 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l-~g~~l~v~  164 (196)
                      ..++++|||+|||..+++++|..+|+.||.|..|.++.++     +|||||+|.+.++|..|+..|||..| +|+.|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            3457899999999999999999999999999999987553     68999999999999999999999988 57899999


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            996

>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=6.1e-20  Score=118.70  Aligned_cols=76  Identities=25%  Similarity=0.428  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..+++|||+||+  +|+++|+++|++||.|.+|.+..+      ++||||+|.+.++|..|+..|||..|.|++|+|.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            356899999996  899999999999999999998754      679999999999999999999999999999999999


Q ss_pred             ccCC
Q 043064          167 FSNG  170 (196)
Q Consensus       167 ~~~~  170 (196)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8765

>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=99.81  E-value=4.2e-21  Score=127.55  Aligned_cols=82  Identities=13%  Similarity=0.266  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+++++|+++|++||.|..+.|+.+ .+|+++|||||+|.+.++|++||+ ||+..|+|+.|+|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            445678999999999999999999999999998888655 589999999999999999999996 999999999999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      |+++
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9764

>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=99.81  E-value=2e-19  Score=120.76  Aligned_cols=81  Identities=27%  Similarity=0.369  Sum_probs=73.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCC--cEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLT--QTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g--~~l~  162 (196)
                      +..+.++|||+|||+++++++|+++|++||.|..+.+..+      ++||||+|.+.++|+.|++.||+..|.|  ++|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEE
Confidence            4556789999999999999999999999999999998754      6799999999999999999999999976  5899


Q ss_pred             EEEcccCCC
Q 043064          163 VDWAFSNGP  171 (196)
Q Consensus       163 v~~a~~~~~  171 (196)
                      |.||++.+.
T Consensus        87 v~~ak~~~~   95 (97)
T d1whya_          87 VDFAKSGPS   95 (97)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999987654

>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=99.80  E-value=1.6e-19  Score=118.57  Aligned_cols=78  Identities=21%  Similarity=0.232  Sum_probs=70.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+++++++|+.+|++||.|..+.+...      +|||||+|.+.++|..|+..|||..|.|+.|+|.||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~------rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc------cEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            3578999999999999999999999999888776543      7899999999999999999999999999999999998


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      |...
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.80  E-value=3.2e-20  Score=120.32  Aligned_cols=76  Identities=25%  Similarity=0.396  Sum_probs=68.8

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCc-eeCCcEeEEEEccc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGG-ELLTQTLTVDWAFS  168 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~-~l~g~~l~v~~a~~  168 (196)
                      ++|||+|||+++|+++|+++|++||.|..+.+...      +|||||+|.+.++|+.|++.|||. .|.|++|+|.||.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            46999999999999999999999999887766554      789999999999999999999986 69999999999988


Q ss_pred             CCC
Q 043064          169 NGP  171 (196)
Q Consensus       169 ~~~  171 (196)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            664

>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=1.8e-19  Score=133.88  Aligned_cols=123  Identities=21%  Similarity=0.363  Sum_probs=97.3

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhcccC-CC-----------CCCCCCCCCCCCCEEEEcCCCccCcHHHHHHhhccC
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFESL-GT-----------DGGPGPQRSIEGWIILVTGVHEEAQEDDLQNVFGEY  113 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~-~~-----------~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~  113 (196)
                      ..++++|++|+.|.+...+.. +....... ..           ............++|||+|||+.+|+++|+++|+.|
T Consensus        43 ~~~~~~g~afv~f~~~~~a~~-a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~  121 (183)
T d1u1qa_          43 NTKRSRGFGFVTYATVEEVDA-AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY  121 (183)
T ss_dssp             TTCCEEEEEEEEESSHHHHHH-HHHTCSCEETTEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGG
T ss_pred             cCCCccCceecccCCHHHHHH-HHHhcCCcccccchhhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccC
Confidence            466889999999995444433 32222111 00           001122334557899999999999999999999999


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064          114 GEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       114 G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      |.|..+.++.+..++.++|||||+|.+.++|.+||+ +++..|.|+.|+|.+|.|+.
T Consensus       122 G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~  177 (183)
T d1u1qa_         122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQ  177 (183)
T ss_dssp             SCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHH
T ss_pred             CceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCcc
Confidence            999999999998899999999999999999999996 78899999999999997753

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.8e-20  Score=123.48  Aligned_cols=75  Identities=13%  Similarity=0.221  Sum_probs=68.8

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccC
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSN  169 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~  169 (196)
                      ++|||+|||+++++++|+++|++||.|..+.++.       .|||||+|.+.++|++||..||+..|.|+.|+|.++.++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            3699999999999999999999999999998864       379999999999999999999999999999999998765


Q ss_pred             CC
Q 043064          170 GP  171 (196)
Q Consensus       170 ~~  171 (196)
                      ..
T Consensus        74 ~~   75 (87)
T d3begb1          74 VD   75 (87)
T ss_dssp             EC
T ss_pred             cC
Confidence            43

>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=99.80  E-value=2e-19  Score=123.15  Aligned_cols=77  Identities=21%  Similarity=0.425  Sum_probs=70.7

Q ss_pred             CCEEEEcCCCc-cCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           89 GWIILVTGVHE-EAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        89 ~~~l~V~nLp~-~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +++|||+||++ .+|+++|+++|+.||.|..|.|+.++     +|||||+|.+.++|.+|++.|||..|.|+.|+|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999965 59999999999999999999998775     7899999999999999999999999999999999987


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.80  E-value=2.6e-19  Score=120.31  Aligned_cols=83  Identities=17%  Similarity=0.316  Sum_probs=74.4

Q ss_pred             CCCCCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           82 GPQRSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        82 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      +|+......+|||+|||+.+++++|+++|++||.|..+.|..       +|||||+|.+.++|++||+.||+..|.|+.|
T Consensus         8 gp~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i   80 (98)
T d1wg4a_           8 GPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEG   80 (98)
T ss_dssp             CCCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTS
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            344455678899999999999999999999999999998863       5799999999999999999999999999999


Q ss_pred             EEEEcccCCC
Q 043064          162 TVDWAFSNGP  171 (196)
Q Consensus       162 ~v~~a~~~~~  171 (196)
                      +|.|++++..
T Consensus        81 ~v~~~~~~~~   90 (98)
T d1wg4a_          81 ETSYIRVYPE   90 (98)
T ss_dssp             CEEEEEEECC
T ss_pred             EEEEEecCCC
Confidence            9999977653

>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=99.80  E-value=1.4e-19  Score=121.21  Aligned_cols=83  Identities=17%  Similarity=0.288  Sum_probs=73.9

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCC-eeEEEEeecC-CCCCcceEEEEEecCHHHHHHHHHHhCC--ceeCCcEeEEEE
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGE-IRNLHLNLDR-RTGFVKGYALIEYENFEEAQNAITAMNG--GELLTQTLTVDW  165 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~-i~~v~i~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~--~~l~g~~l~v~~  165 (196)
                      ++|||+|||..+++++|+++|++||+ |..+.|+.+. .+++++|||||+|.+.++|..|++.|++  ..+.|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            67999999999999999999999996 8999988775 4688999999999999999999999864  456899999999


Q ss_pred             cccCCCC
Q 043064          166 AFSNGPS  172 (196)
Q Consensus       166 a~~~~~~  172 (196)
                      |.|+...
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9886654

>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=99.79  E-value=5.8e-19  Score=118.60  Aligned_cols=75  Identities=21%  Similarity=0.425  Sum_probs=68.0

Q ss_pred             CCCCEEEEcCCC-ccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           87 IEGWIILVTGVH-EEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        87 ~~~~~l~V~nLp-~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ...++|||+||| ..+++.+|+++|++||.|..|.|.        +|||||+|.+.++|++||+.|||..|.|+.|+|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999997 468899999999999999999883        78999999999999999999999999999999999


Q ss_pred             cccC
Q 043064          166 AFSN  169 (196)
Q Consensus       166 a~~~  169 (196)
                      +.+.
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9654

>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=99.79  E-value=1.9e-19  Score=123.63  Aligned_cols=78  Identities=18%  Similarity=0.236  Sum_probs=71.4

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+.+++++|+++|++||.|..|.|..      .+|||||+|.+.++|.+||+.|||..|.|++|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            457899999999999999999999999999998853      36899999999999999999999999999999999997


Q ss_pred             cCCC
Q 043064          168 SNGP  171 (196)
Q Consensus       168 ~~~~  171 (196)
                      ....
T Consensus        83 ~~~~   86 (111)
T d1whxa_          83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            6553

>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=99.79  E-value=5e-19  Score=115.88  Aligned_cols=77  Identities=16%  Similarity=0.304  Sum_probs=72.2

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      .++|||+|||.++|+++|+.+|+.||+|..|.|+.+. ++.++|||||+|.+.++|++||+ +++..+.|+.|.|.|..
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            5689999999999999999999999999999998874 89999999999999999999995 79999999999999874

>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=99.79  E-value=1.5e-19  Score=119.42  Aligned_cols=78  Identities=21%  Similarity=0.350  Sum_probs=70.1

Q ss_pred             CCCCEEEEcCCCccCcHHHH---HHhhccCCCeeEEEEeecCCCCC---cceEEEEEecCHHHHHHHHHHhCCceeCCcE
Q 043064           87 IEGWIILVTGVHEEAQEDDL---QNVFGEYGEIRNLHLNLDRRTGF---VKGYALIEYENFEEAQNAITAMNGGELLTQT  160 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L---~~~F~~~G~i~~v~i~~~~~~g~---~~g~afv~f~~~~~a~~al~~l~~~~l~g~~  160 (196)
                      ...++|||+|||+.+++++|   .++|++||.|..|.++.++.++.   .+|||||+|.+.++|.+|++.|||..|.|++
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34567999999999999999   67899999999999998876654   4589999999999999999999999999999


Q ss_pred             eEEE
Q 043064          161 LTVD  164 (196)
Q Consensus       161 l~v~  164 (196)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=99.79  E-value=1.2e-19  Score=120.37  Aligned_cols=80  Identities=19%  Similarity=0.463  Sum_probs=72.0

Q ss_pred             CCCEEEEcCCCccCcHHHHHH----hhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEE
Q 043064           88 EGWIILVTGVHEEAQEDDLQN----VFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTV  163 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~----~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v  163 (196)
                      |+++|||+|||+.+++++|++    +|++||+|.+|.+..   ++.++|||||+|.+.++|..|+..||+..|.|+.|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            568999999999999988864    689999999988753   5667899999999999999999999999999999999


Q ss_pred             EEcccCC
Q 043064          164 DWAFSNG  170 (196)
Q Consensus       164 ~~a~~~~  170 (196)
                      .||+++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998765

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.2e-19  Score=119.77  Aligned_cols=78  Identities=14%  Similarity=0.248  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ...++|||+|||+.+|+++|+++|++||.|..|.+...     +++||||+|.+.++|+.||.  +++.|.|++|.|.||
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            35678999999999999999999999999999876533     47899999999999999984  788999999999999


Q ss_pred             ccCCC
Q 043064          167 FSNGP  171 (196)
Q Consensus       167 ~~~~~  171 (196)
                      .++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>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=99.78  E-value=4.6e-19  Score=116.81  Aligned_cols=78  Identities=21%  Similarity=0.276  Sum_probs=69.4

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee-CCcEeEEEEc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL-LTQTLTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l-~g~~l~v~~a  166 (196)
                      ++++|||+|||+.+++++|+++|++||.|..+.+..    ++.++||||+|.+.++|..|+..|||..| +|+.|+|.|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            467899999999999999999999999998876653    33478999999999999999999999988 5899999999


Q ss_pred             ccC
Q 043064          167 FSN  169 (196)
Q Consensus       167 ~~~  169 (196)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=3.1e-19  Score=117.15  Aligned_cols=78  Identities=19%  Similarity=0.228  Sum_probs=70.1

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .++|||+|||+++++++|+++|+.||.+....++....++.++|+|||+|.+.++|++|++.||+..|+|++|+|.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            567999999999999999999999999876433344468999999999999999999999999999999999999875

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=9.4e-19  Score=118.42  Aligned_cols=84  Identities=21%  Similarity=0.353  Sum_probs=74.3

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ....+++|||+|||+++|+++|+++|..|| +..+.++.+. ++..+|||||+|.+.++|++|++ +|+..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            455678999999999999999999999997 4577777774 78899999999999999999985 89999999999999


Q ss_pred             EcccCCC
Q 043064          165 WAFSNGP  171 (196)
Q Consensus       165 ~a~~~~~  171 (196)
                      ++.+.+.
T Consensus        88 ~s~~~~~   94 (102)
T d1weza_          88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            9876653

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=9e-20  Score=115.77  Aligned_cols=71  Identities=25%  Similarity=0.485  Sum_probs=68.1

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeE
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLT  162 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~  162 (196)
                      |||+|||+++|+++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|+..|||..|.|+.|+
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            79999999999999999999999999999999988999999999999999999999999999999998764

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.1e-18  Score=115.02  Aligned_cols=76  Identities=20%  Similarity=0.254  Sum_probs=66.0

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ..++|||+|||+++++++|+++|.+|| +..+.+.      ..++||||+|.+.++|++|+..||+..|.|+.|+|.|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee------ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            356799999999999999999999999 3333332      347899999999999999999999999999999999996


Q ss_pred             cCC
Q 043064          168 SNG  170 (196)
Q Consensus       168 ~~~  170 (196)
                      ++.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>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=99.77  E-value=4.6e-18  Score=115.37  Aligned_cols=84  Identities=11%  Similarity=0.099  Sum_probs=75.1

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      .....+|||+|||+++|+++|+++|..+|.|..+.++....+++++|||||+|.+.++|++|++ +|+..|+|+.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3455679999999999999999999999999886666666789999999999999999999995 899999999999999


Q ss_pred             cccCC
Q 043064          166 AFSNG  170 (196)
Q Consensus       166 a~~~~  170 (196)
                      +.+..
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            97654

>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=99.76  E-value=2.2e-18  Score=110.13  Aligned_cols=72  Identities=21%  Similarity=0.411  Sum_probs=64.2

Q ss_pred             EEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcccCC
Q 043064           92 ILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus        92 l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~~~  170 (196)
                      |||+|||+++++++|+++|++|| +..+.+.      +++|||||+|.+.++|++|+..|||..+.|++|+|+|+.+.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 5554443      348999999999999999999999999999999999996543

>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=99.76  E-value=5e-18  Score=111.72  Aligned_cols=80  Identities=14%  Similarity=0.188  Sum_probs=71.3

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM--NGGELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~l~g~~l~  162 (196)
                      ...++++|||+|||+.+++++|.++|++||.|..+.+..+      +++|||+|.+.++|+.|+..+  ++..+.|++|+
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3557889999999999999999999999999999988755      579999999999999999865  57789999999


Q ss_pred             EEEcccCC
Q 043064          163 VDWAFSNG  170 (196)
Q Consensus       163 v~~a~~~~  170 (196)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997553

>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=99.75  E-value=1.3e-17  Score=113.05  Aligned_cols=80  Identities=23%  Similarity=0.276  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCcEeE
Q 043064           85 RSIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM--NGGELLTQTLT  162 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~l~g~~l~  162 (196)
                      ...++.+|||+|||+.+++++|..+|++||.|..+.+..+      +++|||+|.+.++|+.|+..|  ++..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            4456889999999999999999999999999999988754      689999999999999999977  55678999999


Q ss_pred             EEEcccCC
Q 043064          163 VDWAFSNG  170 (196)
Q Consensus       163 v~~a~~~~  170 (196)
                      |.|++.+.
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99997654

>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=99.75  E-value=3.7e-18  Score=109.06  Aligned_cols=74  Identities=16%  Similarity=0.228  Sum_probs=67.3

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ++|||+|||+.+++++|+++|+.||.|..+.++.++..  .++||||+|.+.++|.+|+ .+|+..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999887533  3579999999999999999 58999999999999865

>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=99.75  E-value=3.4e-18  Score=116.77  Aligned_cols=80  Identities=20%  Similarity=0.271  Sum_probs=71.7

Q ss_pred             CCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee--CCcEeEEE
Q 043064           87 IEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL--LTQTLTVD  164 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l--~g~~l~v~  164 (196)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.+..++    .+|+|||+|.+.++|+.|+..|||..|  .++.|+|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            456789999999999999999999999999999988663    479999999999999999999999998  57889999


Q ss_pred             EcccCC
Q 043064          165 WAFSNG  170 (196)
Q Consensus       165 ~a~~~~  170 (196)
                      |++++.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            987654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.6e-18  Score=116.39  Aligned_cols=80  Identities=15%  Similarity=0.077  Sum_probs=70.8

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      ...+|||+|||+++|+++|+++|..||.|..+.++....+|.++|||||+|.+.++|++||. ||+..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            34679999999999999999999999998764444444689999999999999999999995 89999999999999875


Q ss_pred             c
Q 043064          168 S  168 (196)
Q Consensus       168 ~  168 (196)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.72  E-value=2e-17  Score=111.20  Aligned_cols=80  Identities=20%  Similarity=0.219  Sum_probs=70.9

Q ss_pred             CCCCCCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHH--HhCCceeCCcEe
Q 043064           85 RSIEGWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAIT--AMNGGELLTQTL  161 (196)
Q Consensus        85 ~~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~--~l~~~~l~g~~l  161 (196)
                      ...++++|||+|||.. +|+++|..+|++||.|..+.++.+      +|+|||+|.+.++|..|++  .+++..|.|+.|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l   87 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   87 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEE
Confidence            3456789999999985 899999999999999999998765      6899999999999999997  578889999999


Q ss_pred             EEEEcccCC
Q 043064          162 TVDWAFSNG  170 (196)
Q Consensus       162 ~v~~a~~~~  170 (196)
                      +|.|++.+.
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEcCCcc
Confidence            999996543

>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=99.71  E-value=3.1e-17  Score=108.11  Aligned_cols=78  Identities=15%  Similarity=0.153  Sum_probs=69.5

Q ss_pred             CCCCCEEEEcCCCcc-CcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh--CCceeCCcEeE
Q 043064           86 SIEGWIILVTGVHEE-AQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM--NGGELLTQTLT  162 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~-~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~l~g~~l~  162 (196)
                      ..++++|||+|||.. +|+++|.++|++||.|..|.++.+      +++|||+|.+.++|..|+..|  ++..+.|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456788999999986 899999999999999999999765      468999999999999999965  67789999999


Q ss_pred             EEEcccC
Q 043064          163 VDWAFSN  169 (196)
Q Consensus       163 v~~a~~~  169 (196)
                      |.||++.
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999754

>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=99.71  E-value=1e-17  Score=115.08  Aligned_cols=82  Identities=13%  Similarity=0.181  Sum_probs=73.0

Q ss_pred             CCCCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEE
Q 043064           86 SIEGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDW  165 (196)
Q Consensus        86 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~  165 (196)
                      ....++|||+|||+.+|+++|.++|+.||.+..+.++....+|.++|||||+|.+.++|++|++ ||+..|+|+.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3457789999999999999999999999998776555556799999999999999999999995 899999999999988


Q ss_pred             ccc
Q 043064          166 AFS  168 (196)
Q Consensus       166 a~~  168 (196)
                      +.+
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            754

>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=99.71  E-value=1.7e-17  Score=112.42  Aligned_cols=80  Identities=11%  Similarity=0.125  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCccC-c----HHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEe
Q 043064           87 IEGWIILVTGVHEEA-Q----EDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTL  161 (196)
Q Consensus        87 ~~~~~l~V~nLp~~~-t----e~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l  161 (196)
                      ....+|||+||+..+ +    .++|+.+|++||.|..+.++..      +++|||+|.+.++|.+|+..|||..|.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            346789999999976 3    3679999999999999988754      6799999999999999999999999999999


Q ss_pred             EEEEcccCCCC
Q 043064          162 TVDWAFSNGPS  172 (196)
Q Consensus       162 ~v~~a~~~~~~  172 (196)
                      +|.||++....
T Consensus        77 ~v~~a~~~~~~   87 (104)
T d1weya_          77 KLYFAQTLHIG   87 (104)
T ss_dssp             EEECCCCSSCC
T ss_pred             EEeecccCCCC
Confidence            99999776643

>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=99.65  E-value=1.7e-18  Score=114.50  Aligned_cols=77  Identities=17%  Similarity=0.277  Sum_probs=66.7

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEe-----ecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEE
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLN-----LDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVD  164 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~-----~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~  164 (196)
                      ++|||+|||..+|+++|+++|++||.|..+.+.     .+..+++++|||||+|.+.++|+.|+. |||..|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            579999999999999999999999987665442     344567889999999999999999985 99999999999997


Q ss_pred             Ecc
Q 043064          165 WAF  167 (196)
Q Consensus       165 ~a~  167 (196)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.59  E-value=1.6e-16  Score=107.55  Aligned_cols=76  Identities=14%  Similarity=0.232  Sum_probs=71.0

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      ..++|.+++..++++.|+++|++||+|.+|.|+.+ .++.++|+|||+|.+.++|.+|+..|||..++|++|.|.|.
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34788889999999999999999999999999877 58999999999999999999999999999999999999985

>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=99.58  E-value=3.1e-15  Score=102.58  Aligned_cols=74  Identities=19%  Similarity=0.336  Sum_probs=65.2

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCH-HHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENF-EEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~-~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      ..+||+|||+.+|+++|+++|++||+|..|.|+.+      +|||||.|.+. ++|..|+..|++..|.++.+.|.|+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34599999999999999999999999999999855      68999999985 789999999999998888888877655


Q ss_pred             C
Q 043064          169 N  169 (196)
Q Consensus       169 ~  169 (196)
                      .
T Consensus        86 ~   86 (113)
T d1owxa_          86 E   86 (113)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.56  E-value=3.8e-15  Score=100.14  Aligned_cols=65  Identities=23%  Similarity=0.384  Sum_probs=58.5

Q ss_pred             CCCCCEEEEcC--CCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCcee
Q 043064           86 SIEGWIILVTG--VHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGEL  156 (196)
Q Consensus        86 ~~~~~~l~V~n--Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l  156 (196)
                      ..+..+|||.|  ||..+|+++|+.+|++||.|..|.++.+      ++||||+|.+.++|..|+..|||..|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            44567888855  9999999999999999999999988765      57999999999999999999999986

>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=99.56  E-value=1.3e-14  Score=97.14  Aligned_cols=84  Identities=20%  Similarity=0.289  Sum_probs=71.7

Q ss_pred             CCCCCCCCEEEEcCC--CccC---------cHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHh
Q 043064           83 PQRSIEGWIILVTGV--HEEA---------QEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAM  151 (196)
Q Consensus        83 ~~~~~~~~~l~V~nL--p~~~---------te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l  151 (196)
                      |.+...+++|+|.||  |.++         .+++|+..|++||.|..|.+..+    ..+|++||.|.+.++|.+|+..|
T Consensus         2 p~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~l   77 (99)
T d2dita1           2 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTL   77 (99)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHh
Confidence            556677899999999  5432         23688999999999999987643    35799999999999999999999


Q ss_pred             CCceeCCcEeEEEEcccCC
Q 043064          152 NGGELLTQTLTVDWAFSNG  170 (196)
Q Consensus       152 ~~~~l~g~~l~v~~a~~~~  170 (196)
                      ||..++|++|+|.|+.++.
T Consensus        78 ng~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          78 DGRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TTCEETTEECEEEECCSCC
T ss_pred             CCcEECCEEEEEEEeCCcC
Confidence            9999999999999987664

>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=99.52  E-value=5.5e-14  Score=103.63  Aligned_cols=81  Identities=17%  Similarity=0.317  Sum_probs=73.0

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEccc
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAFS  168 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~~  168 (196)
                      .++|||+|||+.+|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|..|+. +++..+.++.+.+.+..+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3689999999999999999999999999999999998899999999999999999999996 466778888888887655


Q ss_pred             CC
Q 043064          169 NG  170 (196)
Q Consensus       169 ~~  170 (196)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            44

>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=99.48  E-value=5.1e-14  Score=90.62  Aligned_cols=73  Identities=18%  Similarity=0.238  Sum_probs=61.2

Q ss_pred             CCCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcE-eEEEEc
Q 043064           88 EGWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQT-LTVDWA  166 (196)
Q Consensus        88 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~-l~v~~a  166 (196)
                      +.+.|+|.++|++++++.| .+|++||.|.++.+..+      ++|+||.|.+.++|++||+ +||..|+|+. |.|...
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3567999999999987665 57999999999987543      6899999999999999995 9999999974 567765


Q ss_pred             cc
Q 043064          167 FS  168 (196)
Q Consensus       167 ~~  168 (196)
                      ..
T Consensus        75 ~~   76 (81)
T d1wwha1          75 ID   76 (81)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=2.6e-13  Score=91.44  Aligned_cols=82  Identities=12%  Similarity=0.240  Sum_probs=68.9

Q ss_pred             CCCCEEEEcCC--CccC--------cHHHHHHhhccCCCeeEEEEeecCCCC--CcceEEEEEecCHHHHHHHHHHhCCc
Q 043064           87 IEGWIILVTGV--HEEA--------QEDDLQNVFGEYGEIRNLHLNLDRRTG--FVKGYALIEYENFEEAQNAITAMNGG  154 (196)
Q Consensus        87 ~~~~~l~V~nL--p~~~--------te~~L~~~F~~~G~i~~v~i~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~  154 (196)
                      .|++.|+|.||  |..+        ..++|++.|++||.|.+|.|+++..+.  ...|++||.|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35788999999  4433        235789999999999999998765442  34689999999999999999999999


Q ss_pred             eeCCcEeEEEEccc
Q 043064          155 ELLTQTLTVDWAFS  168 (196)
Q Consensus       155 ~l~g~~l~v~~a~~  168 (196)
                      .++|+.|.|.|+.+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999854

>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=97.74  E-value=0.00011  Score=43.99  Aligned_cols=61  Identities=20%  Similarity=0.296  Sum_probs=52.0

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEcc
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWAF  167 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a~  167 (196)
                      +.|...|.+++.|.++.+.... .+.  -.|-|...+..+|.-|+..|+...|++++|.|.|+.
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 QLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            5567788999999999886542 333  358999999999999999999999999999999984

>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=97.74  E-value=0.00013  Score=46.43  Aligned_cols=77  Identities=14%  Similarity=0.174  Sum_probs=60.7

Q ss_pred             CEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCC--cceEEEEEecCHHHHHHHHHHhCCceeCC-----cEeE
Q 043064           90 WIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGF--VKGYALIEYENFEEAQNAITAMNGGELLT-----QTLT  162 (196)
Q Consensus        90 ~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~--~~g~afv~f~~~~~a~~al~~l~~~~l~g-----~~l~  162 (196)
                      ++|.|++||+.+|++++.+.++..|.+........+.+-+  .-.-|||.|.+.++...-.+.++|+.+..     .+-.
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            5799999999999999999999988887776665543322  33569999999999999999999998632     2445


Q ss_pred             EEEc
Q 043064          163 VDWA  166 (196)
Q Consensus       163 v~~a  166 (196)
                      |+||
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6666

>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=97.38  E-value=0.00019  Score=45.16  Aligned_cols=54  Identities=17%  Similarity=0.377  Sum_probs=47.5

Q ss_pred             HHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhCCceeCCcEeEEEEc
Q 043064          104 DDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMNGGELLTQTLTVDWA  166 (196)
Q Consensus       104 ~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~l~g~~l~v~~a  166 (196)
                      .+|.+.|..||+|.-++++.+        ..+|+|.+-+.|.+|+. +++..+.|+.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            577888899999999999855        58999999999999995 8999999999999754

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.05  E-value=0.043  Score=34.63  Aligned_cols=56  Identities=21%  Similarity=0.240  Sum_probs=45.1

Q ss_pred             CCEEEEcCCCccCcHHHHHHhhccCCCeeEEEEeecCCCCCcceEEEEEecCHHHHHHHHHHhC
Q 043064           89 GWIILVTGVHEEAQEDDLQNVFGEYGEIRNLHLNLDRRTGFVKGYALIEYENFEEAQNAITAMN  152 (196)
Q Consensus        89 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  152 (196)
                      ...||.-..|..+...+|..+|+.||.|.- .++-+       --|||...+.+.|..++..+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIdd-------TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEE-EEecC-------ceEEEEecCHHHHHHHHHHhc
Confidence            345888899999999999999999998754 34433       159999999999999987654

>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=90.16  E-value=0.083  Score=31.56  Aligned_cols=35  Identities=14%  Similarity=0.180  Sum_probs=24.0

Q ss_pred             CCCCCCCcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           28 SSSPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        28 ~~~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      ..++...+..++++    .+++++||||+.|.+.+.+.+
T Consensus        23 ~~G~i~~v~i~~d~----~tg~~kG~aFV~f~~~~~a~~   57 (77)
T d1uawa_          23 QFGEVKECLVMRDP----LTKRSRGFGFVTFMDQAGVDK   57 (77)
T ss_dssp             TTSCCCCEEEECCC----CSSSCSSEEEECCCCTTHHHH
T ss_pred             HhCCcceeeeeccc----CCCCccceEEEEECCHHHHHH
Confidence            33455566666766    456899999999996555444

>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=88.78  E-value=0.1  Score=32.26  Aligned_cols=43  Identities=21%  Similarity=0.205  Sum_probs=27.2

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCC
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTD   78 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~   78 (196)
                      ++..+..++++    .+++++||||+.|. ....+..+...++.....
T Consensus        35 ~v~~v~~~~d~----~tg~~kg~afV~f~-~~~~A~~Ai~~l~g~~~~   77 (93)
T d1x5ua1          35 PVVNTHMPKDR----VTGQHQGYGFVEFL-SEEDADYAIKIMDMIKLY   77 (93)
T ss_dssp             CEEEEECCBCS----SSCSBCSCEEEEES-SHHHHHHHHHHSSSCBCS
T ss_pred             Cccccceeecc----cccccccceEEEEC-CHHHHHHHHHHcCCCEEC
Confidence            33445555555    45689999999999 455555555566655443

>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=88.69  E-value=0.097  Score=31.80  Aligned_cols=45  Identities=20%  Similarity=0.207  Sum_probs=27.8

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDG   79 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~   79 (196)
                      +++..+..++++    .+++++||||+.|.+...+.. +...+++....+
T Consensus        26 G~v~~v~i~~d~----~tg~~rg~aFV~f~~~~~A~~-a~~~l~~~~l~g   70 (85)
T d2u2fa_          26 GPLKAFNLVKDS----ATGLSKGYAFCEYVDINVTDQ-AIAGLNGMQLGD   70 (85)
T ss_dssp             SCEEEEEEECCC----SSSCCCCEEEEEESSSHHHHH-HHHTSSSCCCSS
T ss_pred             CccceEEeeccc----cccccceeEEEEECCHHHHHH-HHHHhCCCEECC
Confidence            444455556655    445889999999995444444 445555554433

>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=88.22  E-value=0.14  Score=31.20  Aligned_cols=41  Identities=17%  Similarity=0.047  Sum_probs=26.4

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      +++..+..+++.    .+++++||||+.|.+.. .+..+...+++.
T Consensus        30 G~i~~v~i~~d~----~~~~~kg~afV~f~~~~-~A~~ai~~l~~~   70 (89)
T d2cqba1          30 GDITDIQIPLDY----ETEKHRGFAFVEFELAE-DAAAAIDNMNES   70 (89)
T ss_dssp             SCCCCEECCCCS----SSCCCSSEEEECCSSHH-HHHHHHHHHTTE
T ss_pred             CeEEeccccccc----ccccccceeEEEECCHH-HHHHHHHHcCCC
Confidence            455666666665    44588999999999544 444444445443

>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=87.79  E-value=0.11  Score=31.59  Aligned_cols=44  Identities=14%  Similarity=0.124  Sum_probs=27.5

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCC
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDG   79 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~   79 (196)
                      ++..+..+++.    .+++++||||+.|. ...++..+...+++....+
T Consensus        32 ~v~~v~i~~d~----~~g~~kg~afV~f~-~~~~a~~Ai~~lng~~~~G   75 (85)
T d1fxla2          32 RIITSRILVDQ----VTGVSRGVGFIRFD-KRIEAEEAIKGLNGQKPSG   75 (85)
T ss_dssp             CEEEEEEEECT----TTCCEEEEEEEEES-SHHHHHHHHHHHTTCCCTT
T ss_pred             Ccccccccccc----ccccCCCeeEEEEc-CHHHHHHHHHHhCCCEeCC
Confidence            33444555554    45689999999999 4555555555666655443

>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=87.76  E-value=0.28  Score=29.75  Aligned_cols=41  Identities=15%  Similarity=0.176  Sum_probs=25.0

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCC
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTD   78 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~   78 (196)
                      ..+..++..    ..++++|||||.|. ....+..+...+++....
T Consensus        33 ~~~~~~~~~----~~~~~~g~afV~f~-~~~~a~~Ai~~l~~~~~~   73 (90)
T d1x5sa1          33 SEVVVVKDR----ETQRSRGFGFVTFE-NIDDAKDAMMAMNGKSVD   73 (90)
T ss_dssp             CEEEECCCS----SSCSCCSEEEEECS-SHHHHHHHHHHHTTCCTT
T ss_pred             cceeecccc----ccccccceEEEEEC-CHHHHHHHHHHcCCCEEC
Confidence            344444444    45678999999999 455555454555554443

>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=86.72  E-value=0.15  Score=30.73  Aligned_cols=43  Identities=9%  Similarity=0.117  Sum_probs=26.9

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGT   77 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~   77 (196)
                      +++..+..+++.    .+++++||||+.|. ...++..+...++....
T Consensus        31 G~i~~~~~~~d~----~~g~~~g~afV~f~-~~~~A~~Ai~~l~g~~~   73 (85)
T d1b7fa2          31 GSIVQKNILRDK----LTGRPRGVAFVRYN-KREEAQEAISALNNVIP   73 (85)
T ss_dssp             SCEEEEEEEECT----TTCCEEEEEEEEES-SHHHHHHHHHHHTTCCC
T ss_pred             CCEeeeeeeccc----ccccCceeEEEEEC-CHHHHHHHHHHHCCCEe
Confidence            333445555554    45678999999999 45555555556655443

>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=86.23  E-value=0.13  Score=30.54  Aligned_cols=29  Identities=14%  Similarity=0.078  Sum_probs=20.0

Q ss_pred             CcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           34 PQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        34 ~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      .+..++++    .+++++||||+.|.+.+.+.+
T Consensus        28 ~v~i~~d~----~t~~~rG~~FV~f~~~~~a~~   56 (75)
T d1x0fa1          28 SIELPMDN----KTNKRRGFCFITFKEEEPVKK   56 (75)
T ss_dssp             EEECCCCT----TTCCTTCCEEEEESSSHHHHH
T ss_pred             cccccccc----cccccccEEEEEECCHHHHHH
Confidence            34444554    456899999999996665555

>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=85.78  E-value=0.081  Score=31.73  Aligned_cols=40  Identities=8%  Similarity=0.030  Sum_probs=25.5

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      ++..+..++++    .+++++|||||.|. ...++..+...+++.
T Consensus        26 ~i~~v~i~~d~----~tg~~~g~aFV~f~-~~~~a~~ai~~l~g~   65 (80)
T d1cvja1          26 PILSIRVCRDM----ITRRSLGYAYVNFQ-QPADAERALDTMNFD   65 (80)
T ss_dssp             CEEEEEEEECT----TTCCEEEEEEEEES-SHHHHHHHHTTSTTC
T ss_pred             CEeEEEEEecc----cccCCCCceEEEEC-CHHHHHHHHHHcCCC
Confidence            34456666655    45688999999999 455555454455443

>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=84.57  E-value=0.25  Score=30.90  Aligned_cols=42  Identities=26%  Similarity=0.275  Sum_probs=25.9

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLG   76 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~   76 (196)
                      +.+..+..+++.    .+++++|||||.|.+ ...+..+...++...
T Consensus        33 G~i~~v~i~~~~----~tg~~~g~afV~f~~-~~~a~~ai~~l~~~~   74 (104)
T d1p1ta_          33 GPVVSFRLVYDR----ETGKPKGYGFCEYQD-QETALSAMRNLNGRE   74 (104)
T ss_dssp             SCCSEEEEEEET----TTTEEEEEEEEECSC-HHHHHHHHHHSSSBS
T ss_pred             cccccccccccc----ceeccCCceEEEECC-HHHHHHHHHHcCCCE
Confidence            344555555555    345789999999994 444444445555443

>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=84.31  E-value=0.15  Score=31.78  Aligned_cols=38  Identities=18%  Similarity=0.047  Sum_probs=23.4

Q ss_pred             CCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhccc
Q 043064           32 RAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFES   74 (196)
Q Consensus        32 ~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~   74 (196)
                      +..+..+++.    .+++++|||||.|.+ ...+..+...++.
T Consensus        35 v~~v~i~~d~----~tg~~~g~afV~f~~-~~~a~~A~~~l~g   72 (99)
T d1whwa_          35 LSELHYPIDS----LTKKPKGFAFVTFMF-PEHAVKAYAEVDG   72 (99)
T ss_dssp             EEEEECCCCT----TTCCCCSEEEEEESS-HHHHHHHHHHTTT
T ss_pred             ceeeeecccc----cccccCcceEEEECC-HHHHHHHHHHcCC
Confidence            3344455554    456889999999994 4444444444544

>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=84.24  E-value=0.098  Score=30.52  Aligned_cols=45  Identities=16%  Similarity=0.214  Sum_probs=26.7

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccCCCCC
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESLGTDG   79 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~   79 (196)
                      +++.....++..    .+.+++|+||+.|.+ ..++..+...+++....+
T Consensus        23 G~v~~~~~~~~~----~~~~~~g~afV~f~~-~~~A~~Ai~~lng~~~~G   67 (72)
T d1x4ea1          23 GKIVSTKAILDK----TTNKCKGYGFVDFDS-PSAAQKAVTALKASGVQA   67 (72)
T ss_dssp             SCEEEEEEECCS----SSCSCCSEEEEEESC-HHHHHHHHHHHHHHTCCE
T ss_pred             cccccccccccc----ccccccceeEEEECC-HHHHHHHHHHhCCCEECC
Confidence            343444444444    456799999999994 444444555565554443

>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=82.89  E-value=0.33  Score=28.91  Aligned_cols=28  Identities=21%  Similarity=0.137  Sum_probs=18.5

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhccc
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFES   74 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~   74 (196)
                      .+++++|||||.|.+ ..++..+...++.
T Consensus        36 ~~g~~~g~afV~f~~-~~~a~~Ai~~~~g   63 (83)
T d1x5ta1          36 DTGNSKGYAFINFAS-FDASDAAIEAMNG   63 (83)
T ss_dssp             TTCSCCSEEEEEBSS-HHHHHHHHHTTTT
T ss_pred             cccccCceEEEEECC-HHHHHHHHHhCCC
Confidence            456789999999995 4444444444444

>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=82.75  E-value=0.33  Score=28.44  Aligned_cols=32  Identities=16%  Similarity=0.123  Sum_probs=20.4

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      +...+..+++.    .+++++||||+.|.+.+.+..
T Consensus        25 ~i~~~~i~~d~----~t~~~kg~afV~f~~~~~a~~   56 (75)
T d1hd0a_          25 EVVDCTLKLDP----ITGRSRGFGFVLFKESESVDK   56 (75)
T ss_dssp             CEEEEECCCBT----TTTBCCSEEEEEESSHHHHHH
T ss_pred             cccccccccCC----CCCCcCceEEEEECCHHHHHH
Confidence            33344445554    456899999999995544433

>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=82.51  E-value=0.24  Score=31.05  Aligned_cols=33  Identities=9%  Similarity=0.119  Sum_probs=22.1

Q ss_pred             CCCCCcccccccccCCCCCCCcCcccccCCCcHHHHH
Q 043064           30 SPRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        30 ~~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~   66 (196)
                      +.+..+..+++.    .+++++|||||.|.+.+.+..
T Consensus        43 G~V~~v~i~~d~----~tg~~kG~afV~F~~~e~a~~   75 (101)
T d2cq4a1          43 GKVRDVRIISDR----NSRRSKGIAYVEFCEIQSVPL   75 (101)
T ss_dssp             SCEEEEEECCSC----CSSSCCCCEEEEESCGGGHHH
T ss_pred             CeEEEEEeeecC----CCccccceEEEEECCHHHHHH
Confidence            444455555554    456899999999996555444

>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=82.19  E-value=0.67  Score=28.70  Aligned_cols=35  Identities=17%  Similarity=0.280  Sum_probs=24.6

Q ss_pred             CCCCcCcccccCCCcHHHHHHhhhhcccCCCCCCCC
Q 043064           47 PKKTKGRGFREEADSERHSRLADRNFESLGTDGGPG   82 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (196)
                      ..+++|||||.|.+ ..++..+...+++....+.+.
T Consensus        55 ~~~~~g~afV~f~~-~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          55 SGTSRGVGFARMES-TEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             SSCEEEEEEEEESC-HHHHHHHHHHHBTCCCCCCTT
T ss_pred             ccccccceeEEeCC-HHHHHHHHHHhCCCEECCcCC
Confidence            55789999999994 444555556777776666554

>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=81.88  E-value=0.26  Score=30.84  Aligned_cols=40  Identities=10%  Similarity=0.076  Sum_probs=24.9

Q ss_pred             CCCCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           31 PRAPQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        31 ~~~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      +...+..+.+.    .+++++|||||.|.+ ..++..+...+++.
T Consensus        44 ~i~~~~~~~~~----~~g~~kG~afV~f~~-~~~A~~Ai~~lng~   83 (102)
T d2cpza1          44 NVVSAKVFIDK----QTNLSKCFGFVSYDN-PVSAQAAIQSMNGF   83 (102)
T ss_dssp             CCSEEEEEECS----SSCSEEEEEEEECSS-HHHHHHHHHHHTTC
T ss_pred             cccccceeeec----ccCCCccceEEEeCC-HHHHHHHHHHhCCC
Confidence            33445555544    456889999999994 44445454555544

>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=81.32  E-value=0.44  Score=29.19  Aligned_cols=20  Identities=15%  Similarity=0.293  Sum_probs=14.8

Q ss_pred             CCCCcCcccccCCCcHHHHH
Q 043064           47 PKKTKGRGFREEADSERHSR   66 (196)
Q Consensus        47 ~~~~kG~gf~~~~~~~~~~~   66 (196)
                      +++++|||||.|.+.+.+..
T Consensus        47 ~g~~rg~afV~f~~~~~A~~   66 (94)
T d2cpha1          47 TGAHRGFGFVDFITKQDAKK   66 (94)
T ss_dssp             SCSSCSEEEEEESSHHHHHH
T ss_pred             CCCcccEEEEEECCHHHHHH
Confidence            45789999999995444444

>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=80.98  E-value=0.16  Score=30.91  Aligned_cols=38  Identities=11%  Similarity=0.016  Sum_probs=23.5

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      ..+..+++.    .+++++||||+.|.+ ...+..+...+++.
T Consensus        35 ~~v~i~~d~----~tg~~~g~afV~f~~-~~~A~~A~~~lng~   72 (88)
T d1rk8a_          35 KNIHLNLDR----RTGFSKGYALVEYET-HKQALAAKEALNGA   72 (88)
T ss_dssp             EEEEEEECT----TTSSEEEEEEEEESS-HHHHHHHHHHHTTC
T ss_pred             ccccccccc----cccccccceeEEECC-HHHHHHHHHHcCCC
Confidence            344445544    456889999999994 44444444455443

>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=80.70  E-value=0.19  Score=29.99  Aligned_cols=38  Identities=13%  Similarity=0.119  Sum_probs=23.6

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      ..+..+++.    .+++++||||+.|.+ ..++..+...+++.
T Consensus        30 ~~~~i~~~~----~~g~~~g~afV~f~~-~~~A~~ai~~lng~   67 (82)
T d1b7fa1          30 NTCRIMRDY----KTGYSYGYAFVDFTS-EMDSQRAIKVLNGI   67 (82)
T ss_dssp             EEEECCEET----TTTEECSEEEEEESS-HHHHHHHHHHHTTC
T ss_pred             ceeeeeeec----ccCCccccceEEECC-HHHHHHHHHHhCCC
Confidence            344444444    455789999999994 44445454555544

>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=80.57  E-value=0.16  Score=33.67  Aligned_cols=30  Identities=13%  Similarity=0.295  Sum_probs=19.7

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhcccCC
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFESLG   76 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~   76 (196)
                      .+++++|||||.|.+ ..++..+...++...
T Consensus        79 ~t~~~rg~afV~f~~-~~~A~~Ai~~lng~~  108 (139)
T d1u6fa1          79 ETRQSRGYGFVKFQS-GSSAQQAIAGLNGFN  108 (139)
T ss_dssp             TTTEEEEEEEEEESS-HHHHHHHHHHTTTEE
T ss_pred             ccccccceeeEEECC-HHHHHHHHHHhCCCE
Confidence            456789999999994 444444444555443

>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=80.52  E-value=0.45  Score=28.10  Aligned_cols=30  Identities=7%  Similarity=0.162  Sum_probs=16.6

Q ss_pred             CCCCCcCcccccCCCcHHHHHHhhhhcccCC
Q 043064           46 APKKTKGRGFREEADSERHSRLADRNFESLG   76 (196)
Q Consensus        46 ~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~~   76 (196)
                      ..++++||||+.|.+ ..++..+...+++..
T Consensus        38 ~~~~~~g~afV~f~~-~e~A~~Ai~~l~g~~   67 (81)
T d2ghpa1          38 RFNTSRRFAYIDVTS-KEDARYCVEKLNGLK   67 (81)
T ss_dssp             -----CCEEEEECSS-HHHHHHHHHHHTTCE
T ss_pred             ccccccceeEEEECC-HHHHHHHHHHhCCCE
Confidence            355789999999994 444444445555543

>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=80.44  E-value=0.14  Score=30.94  Aligned_cols=41  Identities=15%  Similarity=0.087  Sum_probs=23.3

Q ss_pred             CCcccccccccCCCCCCCcCcccccCCCcHHHHHHhhhhcccC
Q 043064           33 APQPKLKSAITGGAPKKTKGRGFREEADSERHSRLADRNFESL   75 (196)
Q Consensus        33 ~~~~~~r~~~~gg~~~~~kG~gf~~~~~~~~~~~~~~~~~~~~   75 (196)
                      ..+..+++.-+ +...+++|||||.|.+ ..++..+...+++.
T Consensus        26 ~~v~i~~~~~~-~~~~~~kG~afV~f~~-~~~A~~A~~~~~~~   66 (85)
T d2cpfa1          26 KSCTISKKKNK-AGVLLSMGFGFVEYKK-PEQAQKALKQLQGH   66 (85)
T ss_dssp             EEEEEEEEECT-TCCEEEEEEEEEEESS-HHHHHHHHHHSTTC
T ss_pred             cccceeccccc-ccccccceEEEEEECC-HHHHHHHHHHhCCC
Confidence            34444444422 2344679999999994 44444444455443