Citrus Sinensis ID: 025249

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-----
Protein Sequence
MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFGGVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRPSFDRY
Secondary Structure (PSIPRED)
cHHHccccccEEEEEcccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHccEEEEEEcccccccccEEEEcccHHHHHHHHHHHccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mqqclthnndLKIMlerdsgrprgfgfityaDRRAMDDAIREMHGREFGDRVIsvnkaqpkmggevsdhgyrgggyssggrgsygadrpggqddcfkcgrpghwardcpsavggrggaggsfssrsrfggvgvrgdylgggrdryiddrydggrygdrdrydskdskygsrdryvsdryppagdrlagdryggsdrypvngygkergyerdvgaragsdryasggparddgrgyrsraapydrpsrgdrpsfdry
Flexible Loop (DISEMBL)
mqqclthnndlkimlerdsgrprgFGFITYADRRAMDDAIREMHgrefgdrvisvnkaqpkmggevsdhgyrgggysSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGgsfssrsrfggvgvrgdylgggrdryiddrydggrygdrdrydskdskygsrdryvsdryppagdrlagdryggsdrypvngygkergyerdvgaragsdryasggparddgrgyrsraapydrpsrgdrpsfdry
Low Complexity Region (SEG)
MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHgyrgggyssggrgsygADRPGGQDDCFKCGRPGHWARDCPsavggrggaggsfssrsrfggvgvrgdylgggrdryiddrydggrygdrdrydSKDSKYGSRDRYVSDRYPPAGDRLAGDRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRPSFDRY
Disordered region (IsUnstruct)
**********************RGFGFITYADRRAMDDAI******************************************************CFKCGRPGHWARDCPSA***************RFGGVGVRGDYLGGGRDRYIDDRYDG*******************************************************************************************************
Disordered Region (DISOPRED)
MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS*********************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSA*********SFSSRSRFGGVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRS*******************
Disordered Region (DISPRO)
MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA************************************CFKCGRPGHWARDCPS*****************************GGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYD*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFGGVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRPSFDRY
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	255	2.2.26 [Sep-21-2011]
Q03251	169	Glycine-rich RNA-binding	no	no	0.196	0.295	0.6	4e-10
Q05966	169	Glycine-rich RNA-binding	N/A	no	0.2	0.301	0.529	5e-09
Q99070	168	Glycine-rich RNA-binding	N/A	no	0.2	0.303	0.470	3e-08
P10979	157	Glycine-rich RNA-binding,	N/A	no	0.2	0.324	0.470	8e-08
Q03250	176	Glycine-rich RNA-binding	no	no	0.196	0.284	0.52	1e-07
Q03878	157	Glycine-rich RNA-binding	N/A	no	0.235	0.382	0.428	2e-07
P49310	166	Glycine-rich RNA-binding	N/A	no	0.196	0.301	0.5	3e-07
P49311	169	Glycine-rich RNA-binding	N/A	no	0.196	0.295	0.5	4e-07
Q99069	142	Glycine-rich RNA-binding	N/A	no	0.192	0.345	0.489	5e-07
Q43472	161	Glycine-rich RNA-binding	N/A	no	0.203	0.322	0.480	7e-07

>sp|Q03251|RBG8_ARATH Glycine-rich RNA-binding protein 8 OS=Arabidopsis thaliana GN=RBG8 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/50 (60%), Positives = 40/50 (80%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          D KI+ +R+SGR RGFGF+T+ D +AM DAI EM+G+E   RVI+VN+AQ
Sbjct: 34 DSKIINDRESGRSRGFGFVTFKDEKAMRDAIEEMNGKELDGRVITVNEAQ 83

Possibly has a role in RNA transcription or processing during stress.
Arabidopsis thaliana (taxid: 3702)

>sp|Q05966|GRP10_BRANA Glycine-rich RNA-binding protein 10 OS=Brassica napus GN=GRP10 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 27/51 (52%), Positives = 39/51 (76%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          D KI+ +R++GR RGFGF+T+ D ++M DAI EM+G+E   R I+VN+AQ 
Sbjct: 34 DSKIINDRETGRSRGFGFVTFKDEKSMKDAIDEMNGKELDGRTITVNEAQS 84

Possibly has a role in RNA transcription or processing during stress.

Brassica napus (taxid: 3708)

>sp|Q99070|GRP2_SORBI Glycine-rich RNA-binding protein 2 OS=Sorghum bicolor GN=GRP2 PE=2 SV=1

 Score = 58.9 bits (141), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 38/51 (74%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          D K++ +R++GR RGFGF+T++  ++M DAI  M+G+E   R I+VN+AQ 
Sbjct: 36 DSKVITDRETGRSRGFGFVTFSSEQSMLDAIENMNGKELDGRNITVNQAQS 86

Possibly has a role in RNA transcription or processing during stress.

Sorghum bicolor (taxid: 4558)

>sp|P10979|GRPA_MAIZE Glycine-rich RNA-binding, abscisic acid-inducible protein OS=Zea mays GN=RAB15 PE=1 SV=1

 Score = 57.8 bits (138), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 37/51 (72%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          D K++ +R++GR RGFGF+T++   +M DAI  M+G+E   R I+VN+AQ 
Sbjct: 36 DSKVITDRETGRSRGFGFVTFSSENSMLDAIENMNGKELDGRNITVNQAQS 86

Possibly has a role in RNA transcription or processing during stress.

Zea mays (taxid: 4577)

>sp|Q03250|RBG7_ARATH Glycine-rich RNA-binding protein 7 OS=Arabidopsis thaliana GN=RBG7 PE=1 SV=1

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 38/50 (76%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          D KI+ +R++GR RGFGF+T+ D +AM DAI  M+G++   R I+VN+AQ
Sbjct: 36 DSKIINDRETGRSRGFGFVTFKDEKAMKDAIEGMNGQDLDGRSITVNEAQ 85

Possibly has a role in RNA transcription or processing during stress.

Arabidopsis thaliana (taxid: 3702)

>sp|Q03878|GRP1_DAUCA Glycine-rich RNA-binding protein OS=Daucus carota PE=2 SV=1

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 43/63 (68%), Gaps = 3/63 (4%)

Query: 1  MQQCLTHNNDL---KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
          ++Q  +   D+   KI+ +R++GR RGFGF+T+ D ++M DAI  M+G+E   R I+VN+
Sbjct: 22 LEQAFSQFGDITDSKIINDRETGRSRGFGFVTFKDEKSMRDAIEGMNGQELDGRNITVNE 81

Query: 58 AQP 60
          AQ 
Sbjct: 82 AQS 84

May play a role in the biosynthesis and processing of heterogeneous nuclear RNA and in the maturation of specific mRNAs in response to wounding.

Daucus carota (taxid: 4039)

>sp|P49310|GRP1_SINAL Glycine-rich RNA-binding protein GRP1A OS=Sinapis alba PE=2 SV=1

 Score = 55.5 bits (132), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 38/50 (76%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          D KI+ +R++GR RGFGF+T+ D ++M DAI  M+G++   R I+VN+AQ
Sbjct: 36 DSKIINDRETGRSRGFGFVTFKDEKSMKDAIEGMNGQDLDGRSITVNEAQ 85

May play a general role in circadian phenomena associated with meristematic tissue.

Sinapis alba (taxid: 3728)

>sp|P49311|GRP2_SINAL Glycine-rich RNA-binding protein GRP2A OS=Sinapis alba PE=2 SV=1

 Score = 55.5 bits (132), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 38/50 (76%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          D KI+ +R++GR RGFGF+T+ D ++M DAI  M+G++   R I+VN+AQ
Sbjct: 36 DSKIINDRETGRSRGFGFVTFKDEKSMKDAIEGMNGQDLDGRSITVNEAQ 85

May play a general role in circadian phenomena associated with meristematic tissue.

Sinapis alba (taxid: 3728)

>sp|Q99069|GRP1_SORBI Glycine-rich RNA-binding protein 1 (Fragment) OS=Sorghum bicolor GN=GRP1 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 35/49 (71%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          KI+L+R++ R RGFGF+T++   AM  AI  M+G+E   R I+VN+AQ 
Sbjct: 17 KIILDRETQRSRGFGFVTFSTEEAMRSAIEGMNGKELDGRNITVNEAQS 65

Possibly has a role in RNA transcription or processing during stress.

Sorghum bicolor (taxid: 4558)

>sp|Q43472|GRP_HORVU Glycine-rich RNA-binding protein blt801 OS=Hordeum vulgare GN=blt801 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 37/52 (71%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D KI+ +R++GR RGFGF+T+A   AM  AI  M+G++   R I+VN+AQ +
Sbjct: 34 DSKIITDRETGRSRGFGFVTFASDEAMRQAIEAMNGQDLDGRNITVNEAQSR 85

Binds single-stranded DNA and homoribopolymers of guanine, uracil and adenine, but not cytosine. Also binds RNA, with a preference for RNA containing a high proportion of adenine within an open loop structure. Possibly has a role in RNA transcription or processing during stress.

Hordeum vulgare (taxid: 4513)

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	255
224109842	280	predicted protein [Populus trichocarpa]	0.952	0.867	0.751	1e-87
356575516	279	PREDICTED: uncharacterized protein LOC10	0.960	0.878	0.707	2e-78
255645278	279	unknown [Glycine max]	0.960	0.878	0.707	5e-78
296085963	294	unnamed protein product [Vitis vinifera]	0.984	0.853	0.710	1e-77
356536336	279	PREDICTED: uncharacterized protein LOC10	0.960	0.878	0.699	2e-77
225448932	278	PREDICTED: heterogeneous nuclear ribonuc	0.945	0.866	0.730	4e-77
147841866	240	hypothetical protein VITISV_011831 [Viti	0.937	0.995	0.732	3e-75
449449318	286	PREDICTED: uncharacterized protein LOC10	0.952	0.849	0.658	1e-69
255585355	276	glycine-rich RNA-binding protein, putati	0.945	0.873	0.692	2e-69
449465308	283	PREDICTED: uncharacterized protein LOC10	0.960	0.865	0.712	6e-65

>gi|224109842|ref|XP_002315330.1| predicted protein [Populus trichocarpa] gi|222864370|gb|EEF01501.1| predicted protein [Populus trichocarpa]

 Score =  328 bits (841), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 184/245 (75%), Positives = 205/245 (83%), Gaps = 2/245 (0%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGY 71
           ++MLERD+GRPRGFGFIT+ADRRAMDDAIREMHGR+FGDRVISVNKAQPK+GG+ SDHGY
Sbjct: 37  QVMLERDTGRPRGFGFITFADRRAMDDAIREMHGRDFGDRVISVNKAQPKIGGDDSDHGY 96

Query: 72  RGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFGGV 131
           RGG  +    G  G DRP GQD+CFKCGR GHWARDCPSA G  GG GG  SSRSRFGG 
Sbjct: 97  RGGYSTGSRGGYGGGDRPAGQDECFKCGRSGHWARDCPSAGGR-GGGGGLISSRSRFGGA 155

Query: 132 GVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRY 191
           G RGD  GG RDRYIDDRYDGGRYGD+DR+DS+D+KYG RDRY SDRYPP GDR +GDRY
Sbjct: 156 GDRGDRFGGDRDRYIDDRYDGGRYGDKDRFDSRDNKYGGRDRYASDRYPPNGDRFSGDRY 215

Query: 192 GGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRP- 250
           GGSDRY  NGYGK++GY+RDVG R G+DRY SGGP R+D   YR+R APYDRPSRG  P 
Sbjct: 216 GGSDRYAQNGYGKDKGYDRDVGPRGGNDRYGSGGPQRNDRSSYRNRPAPYDRPSRGGHPS 275

Query: 251 SFDRY 255
           SF+RY
Sbjct: 276 SFERY 280

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575516|ref|XP_003555886.1| PREDICTED: uncharacterized protein LOC100809519 [Glycine max]

 Score =  298 bits (762), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 174/246 (70%), Positives = 192/246 (78%), Gaps = 1/246 (0%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           + +IM+ERD+GRPRGFGFIT+ADRR M+DAI+EMHGRE GDR+ISVNKAQPKMGG+  D 
Sbjct: 35  ECQIMMERDTGRPRGFGFITFADRRGMEDAIKEMHGREIGDRIISVNKAQPKMGGDDVDQ 94

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFG 129
           GYRGG  S G       DR G QDDCFKCGRPGHWARDCP A GGRG  G SF SR RFG
Sbjct: 95  GYRGGYSSGGRGSYGAGDRVG-QDDCFKCGRPGHWARDCPLAGGGRGRGGSSFPSRPRFG 153

Query: 130 GVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGD 189
             G  GD LGG RDRY+DDRY+GGRYGDRDR+D++D KYGSRDRY SDRYP +GDR A D
Sbjct: 154 AAGGNGDRLGGERDRYVDDRYEGGRYGDRDRFDNRDYKYGSRDRYASDRYPTSGDRFASD 213

Query: 190 RYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDR 249
           RYGG   YP NGYGKERGY+R  G R G+DRY SG   RD+GR YR R  PYDRPSRG R
Sbjct: 214 RYGGGSDYPQNGYGKERGYDRYGGPRGGADRYGSGMGGRDEGRSYRGRPGPYDRPSRGSR 273

Query: 250 PSFDRY 255
           PS DRY
Sbjct: 274 PSLDRY 279

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255645278|gb|ACU23136.1| unknown [Glycine max]

 Score =  296 bits (759), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 174/246 (70%), Positives = 192/246 (78%), Gaps = 1/246 (0%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           + +IM+ERD+GRPRGFGFIT+ADRR M+DAI+EMHGRE GDR+ISVNKAQPKMGG+  D 
Sbjct: 35  ECQIMMERDTGRPRGFGFITFADRRGMEDAIKEMHGREIGDRIISVNKAQPKMGGDDVDQ 94

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFG 129
           GYRGG  S G       DR G QDDCFKCGRPGHWARDCP A GGRG  G SF SR RFG
Sbjct: 95  GYRGGYSSGGRGSYGAGDRVG-QDDCFKCGRPGHWARDCPLAGGGRGRGGSSFPSRPRFG 153

Query: 130 GVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGD 189
             G  GD LGG RDRY+DDRY+GGRYGDRDR+D++D KYGSRDRY SDRYP +GDR A D
Sbjct: 154 AAGGNGDRLGGERDRYVDDRYEGGRYGDRDRFDNRDYKYGSRDRYASDRYPTSGDRFASD 213

Query: 190 RYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDR 249
           RYGG   YP NGYGKERGY+R  G R G+DRY SG   RD+GR YR R  PYDRPSRG R
Sbjct: 214 RYGGGSDYPQNGYGKERGYDRYGGPRGGADRYGSGMGGRDEGRSYRGRPGPYDRPSRGFR 273

Query: 250 PSFDRY 255
           PS DRY
Sbjct: 274 PSLDRY 279

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296085963|emb|CBI31404.3| unnamed protein product [Vitis vinifera]

 Score =  295 bits (755), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 182/256 (71%), Positives = 206/256 (80%), Gaps = 5/256 (1%)

Query: 2   QQCLTHNNDLK-IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
           Q C + + +L  IMLERD+GRPRGFGFITYADRR M+DAIREMHGR+FGDR+ISVNKAQP
Sbjct: 42  QICSSFSFELVFIMLERDTGRPRGFGFITYADRRGMEDAIREMHGRDFGDRIISVNKAQP 101

Query: 61  KMGGEVSDHGYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGG 120
           KMG E  DHGY GG  S G     G DR  GQDDCFKCGRPGHWARDCPS+ GGRG  G 
Sbjct: 102 KMG-EDPDHGYNGGYSSGGRGSYGGGDRSAGQDDCFKCGRPGHWARDCPSSGGGRGRGGA 160

Query: 121 SFSSRSRFGGVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYP 180
            F SRSRF G   RGD  GG RDRY++DRYDGGRYGDRDR++S+D+KYG+RDRYV+DRY 
Sbjct: 161 PFPSRSRFSGG--RGDRFGGERDRYMEDRYDGGRYGDRDRFESRDNKYGTRDRYVNDRYA 218

Query: 181 PAGDRLAGDRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAP 240
           P+GDR +GDRYGGSDRYP NGYGK+RGY+RD   R G DRYA GG AR++GR YR+R  P
Sbjct: 219 PSGDRFSGDRYGGSDRYPQNGYGKDRGYDRDAAPRGGGDRYAGGGSARNEGRSYRNRPGP 278

Query: 241 YDRPSRGDRP-SFDRY 255
           YDRP+RG RP SFDRY
Sbjct: 279 YDRPNRGGRPSSFDRY 294

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536336|ref|XP_003536695.1| PREDICTED: uncharacterized protein LOC100776333 [Glycine max]

 Score =  294 bits (753), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 172/246 (69%), Positives = 190/246 (77%), Gaps = 1/246 (0%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           + +IM+ERD+GRPRGFGFIT+ADRR M+DAI+EMHGRE GDR+ISVNKAQPKMGG+ +D 
Sbjct: 35  ECQIMMERDTGRPRGFGFITFADRRGMEDAIKEMHGREIGDRIISVNKAQPKMGGDDADQ 94

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFG 129
           GYRGG  S G       DR G QDDCFKCGRPGHWARDCP A GGRG  G SF SR RFG
Sbjct: 95  GYRGGYSSGGRGSYGAGDRVG-QDDCFKCGRPGHWARDCPLAGGGRGRGGSSFPSRPRFG 153

Query: 130 GVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGD 189
             G  GD LGG RDRY+DDRYDGGRYGDRDR+D++D KYGSRDRY  DRYP +GDR A D
Sbjct: 154 AAGGHGDRLGGERDRYVDDRYDGGRYGDRDRFDNRDYKYGSRDRYAGDRYPTSGDRFASD 213

Query: 190 RYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDR 249
           RYG    YP NGYGKERGY+R  G R G+DRY SG   RD+GR YR R  PYDRPSRG R
Sbjct: 214 RYGAGSDYPQNGYGKERGYDRYSGPRGGADRYGSGMGGRDEGRSYRGRPGPYDRPSRGSR 273

Query: 250 PSFDRY 255
            S DRY
Sbjct: 274 SSLDRY 279

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448932|ref|XP_002267178.1| PREDICTED: heterogeneous nuclear ribonucleoprotein G [Vitis vinifera]

 Score =  293 bits (751), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 179/245 (73%), Positives = 201/245 (82%), Gaps = 4/245 (1%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGY 71
           +IMLERD+GRPRGFGFITYADRR M+DAIREMHGR+FGDR+ISVNKAQPKMG E  DHGY
Sbjct: 37  QIMLERDTGRPRGFGFITYADRRGMEDAIREMHGRDFGDRIISVNKAQPKMG-EDPDHGY 95

Query: 72  RGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFGGV 131
            GG  S G     G DR  GQDDCFKCGRPGHWARDCPS+ GGRG  G  F SRSRF G 
Sbjct: 96  NGGYSSGGRGSYGGGDRSAGQDDCFKCGRPGHWARDCPSSGGGRGRGGAPFPSRSRFSGG 155

Query: 132 GVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRY 191
             RGD  GG RDRY++DRYDGGRYGDRDR++S+D+KYG+RDRYV+DRY P+GDR +GDRY
Sbjct: 156 --RGDRFGGERDRYMEDRYDGGRYGDRDRFESRDNKYGTRDRYVNDRYAPSGDRFSGDRY 213

Query: 192 GGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRP- 250
           GGSDRYP NGYGK+RGY+RD   R G DRYA GG AR++GR YR+R  PYDRP+RG RP 
Sbjct: 214 GGSDRYPQNGYGKDRGYDRDAAPRGGGDRYAGGGSARNEGRSYRNRPGPYDRPNRGGRPS 273

Query: 251 SFDRY 255
           SFDRY
Sbjct: 274 SFDRY 278

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147841866|emb|CAN66927.1| hypothetical protein VITISV_011831 [Vitis vinifera]

 Score =  287 bits (734), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 178/243 (73%), Positives = 199/243 (81%), Gaps = 4/243 (1%)

Query: 14  MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
           MLERD+GRPRGFGFITYADRR M+DAIREMHGR+FGDR+ISVNKAQPKMG E  DHGY G
Sbjct: 1   MLERDTGRPRGFGFITYADRRGMEDAIREMHGRDFGDRIISVNKAQPKMG-EDPDHGYNG 59

Query: 74  GGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFGGVGV 133
           G  S G     G DR  GQDDCFKCGRPGHWARDCPS+ GGRG  G  F SRSRF   G 
Sbjct: 60  GYSSGGRGSYGGGDRSAGQDDCFKCGRPGHWARDCPSSGGGRGRGGAPFPSRSRF--SGG 117

Query: 134 RGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDRYGG 193
           RGD  GG RDRY++DRYDGGRYGDRDR++S+D+KYG+RDRYV+DRY P+GDR +GDRYGG
Sbjct: 118 RGDRFGGERDRYMEDRYDGGRYGDRDRFESRDNKYGTRDRYVNDRYAPSGDRFSGDRYGG 177

Query: 194 SDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRP-SF 252
           SDRYP NGYGK+RGY+RD   R G DRYA GG AR++GR YR+R  PYDRP+RG RP SF
Sbjct: 178 SDRYPQNGYGKDRGYDRDAAPRGGGDRYAGGGSARNEGRSYRNRPGPYDRPNRGGRPSSF 237

Query: 253 DRY 255
           DRY
Sbjct: 238 DRY 240

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449318|ref|XP_004142412.1| PREDICTED: uncharacterized protein LOC101202917 [Cucumis sativus] gi|449487254|ref|XP_004157539.1| PREDICTED: uncharacterized protein LOC101231083 [Cucumis sativus]

 Score =  268 bits (686), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 168/255 (65%), Positives = 192/255 (75%), Gaps = 12/255 (4%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           D +IMLE+++GRPRGFGFIT++DRR MDDAIREMHG+EFG+R+ISVNKA+PKM GE  DH
Sbjct: 35  DSQIMLEKNTGRPRGFGFITFSDRRGMDDAIREMHGQEFGERIISVNKAEPKM-GEDMDH 93

Query: 70  ----GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSR 125
               G    G      G  G DR   QD+CFKCGR GHWARDCPS  GGRG  G SF +R
Sbjct: 94  GYRGGGYSTGGRGSYGGGGGGDRSARQDECFKCGRLGHWARDCPSVGGGRGRGGDSFLAR 153

Query: 126 SRFGGVGVRGDYLGGGRDRYIDDRYD-GGRYGDRDRYD--SKDSKYGSRDRYVSDRYPPA 182
           SR G    RGD   G  +RY+DDRYD GGR+GDRDR+D  S+D+KYGSRDRYVSDRYPP 
Sbjct: 154 SRLGDSD-RGDRFAGDANRYVDDRYDGGGRFGDRDRFDSSSRDNKYGSRDRYVSDRYPPG 212

Query: 183 GDRLAGDRYGG-SDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPY 241
           GDR    RY   SDR+PVNGYGK+RGY RD G R G D+Y SGGPARD+GR YR+R APY
Sbjct: 213 GDRFGSSRYTNDSDRFPVNGYGKDRGYYRDGGPR-GVDKYGSGGPARDEGRSYRNRPAPY 271

Query: 242 DRPSRGDRP-SFDRY 255
           DRP+RG RP SFDRY
Sbjct: 272 DRPNRGGRPSSFDRY 286

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585355|ref|XP_002533374.1| glycine-rich RNA-binding protein, putative [Ricinus communis] gi|223526781|gb|EEF29005.1| glycine-rich RNA-binding protein, putative [Ricinus communis]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 171/247 (69%), Positives = 194/247 (78%), Gaps = 6/247 (2%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           + ++MLERD+GRPRGFGFIT++DRR+MDDAIREMHGREFGDRVISVNKAQPKMG ++   
Sbjct: 35  ECQVMLERDTGRPRGFGFITFSDRRSMDDAIREMHGREFGDRVISVNKAQPKMGDDLDHG 94

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFG 129
              G   S G  G YG DRP GQD+CFKCGR GHWARDC ++ GGRGG G SFSSRSR G
Sbjct: 95  YRGGYSSSGGRGGGYGGDRPLGQDECFKCGRIGHWARDC-TSAGGRGGGGSSFSSRSRLG 153

Query: 130 GVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGD 189
           G   RGD   G RDR++DDRYDGGR+GDRDR+DS+D KY SRDRY S+RYPP+GDR A D
Sbjct: 154 GASERGDRFAGDRDRFMDDRYDGGRFGDRDRFDSRD-KY-SRDRYASERYPPSGDRFASD 211

Query: 190 RYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDR 249
           RYGGSDRY  N YGK+RGYERD   R GSDRY +GGP  D  R YRSR  PY+RPSRG  
Sbjct: 212 RYGGSDRYAHNSYGKDRGYERDAVTRGGSDRYGNGGPRGD--RSYRSRPGPYERPSRGGH 269

Query: 250 P-SFDRY 255
           P SF+RY
Sbjct: 270 PSSFERY 276

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465308|ref|XP_004150370.1| PREDICTED: uncharacterized protein LOC101207282 [Cucumis sativus] gi|449524890|ref|XP_004169454.1| PREDICTED: uncharacterized LOC101207282 [Cucumis sativus]

 Score =  253 bits (645), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 178/250 (71%), Positives = 203/250 (81%), Gaps = 5/250 (2%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           + +IMLERD+GRPRGFGFIT+ADRR MDDAIREMHG+E G+R+ISVNKA+PKM G+ ++ 
Sbjct: 35  ETQIMLERDTGRPRGFGFITFADRRGMDDAIREMHGQELGERIISVNKAEPKMEGDDTEQ 94

Query: 70  GYRGGGYSSGGRGSY--GADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSR 127
           G+RGGGYSSGGR S+  G DR  GQD+CFKCGRPGHWARDCPS  GGRGG  GSFSSRSR
Sbjct: 95  GFRGGGYSSGGRASFGRGKDRSVGQDECFKCGRPGHWARDCPSVGGGRGGGRGSFSSRSR 154

Query: 128 FGGVGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLA 187
           F   G RGD  GG RDRY+D+RY+GGRYGDRDR+D +D KYGSRDRY  DRYP AGDR  
Sbjct: 155 FDSDG-RGDRFGGDRDRYVDERYNGGRYGDRDRFDRRDDKYGSRDRYFDDRYPSAGDRFT 213

Query: 188 G-DRYGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSR 246
           G DRY  SDRYP NGY K+R Y+RD+G R+GSDRY SGGP R +GR YR R  PYDRPSR
Sbjct: 214 GSDRYDVSDRYPQNGYVKDRVYDRDIGPRSGSDRYGSGGPGRHEGRSYRDRTGPYDRPSR 273

Query: 247 GDRP-SFDRY 255
             RP S+DRY
Sbjct: 274 VGRPSSYDRY 283

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	255
TAIR|locus:2179939	310	AtRZ-1c "AtRZ-1c" [Arabidopsis	0.392	0.322	0.564	2.3e-52
TAIR|locus:2036520	292	AtRZ-1b "AtRZ-1b" [Arabidopsis	0.360	0.315	0.56	1.8e-50
TAIR|locus:2079276	245	ATRZ-1A [Arabidopsis thaliana	0.403	0.420	0.427	3.8e-31
TAIR|locus:2136298	169	CCR1 "cold, circadian rhythm,	0.215	0.325	0.563	4.1e-16
TAIR|locus:2049359	176	GRP7 "AT2G21660" [Arabidopsis	0.235	0.340	0.466	5.7e-15
UNIPROTKB|Q43472	161	blt801 "Glycine-rich RNA-bindi	0.203	0.322	0.480	4.6e-12
TAIR|locus:2159401	309	GR-RBP3 "glycine-rich RNA-bind	0.215	0.177	0.4	1.1e-11
MGI|MGI:1343045	388	Rbmxl1 "RNA binding motif prot	0.317	0.208	0.448	2.7e-11
UNIPROTKB|Q96E39	390	RBMXL1 "RNA binding motif prot	0.337	0.220	0.447	2.9e-11
RGD|1306751	388	Rbmxrtl "RNA binding motif pro	0.317	0.208	0.448	5.1e-11

TAIR|locus:2179939 AtRZ-1c "AtRZ-1c" [Arabidopsis thaliana (taxid:3702)]

 Score = 313 (115.2 bits), Expect = 2.3e-52, Sum P(2) = 2.3e-52
 Identities = 61/108 (56%), Positives = 75/108 (69%)

Query:    10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSD- 68
             D +IMLERD+GR RGFGFIT+ADRRAMD++IREMHGR+FGDRVISVN+A+PK+G +  + 
Sbjct:    35 DCQIMLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGRDDGES 94

Query:    69 HXXXXXXXXXXXXXXXXADRPGG-------QDDCFKCGRPGHWARDCP 109
             H                +   GG       +D+CFKCGR GHWARDCP
Sbjct:    95 HGSRGGRDSGYSIAGKGSFGGGGGGGGRVGEDECFKCGRVGHWARDCP 142

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;IDA

GO:0003723 "RNA binding" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0009409 "response to cold" evidence=IGI;IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

TAIR|locus:2036520 AtRZ-1b "AtRZ-1b" [Arabidopsis thaliana (taxid:3702)]

 Score = 296 (109.3 bits), Expect = 1.8e-50, Sum P(2) = 1.8e-50
 Identities = 56/100 (56%), Positives = 68/100 (68%)

Query:    10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
             + +IM+ RD+GRPRGFGFIT+ DRR  DDAI+ MHGRE G++VISVNKA+PK+GGE  D 
Sbjct:    40 ECQIMVGRDTGRPRGFGFITFTDRRGADDAIKHMHGRELGNKVISVNKAEPKVGGEDVDQ 99

Query:    70 XXXXXXXXXXXXXXXXADRPGGQDDCFKCGRPGHWARDCP 109
                                 G +D+CFKC RPGHWARDCP
Sbjct:   100 LKKGGGYSSRGK--------GTEDECFKCRRPGHWARDCP 131

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;IDA

GO:0003723 "RNA binding" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0009409 "response to cold" evidence=IGI;IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

TAIR|locus:2079276 ATRZ-1A [Arabidopsis thaliana (taxid:3702)]

 Score = 232 (86.7 bits), Expect = 3.8e-31, Sum P(2) = 3.8e-31
 Identities = 44/103 (42%), Positives = 62/103 (60%)

Query:     7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV 66
             H  + K++L++ SGR RGFGFIT+ +++AMD+AI  M+G +   R I+V+KAQP  GG  
Sbjct:    32 HLVEAKVVLDKFSGRSRGFGFITFDEKKAMDEAIAAMNGMDLDGRTITVDKAQPHQGGAG 91

Query:    67 SDHXXXXXXXXXXXXXXXXADRPGGQDDCFKCGRPGHWARDCP 109
              D+                     G  DCFKCG+PGH+AR+CP
Sbjct:    92 RDNDGDRGRDRGYDRDRSRPSGGRGGGDCFKCGKPGHFARECP 134

GO:0000166 "nucleotide binding" evidence=IEA;IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IMP

GO:0009631 "cold acclimation" evidence=IGI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2136298 CCR1 "cold, circadian rhythm, and RNA binding 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 4.1e-16, Sum P(2) = 4.1e-16
 Identities = 31/55 (56%), Positives = 42/55 (76%)

Query:    10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
             D KI+ +R+SGR RGFGF+T+ D +AM DAI EM+G+E   RVI+VN+AQ +  G
Sbjct:    34 DSKIINDRESGRSRGFGFVTFKDEKAMRDAIEEMNGKELDGRVITVNEAQSRGSG 88

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005618 "cell wall" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009651 "response to salt stress" evidence=IEP

GO:0005777 "peroxisome" evidence=IDA

GO:0010043 "response to zinc ion" evidence=IEP

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0007623 "circadian rhythm" evidence=RCA

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=IMP

TAIR|locus:2049359 GRP7 "AT2G21660" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 5.7e-15, Sum P(2) = 5.7e-15
 Identities = 28/60 (46%), Positives = 41/60 (68%)

Query:    10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
             D KI+ +R++GR RGFGF+T+ D +AM DAI  M+G++   R I+VN+AQ +  G    H
Sbjct:    36 DSKIINDRETGRSRGFGFVTFKDEKAMKDAIEGMNGQDLDGRSITVNEAQSRGSGGGGGH 95

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

GO:0005739 "mitochondrion" evidence=ISM

GO:0005634 "nucleus" evidence=ISS;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IGI;IEP

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP;RCA

GO:0046686 "response to cadmium ion" evidence=IEP;RCA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0045087 "innate immune response" evidence=IMP;IDA

GO:0005777 "peroxisome" evidence=IDA

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

GO:0006970 "response to osmotic stress" evidence=IMP

GO:0010119 "regulation of stomatal movement" evidence=IMP

GO:0009507 "chloroplast" evidence=IDA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA;IMP

GO:0010043 "response to zinc ion" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006096 "glycolysis" evidence=RCA

GO:0006833 "water transport" evidence=RCA

GO:0006972 "hyperosmotic response" evidence=RCA

GO:0007030 "Golgi organization" evidence=RCA

GO:0007623 "circadian rhythm" evidence=IEP;RCA;TAS

GO:0009266 "response to temperature stimulus" evidence=RCA

GO:0000380 "alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0003729 "mRNA binding" evidence=IDA

UNIPROTKB|Q43472 blt801 "Glycine-rich RNA-binding protein blt801" [Hordeum vulgare (taxid:4513)]

 Score = 130 (50.8 bits), Expect = 4.6e-12, Sum P(2) = 4.6e-12
 Identities = 25/52 (48%), Positives = 37/52 (71%)

Query:    10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             D KI+ +R++GR RGFGF+T+A   AM  AI  M+G++   R I+VN+AQ +
Sbjct:    34 DSKIITDRETGRSRGFGFVTFASDEAMRQAIEAMNGQDLDGRNITVNEAQSR 85

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IDA

GO:0009737 "response to abscisic acid stimulus" evidence=IDA

TAIR|locus:2159401 GR-RBP3 "glycine-rich RNA-binding protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 126 (49.4 bits), Expect = 1.1e-11, Sum P(2) = 1.1e-11
 Identities = 22/55 (40%), Positives = 35/55 (63%)

Query:    10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
             D +++L+R++GR RGFGF+T+    A   AI+ + GR+   RV+ VN A  +  G
Sbjct:    68 DTRVILDRETGRSRGFGFVTFTSSEAASSAIQALDGRDLHGRVVKVNYANDRTSG 122

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005524 "ATP binding" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0034968 "histone lysine methylation" evidence=RCA

MGI|MGI:1343045 Rbmxl1 "RNA binding motif protein, X linked-like-1" [Mus musculus (taxid:10090)]

 Score = 121 (47.7 bits), Expect = 2.7e-11, Sum P(2) = 2.7e-11
 Identities = 44/98 (44%), Positives = 49/98 (50%)

Query:   163 SKDSKYGSRDRYVSDR----Y-PPAGDRLAGDRYGGSDR--YPVNGYGKERGYERDVGAR 215
             +KDS Y SRD Y S R    Y PP  D    D    S R  YP  GYG   GY RD   R
Sbjct:   213 TKDS-YSSRD-YPSSRDTRDYAPPPRDYTYRDYSHSSSRDDYPSRGYGDRDGYGRD---R 267

Query:   216 AGSDRYASGGPARDDGRGY-RSRAAPYDRPSRGDRPSF 252
               SD + SGG  RD    Y  SR+AP   P+RG  PS+
Sbjct:   268 DYSD-HPSGGSYRDSYESYGNSRSAP---PTRGPPPSY 301

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=ISO

GO:0001047 "core promoter binding" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IDA

GO:0003723 "RNA binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0006376 "mRNA splice site selection" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0044530 "supraspliceosomal complex" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISO

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=ISO

GO:0051260 "protein homooligomerization" evidence=ISO

UNIPROTKB|Q96E39 RBMXL1 "RNA binding motif protein, X-linked-like-1" [Homo sapiens (taxid:9606)]

 Score = 124 (48.7 bits), Expect = 2.9e-11, Sum P(2) = 2.9e-11
 Identities = 47/105 (44%), Positives = 51/105 (48%)

Query:   163 SKDSKYGSRDRYVSDR----Y-PPAGDRLAGDRYGGS---DRYPVNGYGKERGYERDVGA 214
             +KDS Y SRD Y S R    Y PP  D    D YG S   D YP  GYG   GY RD   
Sbjct:   216 TKDS-YSSRD-YPSSRDTRDYAPPPRDYTYRD-YGHSSSRDDYPSRGYGDRDGYGRD--- 269

Query:   215 RAGSDRYASGGPARDDGRGY-RSRAAPYDR---PSRGDRPSFDRY 255
             R  SD + SGG  RD    Y  SR+AP  R   PS G    +D Y
Sbjct:   270 RDYSD-HPSGGSYRDSYESYGNSRSAPLTRGPPPSYGGSSRYDDY 313

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|1306751 Rbmxrtl "RNA binding motif protein, X chromosome retrogene-like" [Rattus norvegicus (taxid:10116)]

 Score = 122 (48.0 bits), Expect = 5.1e-11, Sum P(2) = 5.1e-11
 Identities = 44/98 (44%), Positives = 49/98 (50%)

Query:   163 SKDSKYGSRDRYVSDR----Y-PPAGDRLAGDRYGGSDR--YPVNGYGKERGYERDVGAR 215
             +KDS Y SRD Y S R    Y PP  D    D    S R  YP  GYG   GY RD   R
Sbjct:   213 TKDS-YSSRD-YPSSRDTRDYAPPPRDYTYRDYSHSSSRDDYPSRGYGDRDGYGRD---R 267

Query:   216 AGSDRYASGGPARDDGRGY-RSRAAPYDRPSRGDRPSF 252
               SD + SGG  RD    Y  SR+AP   P+RG  PS+
Sbjct:   268 EYSD-HPSGGSYRDSYESYGNSRSAP---PTRGPPPSY 301

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IDA

GO:0001047 "core promoter binding" evidence=ISO

GO:0003682 "chromatin binding" evidence=ISO

GO:0003723 "RNA binding" evidence=IDA

GO:0003729 "mRNA binding" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO;ISS

GO:0005719 "nuclear euchromatin" evidence=ISS

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

GO:0006376 "mRNA splice site selection" evidence=IDA

GO:0006509 "membrane protein ectodomain proteolysis" evidence=ISS

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0044530 "supraspliceosomal complex" evidence=IDA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO;ISS

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IDA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IDA

GO:0051260 "protein homooligomerization" evidence=IDA

GO:0070062 "extracellular vesicular exosome" evidence=ISS

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

GO:0071347 "cellular response to interleukin-1" evidence=ISS

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	255
smart00360	73	smart00360, RRM, RNA recognition motif	2e-12
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	6e-06
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	6e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-05
smart00343	17	smart00343, ZnF_C2HC, zinc finger	2e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-05
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	6e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-04
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	6e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-04
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	0.001
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.001
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.001
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	0.002
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.003
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.003
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.003
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.003
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.003
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.003
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.004
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.004
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.004
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.004
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.004
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.004

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

 Score = 60.7 bits (148), Expect = 2e-12
 Identities = 9/46 (19%), Positives = 27/46 (58%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
           ++++ ++++G+ +GF F+ +      + A+  ++G+E   R + V
Sbjct: 28 SVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

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

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 18/52 (34%), Positives = 34/52 (65%)

Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
             +++ +R++GR RGFGF+        + AI +++G +FG R ++VN+A+P
Sbjct: 27 TSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEARP 78

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|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 = 54.2 bits (131), Expect = 6e-10
 Identities = 20/46 (43%), Positives = 30/46 (65%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          +M + ++G  RGFGF+T+      D AIR+++G+E   RVI V KA
Sbjct: 33 LMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVEKA 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|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 = 52.6 bits (127), Expect = 2e-09
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           +++ +RD+G+P+G+GF  + D      AIR ++G EF  R + V+ A
Sbjct: 28 FRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVDFA 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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 13 IMLERDS-GRPRGFGFITYADRRAMDDAIREMHGREFGDRVI 53
          I + RD  GR +GF F+ + D    + A+  ++G+E G R +
Sbjct: 28 IRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGREL 69

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

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

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 9/43 (20%), Positives = 22/43 (51%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          ++    G+ +GF F+ +      + A+  ++G+E   R + V+
Sbjct: 30 IVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKLKVS 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 15/49 (30%), Positives = 28/49 (57%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
            +++ +R++GR RGFG++ +        AI  M G+E   R I+V+ +
Sbjct: 28 GARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          K+M + D G+ +GFGF+ + +  A   A+ E++G+E   + + V +AQ K
Sbjct: 32 KVMKD-DEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYVGRAQKK 80

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

 Score = 53.0 bits (126), Expect = 3e-08
 Identities = 17/55 (30%), Positives = 33/55 (60%)

Query: 7   HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
               ++++ +R++G+ RGF F+ +    + + AI E++G+E   R + V KAQP 
Sbjct: 141 PVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPA 195

Length = 306

>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 = 48.5 bits (116), Expect = 6e-08
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          D ++M + D+GR RGFGF+T+    A++         E G + + V +A
Sbjct: 28 DAQLMQDHDTGRSRGFGFVTFDSESAVERVF-SAGMLELGGKQVEVKRA 75

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

 Score = 49.7 bits (118), Expect = 1e-07
 Identities = 33/81 (40%), Positives = 44/81 (54%), Gaps = 5/81 (6%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ-----PKMGG 64
           D K++++R++GR RGFGF+ + D  A   AI EM G+E   R I VN A      P+  G
Sbjct: 63  DAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAPRAYG 122

Query: 65  EVSDHGYRGGGYSSGGRGSYG 85
               +   GGGY  GG G  G
Sbjct: 123 GGGGYSGGGGGYGGGGDGGGG 143

Length = 144

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 20/47 (42%), Positives = 29/47 (61%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          KIM + D+G  +GF FI+Y    A D AI  M+G+   +R I+V+ A
Sbjct: 33 KIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITVSYA 79

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

 Score = 49.8 bits (119), Expect = 5e-07
 Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           K+ML+ + G  RGFGF+ +++    + A+ EMHGR  G + + V  AQ K
Sbjct: 316 KVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK 364

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

 Score = 42.9 bits (101), Expect = 5e-06
 Identities = 18/47 (38%), Positives = 31/47 (65%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          D ++M +  SGR RG+GF+++  ++  ++AI EM+G+  G R I  N
Sbjct: 28 DARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPIRCN 74

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

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

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIRE 42
          D  IM +  +GR RGFGF+T+AD  ++D  +  
Sbjct: 27 DCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 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|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 41.7 bits (99), Expect = 6e-06
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 95  CFKCGRPGHWARDCPS 110
           C+ CG+ GH ARDCP 
Sbjct: 3   CYNCGKEGHLARDCPE 18

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>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 = 42.2 bits (100), Expect = 1e-05
 Identities = 12/45 (26%), Positives = 29/45 (64%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          K+ +++++G+ + FGF++Y +  +   AI+ M+G + G + + V 
Sbjct: 29 KVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKVQ 73

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

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          ++ +M + +  RPRGFGFIT+    ++D  +   H  +   + + V +A+P
Sbjct: 31 EVVVMYDHEKKRPRGFGFITFESEDSVDQVV-NEHFHDINGKKVEVKRAEP 80

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|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 = 41.8 bits (98), Expect = 2e-05
 Identities = 16/44 (36%), Positives = 27/44 (61%)

Query: 16 ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          +R++ R RGFGF+T+ +     DA+  M+G+    R I V++A 
Sbjct: 35 DRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRVDQAG 78

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 15/47 (31%), Positives = 25/47 (53%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          D++I L+ ++ + RGF F+ + +      AI  M+  E   R I VN
Sbjct: 27 DIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTIRVN 73

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

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 40.1 bits (95), Expect = 2e-05
 Identities = 11/16 (68%), Positives = 13/16 (81%)

Query: 95  CFKCGRPGHWARDCPS 110
           C+ CG+ GH ARDCPS
Sbjct: 2   CYNCGKEGHIARDCPS 17

Length = 17

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

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 10/46 (21%), Positives = 25/46 (54%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
          D+ + ++R+   PRG+ ++ +      + AI+ M G +   + ++V
Sbjct: 27 DVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           GF F+ ++   A + A++ ++G  FG R + V+ +
Sbjct: 21 PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 11/39 (28%), Positives = 21/39 (53%)

Query: 22 PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
           + + F+ + +R     A+ EM+G+E     I V+ A+P
Sbjct: 34 IKDYAFVHFEERDDAVKAMEEMNGKELEGSPIEVSLAKP 72

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

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
          D+ I  +R +   RGF F+ + D+R  +DA+  M G+E   R + V
Sbjct: 27 DVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRV 72

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 13/35 (37%), Positives = 23/35 (65%), Gaps = 1/35 (2%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
           GF F+T+ D  + ++A+ +++G E G R ISV+ 
Sbjct: 45 NGFAFVTFKDASSAENAL-QLNGTELGGRKISVSL 78

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

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          K+M + + GR +GFGF+ ++       A+ EM+GR  G + + V  AQ
Sbjct: 32 KVMTD-EKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQ 78

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

>gnl|CDD|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 = 39.8 bits (93), Expect = 8e-05
 Identities = 15/48 (31%), Positives = 30/48 (62%)

Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           +++ +R++G+P+G+GF  Y D+     A+R ++G E   R + V+ A
Sbjct: 28 FRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVDNA 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 12/42 (28%), Positives = 23/42 (54%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVI 53
           + L R+  RPRGF F+ +A     + A+++++G     R +
Sbjct: 27 GVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

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

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

 Score = 41.7 bits (98), Expect = 2e-04
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 19  SGRPRGFGFITYADRRAMDDAIREMHGREFGD----RVISVNKAQPK 61
           SGR RGF F+ +        A+ EM+G++ G     + + V +AQ +
Sbjct: 215 SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKR 261

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 15/47 (31%), Positives = 28/47 (59%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          K++++  +GR +G+GF+ + D    D A+ EM+G     R + V+ A
Sbjct: 33 KVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPMRVSPA 79

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

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 10/45 (22%), Positives = 26/45 (57%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          +  +  G+ +GF F+ +  +   + AI+ ++G++   R ++V+ A
Sbjct: 31 IPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVDWA 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|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 12/40 (30%), Positives = 27/40 (67%)

Query: 16 ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
          ++++G+ RGF F+T+  R   + AI +++G  + + ++SV
Sbjct: 34 DKETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNLILSV 73

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 13/47 (27%), Positives = 30/47 (63%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          D +++ +  +G+ +G+GF+++  +   ++AI+ M+G+  G R I  N
Sbjct: 28 DARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAIRTN 74

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

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 16/47 (34%), Positives = 26/47 (55%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          KIM +  +G  RG+GF+ ++D      A+ EM G   G R + ++ A
Sbjct: 33 KIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 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 = 80

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 10/39 (25%), Positives = 23/39 (58%)

Query: 20 GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          G+PRG+ F+T+  +   + A++ ++G+    + + V  A
Sbjct: 41 GQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWA 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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 37.3 bits (87), Expect = 5e-04
 Identities = 17/44 (38%), Positives = 21/44 (47%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
          KI+    S   R FGF+T A        I+ +H  E   RVISV
Sbjct: 30 KIVTNARSPGARCFGFVTMASVEEAAKCIQHLHRTELHGRVISV 73

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

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 11/39 (28%), Positives = 20/39 (51%)

Query: 18 DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
           +G+ + FGF  + D      A+R ++G E G + + V 
Sbjct: 37 STGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKLLVK 75

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

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 13/46 (28%), Positives = 28/46 (60%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
          D+ ++ ++ +G+ +GF F+ Y D+R+   A+  ++G +   R I V
Sbjct: 38 DINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRTIRV 83

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

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           P GF F+ + D R  +DA+R + GR      + V  +
Sbjct: 34 NPPGFAFVEFEDPRDAEDAVRALDGRRICGNRVRVELS 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|240968 cd12524, RRM1_MEI2_like, RNA recognition motif 1 in plant Mei2-like proteins

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 8/60 (13%)

Query: 10 DLKIMLER--------DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +L+ + E+         + + RGF  ++Y D RA   A R + G E G R + ++ + PK
Sbjct: 17 ELRALFEQFGDIRTLYTACKHRGFIMVSYYDIRAARRAKRALQGTELGGRKLDIHFSIPK 76

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

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
           ++++  R SG+P+G  ++ Y +  +   A+ +M G E  ++ ISV  + P
Sbjct: 31 SVRLVTNR-SGKPKGLAYVEYENESSASQAVLKMDGTEIKEKTISVAISNP 80

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

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 14/47 (29%), Positives = 33/47 (70%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          K++ ++ +G+ +G+GF++++D      A++EM+G+  G+R I + K+
Sbjct: 37 KVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRPIKLRKS 83

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>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 = 37.1 bits (87), Expect = 7e-04
 Identities = 10/36 (27%), Positives = 22/36 (61%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHG 45
          ++ I+ ++D+G+ +G  F+ ++ R     AI  +HG
Sbjct: 28 EVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
           +++  + ++GR +G+GFI +AD      A+ +++G E   R I V 
Sbjct: 27 FVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73

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

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 9/29 (31%), Positives = 20/29 (68%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAI 40
          +I+ ++++G+ RGF F+T+ D   +D  +
Sbjct: 30 EIVTDKETGKKRGFAFVTFDDYDPVDKIV 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 11 LKIMLERD--SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
              L  D  +G+ +G+GFI Y + ++  DAI  M+  + G + + V KA
Sbjct: 28 KSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQLRVGKA 77

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

>gnl|CDD|240759 cd12313, RRM1_RRM2_RBM5_like, RNA recognition motif 1 and 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 10 DLKIMLERDSGRPRGFGFITY---ADRRAMDDAIREMHGREFGDRVISVNKA 58
          D++++ ++ +G  RGF F+ +    D     DA+  +       RV+ V+ A
Sbjct: 33 DVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84

This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 84

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

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 15/47 (31%), Positives = 27/47 (57%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          KI+ +R +G+  G+GF+ Y D      AI  ++G E  ++ + V+ A
Sbjct: 31 KIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKVSYA 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|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          ++ +R +G+ RG+GF+T+ D+ + + A ++ +      R  +VN A
Sbjct: 32 VITDRQTGKSRGYGFVTFKDKESAERACKDPNPI-IDGRKANVNLA 76

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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 10/40 (25%), Positives = 21/40 (52%)

Query: 18 DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK 57
          ++G  +G+GF+ +    A   AI +++G    D+ + V  
Sbjct: 38 ENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFVGP 77

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

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

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 11/42 (26%), Positives = 23/42 (54%)

Query: 20  GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           G+ RG+GF+ +    +   AI++++G    D+ + V +   K
Sbjct: 126 GKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK 167

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|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 37.1 bits (86), Expect = 0.003
 Identities = 16/24 (66%), Positives = 19/24 (79%)

Query: 95  CFKCGRPGHWARDCPSAVGGRGGA 118
           C+KCG PGH +R+CPSA GGRG  
Sbjct: 30  CYKCGEPGHLSRECPSAPGGRGER 53

Length = 148

>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 = 35.3 bits (82), Expect = 0.003
 Identities = 13/42 (30%), Positives = 23/42 (54%)

Query: 17 RDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
            +G  +G+ F  Y D    D AI  ++G + GD+ ++V +A
Sbjct: 36 SATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTVQRA 77

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 15/49 (30%), Positives = 28/49 (57%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          +L + L+R +G  +G+  I Y  ++    AI  ++G+E   + ISV+ A
Sbjct: 35 NLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQTISVDWA 83

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

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 15/49 (30%), Positives = 29/49 (59%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          K++ ++ +G+  G+GF+ Y D    D AI  ++G +   + I V+ A+P
Sbjct: 34 KLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYARP 82

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D++I  + D GR +GFG + +A       A+ E  G E   R I V+ A  +
Sbjct: 28 DVRIA-QDDDGRSKGFGHVEFATEEGAQKAL-EKSGEELLGREIRVDLATER 77

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|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 36.3 bits (84), Expect = 0.004
 Identities = 21/63 (33%), Positives = 26/63 (41%), Gaps = 10/63 (15%)

Query: 89  PGGQDDCFKCGRPGHWARDCPSAVGGRG-------GAGGSFSSR---SRFGGVGVRGDYL 138
             G+  C+ CG+ GH +R+CP A  G G       G  G  S        GG   R  Y 
Sbjct: 49  GRGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYN 108

Query: 139 GGG 141
            GG
Sbjct: 109 CGG 111

Length = 148

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 15/48 (31%), Positives = 30/48 (62%)

Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          N++K++ + ++ + +GFGF+T  +      AI  ++G   GDRV+ V+
Sbjct: 31 NNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVS 78

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 8/34 (23%), Positives = 18/34 (52%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
          +G+GF+ + +      A+   +GRE   + + +N
Sbjct: 35 KGYGFVQFDNEEDARAAVAGENGREIAGQKLDIN 68

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

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 14/49 (28%), Positives = 29/49 (59%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          K++ ++ +G+  G+GF+ Y D +  + AI  ++G     + I V+ A+P
Sbjct: 35 KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 83

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

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 14/52 (26%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D  +M +  +GR RGFGF+T+   +++++ +++ H      ++I   +A P+
Sbjct: 27 DCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEH--ILDGKIIDPKRAIPR 76

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

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 12 KIMLERD--SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          KI L +D  +G P+G   +TY D  A   AI   + ++F    I V+ A
Sbjct: 35 KIWLYKDKDTGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKVSLA 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	255
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.64
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.45
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.4
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.39
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.36
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.34
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.34
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.33
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.33
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.32
KOG0122	270	consensus Translation initiation factor 3, subunit	99.32
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.3
smart00361	70	RRM_1 RNA recognition motif.	99.29
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.18
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.16
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.15
smart00360	71	RRM RNA recognition motif.	99.13
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.12
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.12
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.11
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.09
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.09
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.07
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.06
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.03
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.03
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.03
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.03
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.98
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.96
smart00362	72	RRM_2 RNA recognition motif.	98.95
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.95
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.93
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.92
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.89
PLN03213	759	repressor of silencing 3; Provisional	98.89
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.89
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.89
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.87
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.87
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.86
PLN03120	260	nucleic acid binding protein; Provisional	98.84
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.84
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.82
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.81
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.81
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.8
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.78
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.77
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.77
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.77
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.77
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.75
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.74
PLN03121	243	nucleic acid binding protein; Provisional	98.64
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.64
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.61
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.61
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.57
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.46
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.4
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.39
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.38
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.31
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.31
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.29
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.29
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.27
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.24
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.03
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.03
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.02
KOG0226	290	consensus RNA-binding proteins [General function p	98.01
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.01
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.0
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.74
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.69
KOG2314	698	consensus Translation initiation factor 3, subunit	97.67
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	97.65
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.62
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.41
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.33
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.25
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.22
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.17
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.13
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.12
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.98
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.95
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	96.95
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.9
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.9
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.64
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.64
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	96.63
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.55
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.27
KOG0151	877	consensus Predicted splicing regulator, contains R	96.24
KOG4210	285	consensus Nuclear localization sequence binding pr	96.14
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.76
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.71
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.57
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	95.29
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.15
KOG2068	327	consensus MOT2 transcription factor [Transcription	94.74
KOG1855	484	consensus Predicted RNA-binding protein [General f	94.37
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	94.19
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	92.6
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	92.5
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	92.42
KOG4660	549	consensus Protein Mei2, essential for commitment t	91.56
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	91.38
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	91.27
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	91.24
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.73
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	90.57
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.24
KOG2135	526	consensus Proteins containing the RNA recognition	89.69
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	89.14
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	88.63
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	88.32
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	86.87
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	86.5
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	85.45
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	83.22
PF13696	32	zf-CCHC_2: Zinc knuckle	82.16
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	81.89
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	81.87
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	80.44

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

Probab=99.64  E-value=1.6e-15  Score=125.65  Aligned_cols=66  Identities=35%  Similarity=0.604  Sum_probs=61.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++|++|+++++||||+|+++++|++||++||+++|++++|+|+++++++....
T Consensus        54 ~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~~~~  119 (144)
T PLN03134         54 AFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAPR  119 (144)
T ss_pred             HHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCCCCC
Confidence            689999999999999999999999999999999999999999999999999999999987765543

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

Probab=99.45  E-value=1.8e-13  Score=115.69  Aligned_cols=90  Identities=27%  Similarity=0.574  Sum_probs=71.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCCCCCCCCCCCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSGG   80 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~~~~g~~GGG~~~gg   80 (255)
                      +|.+||+|.+|+|.++     +.|||||||+++.+|+.||..|++++|.+..|.|++++.+......      +    +.
T Consensus        30 ~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r~~r~------g----g~   94 (195)
T KOG0107|consen   30 AFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPRGSRR------G----GS   94 (195)
T ss_pred             HHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcccccc------C----CC
Confidence            5899999999999986     6799999999999999999999999999999999999865543220      0    00


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025249           81 RGSYGADRPGGQDDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        81 rGg~ggGg~~g~~~~~~~g~~Gh~~~~cp~~  111 (255)
                      + ..     .+...|+.|+..|||.+.|-..
T Consensus        95 ~-~~-----~g~~~~~r~G~rg~~~r~~~~s  119 (195)
T KOG0107|consen   95 R-PP-----RGRGFCYRCGERGHIGRNCKDS  119 (195)
T ss_pred             C-Cc-----ccccccccCCCccccccccccc
Confidence            1 01     1112299999999999999774

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.40  E-value=5.5e-13  Score=123.12  Aligned_cols=63  Identities=21%  Similarity=0.368  Sum_probs=60.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++|+.|+++||||||+|.+.++|.+||++||+.+|+++.|+|+++..+..
T Consensus       289 ~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       289 LFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            689999999999999999999999999999999999999999999999999999999988754

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

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.39  E-value=4.5e-13  Score=120.87  Aligned_cols=86  Identities=23%  Similarity=0.586  Sum_probs=76.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCCCCCCCCCCCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSGG   80 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~~~~g~~GGG~~~gg   80 (255)
                      +|++||+|++|+|++|        |+||.|+-.++|..||+.||+.+|.|+++.|+++..+-....              
T Consensus        98 ~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrlrtap--------------  155 (346)
T KOG0109|consen   98 KFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTAP--------------  155 (346)
T ss_pred             hhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeeccccccCC--------------
Confidence            5999999999999998        999999999999999999999999999999999987765533              


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 025249           81 RGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGR  115 (255)
Q Consensus        81 rGg~ggGg~~g~~~~~~~g~~Gh~~~~cp~~~gg~  115 (255)
                             +.+.+.+|+.|++.|||+.+||.-..++
T Consensus       156 -------gmgDq~~cyrcGkeghwskEcP~~~~~r  183 (346)
T KOG0109|consen  156 -------GMGDQSGCYRCGKEGHWSKECPVDRTGR  183 (346)
T ss_pred             -------CCCCHHHheeccccccccccCCccCCCc
Confidence                   1234678999999999999999887655

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.36  E-value=4.9e-13  Score=115.78  Aligned_cols=62  Identities=26%  Similarity=0.431  Sum_probs=59.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |||+||.|.+|.|++|+.|.+++|||||-|.+..+|+.||++|++.+|+++.|.|++|+-..
T Consensus        33 vFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~arygr   94 (256)
T KOG4207|consen   33 VFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARYGR   94 (256)
T ss_pred             HHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhcCC
Confidence            69999999999999999999999999999999999999999999999999999999997543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.34  E-value=4.6e-12  Score=118.78  Aligned_cols=64  Identities=17%  Similarity=0.285  Sum_probs=58.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|++|+.|+++|+||||+|+++++|++||++||+++|.+  ++|+|.+|+.+...
T Consensus       213 ~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       213 IFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             HHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccccc
Confidence            68999999999999999999999999999999999999999999998876  68999999865443

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).

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.34  E-value=2e-12  Score=117.03  Aligned_cols=71  Identities=17%  Similarity=0.318  Sum_probs=65.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGY   71 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~~~~g~   71 (255)
                      .|++||+|+.|.||.|+.|+++||||||+|+++.+|++|.+..++++|+++.|.|++...+..+.+....-
T Consensus       121 eF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRTvkgW~PRRL  191 (335)
T KOG0113|consen  121 EFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRTVKGWLPRRL  191 (335)
T ss_pred             HHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccccccccccccc
Confidence            38999999999999999999999999999999999999999999999999999999999888877755444

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.33  E-value=1.1e-12  Score=120.02  Aligned_cols=60  Identities=30%  Similarity=0.519  Sum_probs=55.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+||.+ +. -+|||+||||++.++|++|-++||+.+|.|++|+|+.|.++-
T Consensus       116 MF~kfG~VldVEIIfN-ER-GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  116 MFEKFGKVLDVEIIFN-ER-GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARV  175 (376)
T ss_pred             HHHhhCceeeEEEEec-cC-CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhh
Confidence            7999999999999997 33 389999999999999999999999999999999999998653

>PF13893 RRM_5: RNA recognition motif

Probab=99.33  E-value=3.8e-12  Score=88.08  Aligned_cols=53  Identities=28%  Similarity=0.569  Sum_probs=48.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||++||+|++|.++.++     +++|||+|.+.++|++|++.||+..|.+++|+|++|
T Consensus         4 ~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    4 LFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             HhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            58999999999998764     579999999999999999999999999999999986

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.32  E-value=1.8e-12  Score=121.47  Aligned_cols=62  Identities=19%  Similarity=0.400  Sum_probs=58.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++|+.|++++|||||+|+++++|++||++||+++|.+++|+|+++++..
T Consensus       127 lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~  188 (346)
T TIGR01659       127 LFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGG  188 (346)
T ss_pred             HHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccccc
Confidence            68999999999999999999999999999999999999999999999999999999987643

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.32  E-value=2.9e-12  Score=113.26  Aligned_cols=61  Identities=18%  Similarity=0.471  Sum_probs=59.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||.+||.|..|.|++|++|+.+||||||+|.+.++|++||+.||++-+++..|.|++++|+
T Consensus       209 Lf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  209 LFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             HhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            7899999999999999999999999999999999999999999999999999999999986

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.30  E-value=3.8e-12  Score=117.55  Aligned_cols=63  Identities=19%  Similarity=0.481  Sum_probs=60.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+||+|+.|++++|||||+|.++++|++||+.||++.|.+++|+|++++++..
T Consensus        23 ~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~   85 (352)
T TIGR01661        23 LFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD   85 (352)
T ss_pred             HHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc
Confidence            699999999999999999999999999999999999999999999999999999999987653

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

>smart00361 RRM_1 RNA recognition motif

Probab=99.29  E-value=6.1e-12  Score=91.39  Aligned_cols=54  Identities=20%  Similarity=0.421  Sum_probs=49.6

Q ss_pred             CCCccceEEE-EeecCCC--CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 025249            3 QCLTHNNDLK-IMLERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN   56 (255)
Q Consensus         3 ekFG~I~~V~-Iv~Dk~T--g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~   56 (255)
                      ++||+|++|. |+.++.|  +.++||+||+|.++++|++||+.||+..|.+++|+|.
T Consensus        14 ~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361       14 EYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             HhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            3999999995 8888777  9999999999999999999999999999999999873

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.18  E-value=1.3e-11  Score=108.54  Aligned_cols=58  Identities=21%  Similarity=0.404  Sum_probs=54.0

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||+||+|+++.||.||.|+++|||+||||.+.|+|++|++..| -.|+|++..|++|.-
T Consensus        33 FeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   33 FEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKANCNLASL   90 (247)
T ss_pred             HHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccccchhhh
Confidence            8999999999999999999999999999999999999998665 679999999998853

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.16  E-value=3.6e-11  Score=107.76  Aligned_cols=61  Identities=26%  Similarity=0.570  Sum_probs=59.0

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |.+||+|.+++||+|..|+++|||+||.|.+.++|++||++||++=|..+.|..++|..|+
T Consensus        83 F~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   83 FAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             hccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            7899999999999999999999999999999999999999999999999999999998776

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.15  E-value=4.4e-11  Score=113.18  Aligned_cols=59  Identities=22%  Similarity=0.502  Sum_probs=55.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A~   59 (255)
                      |||+.|+|.+|+||+|+.++.+||||||+|.++++|++||+.||+++|. |+.|.|+++.
T Consensus       103 lfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen  103 LFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             HHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            7999999999999999999999999999999999999999999999996 7888887765

>smart00360 RRM RNA recognition motif

Probab=99.13  E-value=1.1e-10  Score=80.67  Aligned_cols=56  Identities=18%  Similarity=0.571  Sum_probs=52.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN   56 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~   56 (255)
                      +|++||+|+.|.|+.++.+++++++|||+|.+.++|++||+.|++..|.+++|.|+
T Consensus        16 ~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       16 LFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             HHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            47899999999999998889999999999999999999999999999999998874

>PF00076 RRM_1: RNA recognition motif

Probab=99.12  E-value=9e-11  Score=82.95  Aligned_cols=53  Identities=21%  Similarity=0.547  Sum_probs=49.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS   54 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~   54 (255)
                      +|++||+|+.|+|+.+ .++++++||||+|+++++|++||++||+++|.+++|+
T Consensus        18 ~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   18 FFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             HHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             HHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            5889999999999998 7888999999999999999999999999999999884

(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 ....

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.12  E-value=3.8e-11  Score=105.04  Aligned_cols=63  Identities=30%  Similarity=0.450  Sum_probs=59.5

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      |=.||.|+.|+|+.|-+++++++|+||+|+..|+|.+||..||..+|.+++|.|++|+|..-+
T Consensus        31 FIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~kik   93 (298)
T KOG0111|consen   31 FIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKIK   93 (298)
T ss_pred             cccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCcccc
Confidence            567999999999999999999999999999999999999999999999999999999986544

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

Probab=99.11  E-value=1.3e-10  Score=115.58  Aligned_cols=64  Identities=17%  Similarity=0.317  Sum_probs=60.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|++|+.|+++||||||+|++.++|++||++||+.+|.|+.|+|.+|.+++..
T Consensus       224 lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       224 VFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             HHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccc
Confidence            6999999999999999999999999999999999999999999999999999999999876544

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.

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.09  E-value=2.9e-11  Score=103.04  Aligned_cols=59  Identities=22%  Similarity=0.477  Sum_probs=56.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|+.|.||+|+.|+++|||||+.|++..+..-||..||++.|.+++|.|+...
T Consensus        55 VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   55 VFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             EeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            59999999999999999999999999999999999999999999999999999998764

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.09  E-value=1.2e-10  Score=104.22  Aligned_cols=64  Identities=20%  Similarity=0.481  Sum_probs=61.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||...|+|++|+||+||.|+++.||+||.|.++++|++||..||+..|..++|+|++|.|....
T Consensus        61 LF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~  124 (360)
T KOG0145|consen   61 LFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDS  124 (360)
T ss_pred             HhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhh
Confidence            6888999999999999999999999999999999999999999999999999999999987654

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.07  E-value=2.7e-10  Score=101.87  Aligned_cols=62  Identities=24%  Similarity=0.431  Sum_probs=59.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||..||.|+.|+|++|..|+++|||+||++.+-++|..||..||+..|.++.|.|++...+.
T Consensus       298 lFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk~  359 (360)
T KOG0145|consen  298 LFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKA  359 (360)
T ss_pred             HhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCCC
Confidence            79999999999999999999999999999999999999999999999999999999987653

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

Probab=99.06  E-value=3.1e-10  Score=108.74  Aligned_cols=61  Identities=30%  Similarity=0.548  Sum_probs=58.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|+.|.|++++.|+++++||||+|.+.++|++||++||+++|.+++|.|.+|+..
T Consensus       206 ~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~  266 (457)
T TIGR01622       206 IFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS  266 (457)
T ss_pred             HHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCC
Confidence            6899999999999999999999999999999999999999999999999999999998743

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.

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

Probab=99.03  E-value=4e-10  Score=109.26  Aligned_cols=61  Identities=21%  Similarity=0.455  Sum_probs=58.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||.|+.|.|++++.|++++|||||+|.++++|++||++||+++|.+++|.|.+|...
T Consensus       315 ~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       315 LLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             HHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            6899999999999999999999999999999999999999999999999999999999754

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

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

Probab=99.03  E-value=2.7e-10  Score=113.42  Aligned_cols=59  Identities=22%  Similarity=0.447  Sum_probs=56.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|++|+.|++++|||||+|+++++|++||++||+++|.++.|+|....
T Consensus       127 lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       127 AFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             HHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            68999999999999999999999999999999999999999999999999999998654

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

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

Probab=99.03  E-value=3.7e-10  Score=111.37  Aligned_cols=62  Identities=32%  Similarity=0.567  Sum_probs=58.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.| .+++++|||||+|.+.++|++||++||++.|.+++|.|.+|+.+..
T Consensus       305 ~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~  366 (562)
T TIGR01628       305 LFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ  366 (562)
T ss_pred             HHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHH
Confidence            5899999999999999 8899999999999999999999999999999999999999987653

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

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.03  E-value=1.7e-10  Score=94.28  Aligned_cols=63  Identities=19%  Similarity=0.309  Sum_probs=59.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      +|..||+|+.|.|-.|+.|+-.||||+|+|++.++|++||.+||+.+|.+++|+|+|+..+.+
T Consensus        92 ~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~gp  154 (170)
T KOG0130|consen   92 KFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVKGP  154 (170)
T ss_pred             HHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEecCC
Confidence            478999999999999999999999999999999999999999999999999999999976544

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.98  E-value=2.3e-10  Score=102.72  Aligned_cols=64  Identities=23%  Similarity=0.468  Sum_probs=60.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||-.||.|++.+|..|+.|+++|+|+||.|+++.++++||.+||+.+|.-++|+|.+..||...
T Consensus       305 mF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdan  368 (371)
T KOG0146|consen  305 MFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDAN  368 (371)
T ss_pred             HhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccccC
Confidence            5788999999999999999999999999999999999999999999999999999999988654

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.97  E-value=1.6e-09  Score=77.53  Aligned_cols=53  Identities=19%  Similarity=0.520  Sum_probs=49.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS   54 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~   54 (255)
                      +|+.|+.|+.|.++.++. ++++++|||+|.++++|++||+.+++++|++++|+
T Consensus        18 ~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   18 FFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             HCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             HHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            488999999999999977 89999999999999999999999999999999875

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=98.96  E-value=8.6e-10  Score=108.74  Aligned_cols=60  Identities=13%  Similarity=0.323  Sum_probs=57.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||+.||.+.|.++.|+|.+++.
T Consensus        20 ~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628        20 LFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             HHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            589999999999999999999999999999999999999999999999999999998864

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

>smart00362 RRM_2 RNA recognition motif

Probab=98.95  E-value=1.6e-09  Score=75.12  Aligned_cols=54  Identities=22%  Similarity=0.525  Sum_probs=49.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN   56 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~   56 (255)
                      +|++||+|..|.|+.++  +.++++|||+|.+.++|++||+.|++.+|.+++|+|+
T Consensus        19 ~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       19 LFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             HHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            47899999999999886  6788999999999999999999999999999998874

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

Probab=98.95  E-value=1.1e-09  Score=104.80  Aligned_cols=60  Identities=20%  Similarity=0.379  Sum_probs=56.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|++|+||+|+.|++++|||||+|.++++|++||+ ||++.|.+++|.|..++..
T Consensus       109 ~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~~  168 (457)
T TIGR01622       109 FFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQAE  168 (457)
T ss_pred             HHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecchh
Confidence            58999999999999999999999999999999999999997 9999999999999887643

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.

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.93  E-value=7.2e-10  Score=102.67  Aligned_cols=63  Identities=17%  Similarity=0.299  Sum_probs=59.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||+.||+|++|.||+|+.|+.+.-||||+|++++++++|.-+|++..|+.+.|.|++++.-..
T Consensus       259 IFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVsk  321 (479)
T KOG0415|consen  259 IFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVSK  321 (479)
T ss_pred             HHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhhh
Confidence            799999999999999999999999999999999999999999999999999999999986443

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.92  E-value=1.4e-09  Score=105.16  Aligned_cols=63  Identities=22%  Similarity=0.563  Sum_probs=58.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      |||.||+|+.|.+++|.+|+++|||+||+|.+.++|.+|+++||+.+|.|+.|+|...+-+..
T Consensus       298 ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  298 IFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             hccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            799999999999999999999999999999999999999999999999999999987764443

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

Probab=98.89  E-value=1.5e-09  Score=107.78  Aligned_cols=57  Identities=21%  Similarity=0.476  Sum_probs=50.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A   58 (255)
                      ||++||+|++|+||+| .|++++|||||+|.++++|++||+.||+.+|. ++.|.|.++
T Consensus        78 ~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        78 LFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             HHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            6899999999999999 89999999999999999999999999998885 666655433

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=98.89  E-value=1.7e-09  Score=103.78  Aligned_cols=56  Identities=14%  Similarity=0.366  Sum_probs=51.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCH--HHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADR--RAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~--e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|.+|.||  ++|+  ||||||+|.+.  +++++||+.||+.+|+|+.|+|+.|++
T Consensus        30 vFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         30 IFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             HHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            58999999999999  5677  89999999987  789999999999999999999999985

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

Probab=98.89  E-value=2.7e-09  Score=91.16  Aligned_cols=60  Identities=28%  Similarity=0.655  Sum_probs=57.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|..|.|+.|+.|+++++||||+|.++++|..||+.|++..|.++.|.|.++.+
T Consensus       135 ~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         135 LFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             HHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            589999999999999999999999999999999999999999999999999999999653

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.89  E-value=1.3e-09  Score=103.04  Aligned_cols=64  Identities=17%  Similarity=0.398  Sum_probs=56.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee-C--CeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF-G--DRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i-~--Gr~I~V~~A~~k~~~   64 (255)
                      |||+||.|.+|.|++||.|+.++|||||+|.+.++|.+||.+||++.. -  ...|.|++|....++
T Consensus        54 lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er  120 (510)
T KOG0144|consen   54 LFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER  120 (510)
T ss_pred             HHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc
Confidence            699999999999999999999999999999999999999999997543 3  478999999865544

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.87  E-value=1.9e-09  Score=104.31  Aligned_cols=64  Identities=19%  Similarity=0.321  Sum_probs=58.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|.|++.+.+..+ |||||+|....+|.+||+.||+.+|++++|.|+||.++....
T Consensus       137 vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye  200 (678)
T KOG0127|consen  137 VFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYE  200 (678)
T ss_pred             HHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccccc
Confidence            6899999999999987766666 999999999999999999999999999999999999887553

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=98.87  E-value=1.4e-09  Score=102.70  Aligned_cols=65  Identities=18%  Similarity=0.334  Sum_probs=57.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee-C--CeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF-G--DRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i-~--Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||.|++|.|++| ..+.+||||||+|++.|.|..||++||+... .  ..+|.|+||.+++++..
T Consensus       144 iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  144 IFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            7999999999999999 6789999999999999999999999998543 3  47899999999887653

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=98.86  E-value=5.4e-09  Score=89.58  Aligned_cols=59  Identities=17%  Similarity=0.286  Sum_probs=51.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||.|||.|++|.|..-   -.+..||||+|+++.+|+.||..-++..+++..|.|+++..-.
T Consensus        26 lFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr   84 (241)
T KOG0105|consen   26 LFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGR   84 (241)
T ss_pred             HHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCC
Confidence            7999999999988553   2356799999999999999999999999999999999998544

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.84  E-value=4.6e-09  Score=94.55  Aligned_cols=56  Identities=13%  Similarity=0.287  Sum_probs=51.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||+.||+|++|.|+.|++   +++||||+|+++++|+.||. ||+.+|.++.|.|..+..
T Consensus        24 fFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         24 FFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             HHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            689999999999999865   46899999999999999996 999999999999999874

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.84  E-value=2.8e-09  Score=102.45  Aligned_cols=64  Identities=28%  Similarity=0.628  Sum_probs=60.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++.|.|.+++++.|++|+++|||+||+|.++++|+.||+.||+.++.+++|+|+++...+..
T Consensus        38 ~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~~~~  101 (435)
T KOG0108|consen   38 IFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNRKNA  101 (435)
T ss_pred             HHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccccchh
Confidence            5788999999999999999999999999999999999999999999999999999999866554

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=98.82  E-value=3.2e-09  Score=100.71  Aligned_cols=58  Identities=21%  Similarity=0.352  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+.++|        ||||+|.+.++|.+||++||+++|+|..|+|.+|+|..+...
T Consensus       279 ~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  279 LFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             HHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhcc
Confidence            6899999999999988        999999999999999999999999999999999998665543

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

Probab=98.81  E-value=6.2e-09  Score=100.95  Aligned_cols=60  Identities=27%  Similarity=0.305  Sum_probs=53.6

Q ss_pred             CCCCCccceEEEEeecC---CCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLER---DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk---~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|++|+|+++.   .+...+|++||+|+++++|++||++||+.+|++++|.|.+...
T Consensus       439 ~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       439 EFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            48899999999999753   4456789999999999999999999999999999999998764

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

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

Probab=98.81  E-value=6.4e-09  Score=101.29  Aligned_cols=56  Identities=14%  Similarity=0.190  Sum_probs=52.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|++|+|+++     +++||||+|.++++|++||+.||+.+|.+++|+|++++.+
T Consensus       296 lF~~yG~V~~vki~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       296 LFCVYGNVERVKFMKN-----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             HHHhcCCeEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            6999999999999997     3689999999999999999999999999999999998754

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).

>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=98.80  E-value=1.5e-08  Score=70.60  Aligned_cols=56  Identities=21%  Similarity=0.585  Sum_probs=50.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK   57 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~   57 (255)
                      +|+.|++|..+.|+.++.+ .++++|||+|.+.++|+.|++.|++..|++++|.|.+
T Consensus        19 ~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          19 LFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             HHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4778899999999998766 7789999999999999999999999999999999864

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).

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

Probab=98.78  E-value=8.7e-09  Score=102.37  Aligned_cols=56  Identities=21%  Similarity=0.363  Sum_probs=51.5

Q ss_pred             CCCCC--ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCL--THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekF--G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|  |+|++|+++++        ||||+|++.++|++||++||+++|++++|+|++|+|+...
T Consensus       253 ~F~~f~~G~I~rV~~~rg--------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       253 SFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HHHhcCCCceEEEEeecC--------eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcc
Confidence            58999  99999998764        9999999999999999999999999999999999986544

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.

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.77  E-value=4.5e-09  Score=89.68  Aligned_cols=62  Identities=24%  Similarity=0.307  Sum_probs=56.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||-+.|+|+.|+|++|+.|.+++|||||+|.++|+|+=||+.||...|.+++|+|+.|...+
T Consensus        29 L~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~   90 (203)
T KOG0131|consen   29 LFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQ   90 (203)
T ss_pred             HHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEeccccc
Confidence            35567999999999999999999999999999999999999999999999999999998433

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.77  E-value=3.9e-09  Score=95.68  Aligned_cols=55  Identities=25%  Similarity=0.434  Sum_probs=52.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      |||+||+|++|.||++        |+||+.+++..++.||.+||+.+|++..|+|+.++.|..
T Consensus        22 lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKsk   76 (346)
T KOG0109|consen   22 LFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKSK   76 (346)
T ss_pred             HHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccccCC
Confidence            7999999999999998        999999999999999999999999999999999988743

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=9.4e-09  Score=83.40  Aligned_cols=62  Identities=24%  Similarity=0.376  Sum_probs=58.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++.|+|..|.|-.|+.|..+.|||||+|.+.++|+.||+-++++.|+.++|.|++...-.
T Consensus        56 LFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~GF~  117 (153)
T KOG0121|consen   56 LFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAGFV  117 (153)
T ss_pred             HHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccccch
Confidence            68999999999999999999999999999999999999999999999999999999876543

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.77  E-value=6.2e-09  Score=96.92  Aligned_cols=57  Identities=23%  Similarity=0.466  Sum_probs=54.6

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      |..||+|++|.+-+|+.|+++|+||||+|+-+|.|+-|++.||+.+|.+++|+|..-
T Consensus       134 F~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  134 FDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             ccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            788999999999999999999999999999999999999999999999999999743

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.75  E-value=1.6e-08  Score=90.98  Aligned_cols=57  Identities=14%  Similarity=0.363  Sum_probs=52.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      +|+.||.|.+|+|.++      +|||||.|+++|+|..||.+||+++|.++.|+|.+-+....
T Consensus       184 ~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  184 TFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             hcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCC
Confidence            4899999999999997      58999999999999999999999999999999998875443

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.74  E-value=1.4e-08  Score=88.03  Aligned_cols=60  Identities=10%  Similarity=0.311  Sum_probs=54.2

Q ss_pred             CCCC-ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            2 QQCL-THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         2 fekF-G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      |.+| |.|+.+++-+++.||.+|+||||+|++++.|+.|-+.||+..|.++.|+|.+-.|.
T Consensus        70 ~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   70 FRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             hhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            4555 88888888899999999999999999999999999999999999999999887654

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.64  E-value=4.4e-08  Score=87.23  Aligned_cols=55  Identities=13%  Similarity=0.245  Sum_probs=49.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||+.||+|++|+|+.|.++   ++||||+|+++++|+.||. ||+.+|.++.|.|..+.
T Consensus        25 fFS~~G~I~~V~I~~D~et---~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121         25 FFSHCGAIEHVEIIRSGEY---ACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             HHHhcCCeEEEEEecCCCc---ceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            6999999999999998544   4799999999999999996 99999999999998765

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.64  E-value=3.3e-08  Score=93.58  Aligned_cols=62  Identities=18%  Similarity=0.330  Sum_probs=56.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      +|+.||+|++|+|++|.+ + +||| ||+|+++++|++||+.||+..+.+++|.|..+..+.+..
T Consensus        96 ~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~  157 (369)
T KOG0123|consen   96 TFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEERE  157 (369)
T ss_pred             HHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhc
Confidence            589999999999999944 4 9999 999999999999999999999999999999988776654

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

Probab=98.61  E-value=6.4e-08  Score=94.29  Aligned_cols=58  Identities=7%  Similarity=0.125  Sum_probs=50.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++++.    +++|||+|+++++|++||++||+++|.+  .+|+|++|+++.
T Consensus       116 ~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~  175 (481)
T TIGR01649       116 IFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTR  175 (481)
T ss_pred             HHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCC
Confidence            689999999999988643    3689999999999999999999999975  488999988644

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=98.61  E-value=3.3e-08  Score=84.39  Aligned_cols=65  Identities=37%  Similarity=0.483  Sum_probs=59.6

Q ss_pred             CCCCCccceEE-EEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDL-KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V-~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      +|++||.|... +||+|..|+++++|+||.|.+.|.+.+||+.||++.|.+++|+|++|..+..+.
T Consensus       116 tFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  116 TFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             HHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            48999999875 899999999999999999999999999999999999999999999998765443

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.57  E-value=5e-08  Score=95.10  Aligned_cols=60  Identities=25%  Similarity=0.364  Sum_probs=57.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||+|||+|+-++||++..|--.++|+|||+.+.++|.+||+.||-++|.++.|.|+.|+.
T Consensus       425 lFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  425 LFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             HHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            799999999999999988877889999999999999999999999999999999999874

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.46  E-value=9.7e-08  Score=88.39  Aligned_cols=64  Identities=27%  Similarity=0.501  Sum_probs=59.8

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      |++|++|..|.||+|+++.++++|+||+|++++++++++. +.-++|+++.|+|..|.|+.....
T Consensus       118 fe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~~~  181 (311)
T KOG4205|consen  118 FEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVMQS  181 (311)
T ss_pred             hhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhccc
Confidence            8999999999999999999999999999999999999987 577899999999999999987764

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=98.40  E-value=2.8e-07  Score=89.63  Aligned_cols=65  Identities=23%  Similarity=0.448  Sum_probs=60.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      +|+.+|+|..|.|++++.+..++||+||+|.-+|+++.||++++...|.++.|.|++|+++....
T Consensus        25 ~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e   89 (678)
T KOG0127|consen   25 FFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSE   89 (678)
T ss_pred             hhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccch
Confidence            58999999999999999999999999999999999999999999999999999999998765443

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.39  E-value=4.5e-07  Score=86.30  Aligned_cols=57  Identities=16%  Similarity=0.420  Sum_probs=53.4

Q ss_pred             CCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            3 QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         3 ekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      |+.|+|+-|.|+.| +++|++|+|.|||+++|.+++|+++||-++|++++|+|+....
T Consensus        67 ekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   67 EKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             HhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            67899999999999 8899999999999999999999999999999999999986654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.38  E-value=2.9e-07  Score=80.82  Aligned_cols=61  Identities=16%  Similarity=0.290  Sum_probs=55.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|.+.+   |.+.+|-|||+|.+.+.|.+|+.+|++..+.++.+.|++|+.+..-
T Consensus        33 LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdi   93 (221)
T KOG4206|consen   33 LFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDI   93 (221)
T ss_pred             HHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccch
Confidence            799999999997765   5678999999999999999999999999999999999999876543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.31  E-value=7.2e-07  Score=80.46  Aligned_cols=63  Identities=16%  Similarity=0.307  Sum_probs=54.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG---DRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~---Gr~I~V~~A~~k~~~   64 (255)
                      ||+.||+|++|.|++- ..+.+||+|||.|.+..+|+.||..||+....   ...|.|++|...+++
T Consensus        39 lf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~ADTdkER  104 (371)
T KOG0146|consen   39 LFQPFGNIEECTVLRG-PDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKFADTDKER  104 (371)
T ss_pred             HhcccCCcceeEEecC-CCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEeccchHHH
Confidence            6899999999999987 56889999999999999999999999986543   367889999876554

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.31  E-value=1.3e-06  Score=68.77  Aligned_cols=58  Identities=21%  Similarity=0.317  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||-+||+|..|+|-.+++|   +|-|||+|++..+|++|++.|++..+.++.|.|-+-++.
T Consensus        38 lFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   38 LFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             HhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            6899999999999887665   689999999999999999999999999999999887653

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.29  E-value=3.6e-07  Score=84.63  Aligned_cols=63  Identities=22%  Similarity=0.448  Sum_probs=56.4

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      |++||+|++|.||+|+.|+++++|+||+|++.+.+.++|.+ .-++|++++|++..|.++....
T Consensus        27 f~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av~r~~~~   89 (311)
T KOG4205|consen   27 FSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAVSREDQT   89 (311)
T ss_pred             hcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceeccCccccc
Confidence            68999999999999999999999999999999999988874 4578999999999999877544

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.29  E-value=5.3e-07  Score=84.23  Aligned_cols=60  Identities=18%  Similarity=0.351  Sum_probs=56.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +||.||+|++|+|.+++.+..+|||+||+|.+.++..+||..||-..|.++-|.|-.+..
T Consensus       230 VFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  230 VFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             HHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            589999999999999999999999999999999999999999999999999999977754

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.27  E-value=1.3e-06  Score=82.72  Aligned_cols=59  Identities=8%  Similarity=0.148  Sum_probs=55.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      +|+.+++|++|+|.+|. |  +-|||||.|.++++|++||++||-..|++++|.|.+++...
T Consensus        18 ~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen   18 KFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             HhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            58899999999999998 7  99999999999999999999999999999999999987543

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.24  E-value=3.7e-05  Score=71.65  Aligned_cols=54  Identities=30%  Similarity=0.569  Sum_probs=50.6

Q ss_pred             EEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249           10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus        10 ~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      +|+|.+|++|+++|+-|.|+|++...|++||+.++++.|.+.+|+|.+|+.+..
T Consensus       103 ki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  103 KIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRTG  156 (351)
T ss_pred             chhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhccC
Confidence            478899999999999999999999999999999999999999999999987764

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.03  E-value=7.9e-06  Score=81.60  Aligned_cols=59  Identities=15%  Similarity=0.357  Sum_probs=51.5

Q ss_pred             CCCCCccceEEEEeecCCCC---CCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSG---RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg---~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++.|.|.+|.|.+-+..-   .+.||+||+|.++++|++|++.|+++.|+++.|.|+++.
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            47788999999887754321   356999999999999999999999999999999999998

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.03  E-value=5.5e-06  Score=83.43  Aligned_cols=59  Identities=19%  Similarity=0.329  Sum_probs=53.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      |||.||+|++|.|+.      ++++|||++...++|++||++|+...|..+.|+|.||..+..+.
T Consensus       441 ~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~ks  499 (894)
T KOG0132|consen  441 LFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKS  499 (894)
T ss_pred             HHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcch
Confidence            699999999999987      46899999999999999999999999999999999998766544

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.02  E-value=6.7e-06  Score=73.34  Aligned_cols=59  Identities=17%  Similarity=0.409  Sum_probs=55.6

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      |+.+|.|..|.|++|+.++.+|+|+||+|.+.+.+++||+ ||+.+|.++.|+|.....+
T Consensus       122 f~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  122 FESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             eeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            7788999999999999999999999999999999999999 9999999999999888765

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.01  E-value=1.6e-06  Score=77.52  Aligned_cols=61  Identities=26%  Similarity=0.537  Sum_probs=55.4

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |.+|=.....+|++|+.|+++|||+||.|.+.+++..|+.+||++-+..+.|++..+..+.
T Consensus       211 f~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  211 FKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             HHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            6677777788999999999999999999999999999999999999999999887776654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.01  E-value=2.1e-05  Score=75.65  Aligned_cols=63  Identities=22%  Similarity=0.431  Sum_probs=51.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      +|++||.|+++.|..-.-.++..+||||+|++.++++.||++ +-.+|.+++|.|+..++....
T Consensus       308 ~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~~~g  370 (419)
T KOG0116|consen  308 VFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPGFRG  370 (419)
T ss_pred             HHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccccccc
Confidence            489999999988876433344558999999999999999985 578899999999987764433

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.00  E-value=2.7e-06  Score=84.82  Aligned_cols=61  Identities=16%  Similarity=0.352  Sum_probs=56.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||..||.|.+|.|++-.....++|||||+|.++.+|.+|+++|..+.|.|+.|.++||...
T Consensus       633 LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  633 LFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             HHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccc
Confidence            7999999999999987666778999999999999999999999999999999999999754

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=97.74  E-value=3.8e-05  Score=68.94  Aligned_cols=61  Identities=11%  Similarity=0.273  Sum_probs=55.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++|++++.|.|..| +++.+.|.|-|+|+..++|++||+.+|+..|+++.|+|.+..+..
T Consensus       103 LF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~  163 (243)
T KOG0533|consen  103 LFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPS  163 (243)
T ss_pred             HHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcc
Confidence            6899999999999888 788999999999999999999999999999999999998876544

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=97.69  E-value=2.3e-05  Score=76.42  Aligned_cols=60  Identities=18%  Similarity=0.402  Sum_probs=55.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||+.+|+|..|.||.|+.+..+||.|||+|.+++.+..||. |.|+.+.+..|.|...+..
T Consensus       199 fFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sEae  258 (549)
T KOG0147|consen  199 FFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSEAE  258 (549)
T ss_pred             HHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccHHH
Confidence            58999999999999999999999999999999999999995 9999999999999877643

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.67  E-value=4e-05  Score=75.11  Aligned_cols=57  Identities=16%  Similarity=0.372  Sum_probs=50.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A   58 (255)
                      ||+++|+|+.+.++.+.+++ ++||.|++|.+..+|+.||+.||++.|+ .+++.|..-
T Consensus        84 vfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~f  141 (698)
T KOG2314|consen   84 VFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRLF  141 (698)
T ss_pred             HHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceEEeehh
Confidence            68999999999999986666 9999999999999999999999999987 677777543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.65  E-value=6.5e-05  Score=69.89  Aligned_cols=55  Identities=16%  Similarity=0.308  Sum_probs=47.5

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHH-hcCCeeCCeEEEEEecccCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIRE-MHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~-lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |.+||+|..|.|+..      +++|||+|.+.++|+.|.++ +|-..|++++|+|.|..+++
T Consensus       249 FyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~~~  304 (377)
T KOG0153|consen  249 FYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRPKQ  304 (377)
T ss_pred             HhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCCcc
Confidence            789999999999875      45999999999999998654 67778899999999999833

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.62  E-value=3.1e-05  Score=68.27  Aligned_cols=55  Identities=27%  Similarity=0.495  Sum_probs=48.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||.+|++|.+|.|+.        +|+||+|+++.+|+.||..||+++|.+.+|.|++|..+..
T Consensus        21 ~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen   21 FFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             HHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            688999999998765        6999999999999999999999999998888888886543

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.41  E-value=0.00047  Score=61.12  Aligned_cols=66  Identities=9%  Similarity=0.161  Sum_probs=47.7

Q ss_pred             CCCCCccceEEEEe-ecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIM-LERDSGRPRGFGFITYADRRAMDDAIREMHGREFG---DRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv-~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~---Gr~I~V~~A~~k~~~~~   66 (255)
                      ||..|--.+.+.|. +++...-++-+|||+|.+.++|++|+++||+..|+   +.+|.|++|+......+
T Consensus        54 LFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~kr  123 (284)
T KOG1457|consen   54 LFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKRKR  123 (284)
T ss_pred             HhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCccccc
Confidence            34445333434332 34444556789999999999999999999999998   67888888886555433

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.33  E-value=0.00011  Score=64.73  Aligned_cols=57  Identities=9%  Similarity=0.101  Sum_probs=47.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||-+-|+|++|.|+.++.. +.| ||||.|+++..+.-||+.||+..|.+..|+|.+-.
T Consensus        29 lfiqaGPV~kv~ip~~~d~-~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen   29 LFIQAGPVYKVGIPSGQDQ-EQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             HhhccCceEEEeCCCCccC-CCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            3445599999999988554 455 99999999999999999999999999888887654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=97.25  E-value=0.00013  Score=71.47  Aligned_cols=62  Identities=23%  Similarity=0.498  Sum_probs=56.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |.+.|+.|....+++|..|+.+|+|||.+|.+......||+.||+++|.+++|.|..|.+..
T Consensus       309 ll~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  309 LLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             HHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            34678999999999999999999999999999999999999999999999999999887543

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

Probab=97.22  E-value=0.001  Score=51.75  Aligned_cols=56  Identities=11%  Similarity=0.275  Sum_probs=48.4

Q ss_pred             ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC----CeEEEEEecccC
Q 025249            6 THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG----DRVISVNKAQPK   61 (255)
Q Consensus         6 G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~----Gr~I~V~~A~~k   61 (255)
                      ++..-+.|+.|..|..+.|||||.|.+++.|.+-.+.+|++.+.    .+.++|.+|+-+
T Consensus        28 g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAriQ   87 (97)
T PF04059_consen   28 GKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYARIQ   87 (97)
T ss_pred             CcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhHhh
Confidence            45566789999999999999999999999999999999999886    577888888643

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

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.17  E-value=0.0008  Score=63.48  Aligned_cols=57  Identities=12%  Similarity=0.195  Sum_probs=50.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||=.||+|++|++|+.|     .+-|.|++.+..+++.||..||+..|.+.+|.|.++++.-
T Consensus       308 l~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~  364 (494)
T KOG1456|consen  308 LFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNF  364 (494)
T ss_pred             hhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccc
Confidence            56679999999999974     3789999999999999999999999999999999887543

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.13  E-value=0.00074  Score=64.27  Aligned_cols=54  Identities=13%  Similarity=0.258  Sum_probs=50.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||..||+|.+|+|+.+|.     --|+|.+.+...|+-|++.|+++.|.+++|.|.+++
T Consensus       318 lFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  318 LFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             HHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            688999999999999854     369999999999999999999999999999999886

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=97.12  E-value=0.0005  Score=64.10  Aligned_cols=61  Identities=18%  Similarity=0.291  Sum_probs=53.7

Q ss_pred             CCCCCccceE--------EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNND--------LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~--------V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||+++|-|.+        |+|..+. .++.||=|+|+|...|+++-||+.|+..+|.+++|.|+.|+-..
T Consensus       154 ~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~  222 (382)
T KOG1548|consen  154 VMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQM  222 (382)
T ss_pred             HHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhh
Confidence            4778887764        7888884 49999999999999999999999999999999999999998544

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.98  E-value=0.0014  Score=54.47  Aligned_cols=50  Identities=12%  Similarity=0.210  Sum_probs=41.6

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      |++||+|+-|+++-+        --+|||.+-+.|.+|++ |++++|.++.|+|....|
T Consensus        57 ~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   57 FAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE---
T ss_pred             HHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCc
Confidence            678999999988876        46899999999999998 999999999999988765

; PDB: 1UFW_A 2DNR_A.

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=96.95  E-value=0.0017  Score=63.77  Aligned_cols=58  Identities=19%  Similarity=0.269  Sum_probs=47.8

Q ss_pred             CCCCccceEEEEeecCCC---CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            2 QQCLTHNNDLKIMLERDS---GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~T---g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +.+|+.|.+|+|+.+-.+   .-.-|--||+|.+.++++.|+++|+|.+|.+++|.+.+-.
T Consensus       430 c~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  430 CAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             hcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            468999999999887221   2234567999999999999999999999999999887654

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=96.95  E-value=0.00032  Score=61.93  Aligned_cols=46  Identities=17%  Similarity=0.365  Sum_probs=40.0

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV   55 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V   55 (255)
                      |.+||+|+.+.++.        .++||+|+++++|..||+.|++.+|.++.|+|
T Consensus       120 ~~~~g~~~~~~~~~--------~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  120 FRPAGEVTYVDARR--------NFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hcccCCCchhhhhc--------cccceeehhhhhhhhcchhccchhhcCceeee
Confidence            67788886555533        49999999999999999999999999999999

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.90  E-value=0.0015  Score=61.07  Aligned_cols=59  Identities=15%  Similarity=0.246  Sum_probs=45.8

Q ss_pred             CCCCCccceEEEEeecCCC-CCCCcEE--EEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDS-GRPRGFG--FITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~T-g~srGfa--FVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|-+||+|.+|.|-+...+ ...-+.+  ||||.+.|+|..||+++++..++|+.|++.+-.
T Consensus       140 yFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         140 YFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             hhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            4889999999877553211 1112223  999999999999999999999999999987765

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.90  E-value=0.0023  Score=59.78  Aligned_cols=55  Identities=18%  Similarity=0.335  Sum_probs=47.3

Q ss_pred             CCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            3 QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         3 ekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ++||.|.+|.|.-.    .+.|.+.|+|.+.++|+.||+.|+|.-|++++|..++...+
T Consensus       298 ~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  298 EKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            68999999977532    36799999999999999999999999999999988776543

>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=96.64  E-value=0.0037  Score=47.52  Aligned_cols=37  Identities=19%  Similarity=0.330  Sum_probs=29.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249           24 GFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus        24 GfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +.|+|.|.+++.|+.|++.|++..+.+.+|.|+++..
T Consensus        40 ~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~~   76 (90)
T PF11608_consen   40 GTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSPK   76 (90)
T ss_dssp             T-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS--
T ss_pred             CEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcCC
Confidence            5899999999999999999999999999999998854

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=96.64  E-value=0.00047  Score=67.57  Aligned_cols=49  Identities=18%  Similarity=0.374  Sum_probs=43.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS   54 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~   54 (255)
                      ||++||+|.+|+.-.     ..++..||+|-|..+|++|+++||..+|.++.|+
T Consensus        95 ~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   95 IFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             HHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            689999999965544     3668999999999999999999999999999887

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=96.63  E-value=0.0027  Score=61.59  Aligned_cols=53  Identities=23%  Similarity=0.466  Sum_probs=43.2

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      +|+.+.  ..++|+++.|-|||+|+++|++++||+ +|-..|..+-|+|-.+.+..
T Consensus        35 ~I~~~~--~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   35 GIENLE--IPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             ceeEEE--EeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCcc
Confidence            466644  445789999999999999999999998 67788889999998775433

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.55  E-value=0.00059  Score=61.31  Aligned_cols=56  Identities=11%  Similarity=0.215  Sum_probs=47.8

Q ss_pred             CCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            3 QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         3 ekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      .|||+|++++|..+ ..-..+|-++|.|..+++|++|++.||+.-|.+++|.+++..
T Consensus        91 ~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   91 DKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            48999999977665 334567889999999999999999999999999999877654

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.27  E-value=0.0096  Score=56.37  Aligned_cols=55  Identities=11%  Similarity=0.175  Sum_probs=45.5

Q ss_pred             CCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCC
Q 025249            3 QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKM   62 (255)
Q Consensus         3 ekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~   62 (255)
                      ...|+|..|.|++.  ++   --|.|||++.+.|++|.++||+..|.-  .+|+|++|+|..
T Consensus       144 np~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  144 NPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             CCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            35689999988874  33   369999999999999999999998874  578899998754

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=96.24  E-value=0.0048  Score=62.35  Aligned_cols=59  Identities=20%  Similarity=0.347  Sum_probs=50.9

Q ss_pred             CCCCccceEEEEeecCC---CCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            2 QQCLTHNNDLKIMLERD---SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~---Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      |-.||+|..|+||+.+.   ..+.+-++||.|.+..+|++|++.|+++.|....|++-|+++
T Consensus       195 fGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~  256 (877)
T KOG0151|consen  195 FGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKA  256 (877)
T ss_pred             hcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccc
Confidence            56789999999998653   345667999999999999999999999999999999888853

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.14  E-value=0.004  Score=57.29  Aligned_cols=63  Identities=14%  Similarity=0.412  Sum_probs=56.2

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      |..++.|+.|+++.++.|+.+++||+|+|.+...++.||.. +...|.+++|.|....+.....
T Consensus       206 ~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  268 (285)
T KOG4210|consen  206 FVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPKSD  268 (285)
T ss_pred             ccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcccc
Confidence            56778999999999999999999999999999999999886 7889999999999998876553

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.76  E-value=0.015  Score=53.55  Aligned_cols=57  Identities=18%  Similarity=0.192  Sum_probs=45.2

Q ss_pred             CCCCccceEEEEeecCCCCCCC-cEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            2 QQCLTHNNDLKIMLERDSGRPR-GFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~sr-GfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      .+|||+|..|.|..++.--... ---||+|+..++|.+|+..||+.-|.|+.+...+-
T Consensus       307 ceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  307 CEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            4789999999887764322221 23699999999999999999999999999876654

>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=95.71  E-value=0.019  Score=44.90  Aligned_cols=57  Identities=12%  Similarity=0.131  Sum_probs=38.2

Q ss_pred             CCCCccceEEEEe-ecCC------CCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCe-EEEEEecc
Q 025249            2 QQCLTHNNDLKIM-LERD------SGRPRGFGFITYADRRAMDDAIREMHGREFGDR-VISVNKAQ   59 (255)
Q Consensus         2 fekFG~I~~V~Iv-~Dk~------Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr-~I~V~~A~   59 (255)
                      |++||+|++..-+ ++..      .-...-+-.|+|+++.+|++||+ .|+..|.+. .|-|.+++
T Consensus        26 F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   26 FSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             HHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEEE-H
T ss_pred             HHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEEEcH
Confidence            8899999987511 1100      00123488999999999999998 699999885 44576664

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.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=95.57  E-value=0.0099  Score=41.01  Aligned_cols=33  Identities=12%  Similarity=0.285  Sum_probs=27.7

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHH
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAI   40 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI   40 (255)
                      |++||+|+++.+...      .-+.+|+|.+..+|++||
T Consensus        21 F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   21 FASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            678999999888722      239999999999999985

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=95.29  E-value=0.012  Score=31.90  Aligned_cols=17  Identities=71%  Similarity=1.716  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPS  110 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~  110 (255)
                      .||+|+..||++.+||.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            59999999999999984

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>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=95.15  E-value=0.04  Score=40.28  Aligned_cols=43  Identities=14%  Similarity=0.442  Sum_probs=26.2

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      .|-.|+|..+        |+||+-... .|+.+|++|++..+.+++|.|+.|
T Consensus        32 ~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   32 DIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             hEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4556777665        999998775 778899999999999999999876

; PDB: 2G0C_A 3MOJ_B.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=94.74  E-value=0.016  Score=54.00  Aligned_cols=61  Identities=16%  Similarity=0.150  Sum_probs=47.9

Q ss_pred             CCCCccceEEEEeecCCCCC---CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            2 QQCLTHNNDLKIMLERDSGR---PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~---srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |.+||+|.+|.+-.+..+-.   .-.-++|||+.+|+|..||...++..++++.|++.+...+-
T Consensus       101 fgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gttky  164 (327)
T KOG2068|consen  101 FGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASLGTTKY  164 (327)
T ss_pred             ccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhhCCCcc
Confidence            67899999998888763111   11237999999999999999999999999988777776554

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=94.37  E-value=0.014  Score=55.97  Aligned_cols=47  Identities=9%  Similarity=0.135  Sum_probs=37.8

Q ss_pred             CCCCCccceEEEEeec---CCCC--C--------CCcEEEEEeCCHHHHHHHHHHhcCCe
Q 025249            1 MQQCLTHNNDLKIMLE---RDSG--R--------PRGFGFITYADRRAMDDAIREMHGRE   47 (255)
Q Consensus         1 lfekFG~I~~V~Iv~D---k~Tg--~--------srGfaFVtF~~~e~a~~AI~~lnG~~   47 (255)
                      ||.++|.|..|+|+..   +++.  .        .+-+|||+|+..+.|.+|.+.||...
T Consensus       251 iFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e~  310 (484)
T KOG1855|consen  251 IFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPEQ  310 (484)
T ss_pred             HhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchhh
Confidence            7999999999999887   3332  2        25689999999999999999886543

>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=94.19  E-value=0.056  Score=42.47  Aligned_cols=52  Identities=6%  Similarity=0.138  Sum_probs=30.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCC-----eeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR-----EFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~-----~i~Gr~I~V~~A   58 (255)
                      +|++|++|.-|.+...-      -.|+|-|.++++|++||+++.-.     +|.+..+++.+.
T Consensus        21 ~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL   77 (105)
T PF08777_consen   21 AFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL   77 (105)
T ss_dssp             HT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred             HHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence            47889999888886642      27999999999999998876533     556666666553

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=92.60  E-value=0.077  Score=50.03  Aligned_cols=49  Identities=14%  Similarity=0.370  Sum_probs=42.5

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV   55 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V   55 (255)
                      .|.++++..++.++++||||+|...+..++++.++.|-.++|.++.-.|
T Consensus       108 ~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen  108 QFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             HHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            4567788888899999999999999999999999999999999875444

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=92.50  E-value=0.1  Score=50.01  Aligned_cols=50  Identities=10%  Similarity=0.159  Sum_probs=38.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS   54 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~   54 (255)
                      ||++||.|.+|.-.. |..+   =-|+|.|.+.+.|+.|..+|+++.|..-.|.
T Consensus       170 vFS~fG~VlKIiTF~-Knn~---FQALvQy~d~~sAq~AK~aLdGqnIyngcCt  219 (492)
T KOG1190|consen  170 VFSKFGFVLKIITFT-KNNG---FQALVQYTDAVSAQAAKLALDGQNIYNGCCT  219 (492)
T ss_pred             HHhhcceeEEEEEEe-cccc---hhhhhhccchhhHHHHHHhccCCcccCceeE
Confidence            699999999874433 2222   2489999999999999999999998764443

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=92.42  E-value=0.16  Score=49.59  Aligned_cols=47  Identities=23%  Similarity=0.533  Sum_probs=37.4

Q ss_pred             EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249           11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus        11 V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      |.|+.+ ..+++-|-|||.|++.+.|++||+ -|.+.|..+-|+|-.+.
T Consensus       134 i~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  134 ILLPMD-QRGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRSS  180 (510)
T ss_pred             eeeecc-CCCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehhH
Confidence            344555 445688999999999999999998 46678888999987664

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=91.56  E-value=0.35  Score=47.90  Aligned_cols=56  Identities=14%  Similarity=0.275  Sum_probs=44.2

Q ss_pred             CccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC----CeEEEEEeccc
Q 025249            5 LTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG----DRVISVNKAQP   60 (255)
Q Consensus         5 FG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~----Gr~I~V~~A~~   60 (255)
                      .++-.-+.|+.|-.+....|||||.|.+++++..+.+++|++.+.    .+.++|.+|.-
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArI  472 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARI  472 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhh
Confidence            344445777888777788999999999999999999999998776    35556777754

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=91.38  E-value=0.33  Score=47.12  Aligned_cols=56  Identities=18%  Similarity=0.290  Sum_probs=46.4

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      |.--|+|+.|.+-.||+- .++|||.|+|+++-+|.+||..|+...+..++..|...
T Consensus       236 fgmAGkv~~vdf~idKeG-~s~G~~vi~y~hpveavqaIsml~~~g~~~~~~~~Rl~  291 (608)
T KOG4212|consen  236 FGMAGKVQSVDFSIDKEG-NSRGFAVIEYDHPVEAVQAISMLDRQGLFDRRMTVRLD  291 (608)
T ss_pred             hccceeeeeeceeecccc-ccCCeeEEEecchHHHHHHHHhhccCCCccccceeecc
Confidence            344578999998888765 89999999999999999999999987777777666653

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=91.27  E-value=0.077  Score=54.80  Aligned_cols=62  Identities=11%  Similarity=0.213  Sum_probs=53.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      |++++++++++.+++. ..+++||.|||.|.++.++.+++..++...+.-..++|+++.|...
T Consensus       756 l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~~  817 (881)
T KOG0128|consen  756 LASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPERD  817 (881)
T ss_pred             hccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCccc
Confidence            6789999999998876 5689999999999999999999988988888888888888776433

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=91.24  E-value=1.8  Score=44.04  Aligned_cols=45  Identities=4%  Similarity=0.121  Sum_probs=34.4

Q ss_pred             ceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            8 NNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         8 I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      |-.|+|..+        |.||+.... .+++.|+.|+...|.+++|.|+.+...
T Consensus       519 ig~i~i~~~--------~s~v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  563 (629)
T PRK11634        519 IGNIKLFAS--------HSTIELPKG-MPGEVLQHFTRTRILNKPMNMQLLGDA  563 (629)
T ss_pred             CCcEEEeCC--------ceEEEcChh-hHHHHHHHhccccccCCceEEEECCCC
Confidence            445666654        889987764 467788889999999999999988643

>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=90.73  E-value=0.33  Score=41.96  Aligned_cols=56  Identities=13%  Similarity=0.140  Sum_probs=39.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH--GREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln--G~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++|..++.+.+++.      -.=..|.|.+.++|.+|.+.|+  ...|.+..|+|-++++..
T Consensus        15 l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen   15 LFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             HHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             HHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            4677888888777663      2357899999999999999999  899999999999886543

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=90.57  E-value=0.56  Score=39.23  Aligned_cols=52  Identities=6%  Similarity=0.031  Sum_probs=41.6

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      .+.||+|.+|.+.--       --|.|+|.+..+|-+||.+++. ..-+..+.+++-+.-
T Consensus       111 Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWqqrF  162 (166)
T PF15023_consen  111 LSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQQRF  162 (166)
T ss_pred             HHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcC-CCCCceEEeeccccc
Confidence            367999999987542       2699999999999999999886 566777888876643

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.24  E-value=0.11  Score=53.70  Aligned_cols=59  Identities=10%  Similarity=0.076  Sum_probs=49.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC--CeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG--DRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~--Gr~I~V~~A~~k~~~~   65 (255)
                      |+++||+|.+++.+++-.      .|.|+|...+.|..|+++|+++++.  +-+.+|.+|++-+--+
T Consensus       318 l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~~~e  378 (1007)
T KOG4574|consen  318 LCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLPMYE  378 (1007)
T ss_pred             HHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccccccc
Confidence            578999999999988732      7999999999999999999998875  6788999998755443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=89.69  E-value=0.14  Score=49.83  Aligned_cols=54  Identities=15%  Similarity=0.231  Sum_probs=44.6

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |.+||+|+.|.|-...      --|.|||.+..+|-.|.. .++..|+++.|+|-|..+..
T Consensus       394 fA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  394 FAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhcCccccccccCch------hhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            7799999999886642      268999999999977755 68899999999999988743

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=89.14  E-value=0.46  Score=44.07  Aligned_cols=55  Identities=18%  Similarity=0.192  Sum_probs=41.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeE-EEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRV-ISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~-I~V~~A~~k~   62 (255)
                      +|+++|+|+++....   ++   -|-+|-|.+..+|++||. .|+++|++-. |-|+.+..|.
T Consensus       216 ~F~~cG~Vvkhv~~~---ng---NwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtDks  271 (350)
T KOG4285|consen  216 LFSRCGEVVKHVTPS---NG---NWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTDKS  271 (350)
T ss_pred             HHHhhCeeeeeecCC---CC---ceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCCHH
Confidence            589999999875542   22   388999999999999998 6899998764 4566654443

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=88.63  E-value=0.39  Score=45.97  Aligned_cols=48  Identities=25%  Similarity=0.427  Sum_probs=41.1

Q ss_pred             EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249           11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus        11 V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      |.|+.+ ..+++.|-|||+|.++|.|.+|.++.|.+.++.+-|+|-.+.
T Consensus       313 VHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  313 VHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             eEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            677776 568899999999999999999998898888888888886654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=88.32  E-value=0.51  Score=46.45  Aligned_cols=42  Identities=19%  Similarity=0.248  Sum_probs=38.1

Q ss_pred             CCC-CCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHH
Q 025249            1 MQQ-CLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIRE   42 (255)
Q Consensus         1 lfe-kFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~   42 (255)
                      ||+ .||.|+-|-|-+|++-+-+||-+-|||.+..+-.+||++
T Consensus       390 imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  390 IMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             HHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            344 799999999999999999999999999999999999974

>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=86.87  E-value=0.9  Score=32.86  Aligned_cols=29  Identities=17%  Similarity=0.384  Sum_probs=26.1

Q ss_pred             EEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 025249           27 FITYADRRAMDDAIREMHGREFGDRVISV   55 (255)
Q Consensus        27 FVtF~~~e~a~~AI~~lnG~~i~Gr~I~V   55 (255)
                      ||+|.+.++|++|.++.|++.+...+|.+
T Consensus        37 YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   37 YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            89999999999999999999888877665

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=86.50  E-value=1.8  Score=34.40  Aligned_cols=42  Identities=19%  Similarity=0.433  Sum_probs=34.6

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD   50 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G   50 (255)
                      .|+.++|++|...  .+=.+.|+|.+.++|++-.+++||+.++-
T Consensus        40 ~i~~~riird~~p--nrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   40 DIEHIRIIRDGTP--NRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             cEEEEEEeeCCCC--ceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            4667889987443  45589999999999999999999998874

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

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=85.45  E-value=0.31  Score=48.79  Aligned_cols=38  Identities=5%  Similarity=0.253  Sum_probs=32.2

Q ss_pred             CcEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEEeccc
Q 025249           23 RGFGFITYADRRAMDDAIREMHGREFG---DRVISVNKAQP   60 (255)
Q Consensus        23 rGfaFVtF~~~e~a~~AI~~lnG~~i~---Gr~I~V~~A~~   60 (255)
                      |-.|||+|.+.++|.+.+.+||+..|-   .+.|.|.|+..
T Consensus       481 KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~~  521 (718)
T KOG2416|consen  481 KSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVRA  521 (718)
T ss_pred             hcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecch
Confidence            458999999999999999999998874   57788887753

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=83.22  E-value=2  Score=32.70  Aligned_cols=36  Identities=6%  Similarity=0.084  Sum_probs=28.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH   44 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln   44 (255)
                      ||+.||.|.- ..|.|       --|||...+.+.|..|+..+.
T Consensus        28 lFspfG~I~V-sWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   28 LFSPFGQIYV-SWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             HCCCCCCEEE-EEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             HhccCCcEEE-EEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            6899999764 44444       279999999999999988776

; 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.

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=82.16  E-value=0.54  Score=29.30  Aligned_cols=19  Identities=47%  Similarity=1.399  Sum_probs=17.0

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~  111 (255)
                      -.|+.|...|||..+||..
T Consensus         9 Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CEeecCCCCCccHhHCCCC
Confidence            4699999999999999974

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=81.89  E-value=0.86  Score=29.09  Aligned_cols=19  Identities=42%  Similarity=1.017  Sum_probs=12.0

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~  111 (255)
                      .-|++|++.-||+.+|-..
T Consensus         3 ~~CprC~kg~Hwa~~C~sk   21 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSK   21 (36)
T ss_dssp             -C-TTTSSSCS-TTT---T
T ss_pred             ccCcccCCCcchhhhhhhh
Confidence            4699999999999999754

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=81.87  E-value=0.29  Score=50.69  Aligned_cols=47  Identities=13%  Similarity=0.165  Sum_probs=37.5

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF   48 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i   48 (255)
                      |..++.|..|.|+-.+.+++.+|.|+|+|..++++.+||.....+.+
T Consensus       688 ~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  688 FSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             cCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            56777787777775667889999999999999999999985544333

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=80.44  E-value=1.1  Score=46.94  Aligned_cols=56  Identities=20%  Similarity=0.289  Sum_probs=46.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~   62 (255)
                      +|..||.|..|.+-.-      .-||+|.+++...++.|++.|-+..|.+  +.|.|++|.+..
T Consensus       475 ~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  475 EFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             HhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCC
Confidence            4788999998777432      2399999999999999999999988874  778999987543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	255
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-04
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		5e-04

>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 = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 34/55 (61%)
Query: 11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE 65
           +++ +R++G+P+G+GF  Y D+     A+R ++GREF  R + V+ A  +   E
Sbjct: 38 FRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           D ++ML++D+G+ RGFGF+TY    A+D   +     +F DR I + +A+P+
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKF-IDFKDRKIEIKRAEPR 166

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 34/53 (64%), Gaps = 1/53 (1%)
Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           ++ ++ + +  RPRGFGFIT+ D +++D A+  MH  +   + + V +A+P+
Sbjct: 38 TEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPR 89

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	255
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-16
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-16
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-16
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-15
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	8e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-15
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-14
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-06
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-14
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-13
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-13
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-13
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-08
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-12
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-12
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	9e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-11
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-11
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-05
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-10
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-08
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-10
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-10
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-10
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-08
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	8e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-09
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-08
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-08
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-08
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-08
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	7e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-07
2div_A	99	TRNA selenocysteine associated protein; structural	2e-07
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	8e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	9e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	2e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	2e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-05
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	5e-05
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	2e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	7e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	7e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	7e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	3e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	6e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-04

>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 = 71.4 bits (176), Expect = 2e-16
 Identities = 12/50 (24%), Positives = 26/50 (52%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +M +  +G  RG+GF+++  +    +A+  M G++   R + +N A   
Sbjct: 32 HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL 81

>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 = 70.3 bits (173), Expect = 7e-16
 Identities = 17/52 (32%), Positives = 27/52 (51%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D++I L+ ++ + RGF F+ +        AI  M+  E   R I VN A+P 
Sbjct: 41 DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM 92

>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 = 69.5 bits (171), Expect = 8e-16
 Identities = 16/50 (32%), Positives = 26/50 (52%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          D++I L+ ++ + RGF F+ +        AI  M+  E   R I VN A+
Sbjct: 36 DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 70.1 bits (172), Expect = 1e-15
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 6   THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE 65
           T    + +  +R++G+ +G   +++ D  +   AI    G+EF    I V+ A  +    
Sbjct: 40  TGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

Query: 66  VSDHGYRGGGYSSGGRGSYG 85
                 RGGG   GG   + 
Sbjct: 100 ------RGGGNGRGGLEHHH 113

>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 = 68.4 bits (168), Expect = 2e-15
 Identities = 8/52 (15%), Positives = 19/52 (36%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          ++K    R +G+ +GF  +      +    +  +  RE   +   V  +   
Sbjct: 32 EIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL 83

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 69.8 bits (171), Expect = 2e-15
 Identities = 16/49 (32%), Positives = 25/49 (51%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           D++I L+ ++ + RGF F+ +        AI  M+  E   R I VN A
Sbjct: 92  DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 68.4 bits (168), Expect = 3e-15
 Identities = 16/52 (30%), Positives = 31/52 (59%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          ++ ++ +R++ R RGFGF+T+ +     DA+  M+G+    R I V++A   
Sbjct: 41 EVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92

>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 = 67.7 bits (166), Expect = 6e-15
 Identities = 19/65 (29%), Positives = 35/65 (53%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
             +++ +R++G+P+G+GF  Y D+     A+R ++GREF  R + V+ A  +   E    
Sbjct: 37  SFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKS 96

Query: 70  GYRGG 74
              G 
Sbjct: 97  LGTGA 101

>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 = 67.7 bits (166), Expect = 8e-15
 Identities = 14/52 (26%), Positives = 31/52 (59%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +++M++ ++GR +G+GFIT++D      A+ +++G E   R + V     +
Sbjct: 55  SIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>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 = 67.2 bits (165), Expect = 9e-15
 Identities = 15/52 (28%), Positives = 30/52 (57%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          ++ +M + D+GR +G+GFIT++D      A+ +++G E   R + V     +
Sbjct: 34 NIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTER 85

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 67.3 bits (165), Expect = 9e-15
 Identities = 10/52 (19%), Positives = 27/52 (51%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           ++ + L+R +G  +G+  + Y   +    A+  ++G++   + ISV+    +
Sbjct: 52  NIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103

>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 = 66.8 bits (164), Expect = 1e-14
 Identities = 7/53 (13%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 10 DLKIMLER-DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           + + +ER      +G+ ++ + +    + A++ M G +   + I+       
Sbjct: 33 MIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAP 85

>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 = 67.0 bits (164), Expect = 1e-14
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           ++ ++ +R + + RGF FIT+ +     +A ++M+G+    + I V +A+          
Sbjct: 36  EVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRR 94

Query: 70  GYRGGGYSSGGRGSYGADR 88
                  +    GS     
Sbjct: 95  RPPASSRNRSPSGSLEHHH 113

>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 = 66.5 bits (163), Expect = 2e-14
 Identities = 14/52 (26%), Positives = 28/52 (53%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +LK+M +  +GR +G+ FI + D  +   A+R ++G + G R +    +   
Sbjct: 31 NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS 82

>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 = 66.1 bits (162), Expect = 2e-14
 Identities = 20/50 (40%), Positives = 30/50 (60%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          KIM + D+G  +G+ FI +A   A D AI  M+G+   +R I+V+ A  K
Sbjct: 37 KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKK 86

>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 = 66.1 bits (162), Expect = 2e-14
 Identities = 12/49 (24%), Positives = 27/49 (55%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           + IM ++D+ + +G  FI + D+ +  +  R ++ ++   RVI  + A
Sbjct: 45 KVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>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 = 66.2 bits (162), Expect = 2e-14
 Identities = 11/52 (21%), Positives = 24/52 (46%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           ++ + L+R +G  +G+  + Y   +    A   ++G E   + I V+    K
Sbjct: 55  NIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 68.5 bits (168), Expect = 3e-14
 Identities = 13/52 (25%), Positives = 26/52 (50%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              +  +  +G+ +G+GFI Y   ++  DA+  M+  + G + + V KA   
Sbjct: 154 SATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 59.6 bits (145), Expect = 6e-11
 Identities = 11/50 (22%), Positives = 21/50 (42%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +  +  + + +GF F+ Y    A   A+ +M+    G R I V +    
Sbjct: 59  DMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI 108

>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 = 67.2 bits (164), Expect = 3e-14
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           D+ I  +R +   RGF F+ + D+R  +DA+  M G     R + V  A+  
Sbjct: 99  DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 150

>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 = 65.7 bits (161), Expect = 3e-14
 Identities = 13/50 (26%), Positives = 26/50 (52%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +I+ +R++G  +GFGF+ +        A   M   E     ++++ A+PK
Sbjct: 43 RIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92

>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 = 67.7 bits (166), Expect = 5e-14
 Identities = 13/52 (25%), Positives = 25/52 (48%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              ++ +  +G  +G+ F  Y D    D AI  ++G + GD+ + V +A   
Sbjct: 143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 194

>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 = 46.2 bits (110), Expect = 2e-06
 Identities = 6/50 (12%), Positives = 16/50 (32%), Gaps = 1/50 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +L     + + F F+ +        A+    G  F  + + + +    
Sbjct: 40 NPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY 88

>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 = 65.9 bits (161), Expect = 6e-14
 Identities = 12/50 (24%), Positives = 26/50 (52%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           KI+ +R++ + RG+GF+ +    +   AI  ++G    ++ + V  A   
Sbjct: 73  KIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG 122

>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 = 64.5 bits (158), Expect = 6e-14
 Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGY 71
          K++ +R++ +P+GFGF+   +  ++ +AI ++   +F  R I V +A PK   E   H +
Sbjct: 32 KLIYDRETKKPKGFGFVEMQE-ESVSEAIAKLDNTDFMGRTIRVTEANPKKSLEHHHHHH 90

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 64.5 bits (158), Expect = 7e-14
 Identities = 15/52 (28%), Positives = 33/52 (63%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D +++ +  +G+ +G+GF+++ ++   ++AI++M G+  G R I  N A  K
Sbjct: 35 DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86

>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 = 64.6 bits (158), Expect = 7e-14
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +I L    G+ +G  +I +      +  + E  G E   R +S+     K
Sbjct: 42 EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 64.2 bits (157), Expect = 1e-13
 Identities = 12/47 (25%), Positives = 24/47 (51%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           +  +R++G+ +G   +++ D  +   AI    G+EF    I V+ A
Sbjct: 52 NLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>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 = 64.7 bits (158), Expect = 1e-13
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK--MGGEVS 67
           D +++ +  +G+ +G+GF+++ ++   ++AI++M G+  G R I  N A  K        
Sbjct: 44  DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTY 103

Query: 68  DHGYRGGGYSSG 79
           +   +  G SSG
Sbjct: 104 ESNTKQSGPSSG 115

>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 = 63.8 bits (156), Expect = 1e-13
 Identities = 14/50 (28%), Positives = 24/50 (48%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          D+ I+ ++ S R RGF F+ + +     +A    +G E   R I V+   
Sbjct: 44 DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 65.7 bits (161), Expect = 1e-13
 Identities = 13/49 (26%), Positives = 25/49 (51%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
              ++ +  +G  +G+ F  Y D    D AI  ++G + GD+ + V +A
Sbjct: 123 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 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 = 49.2 bits (118), Expect = 1e-07
 Identities = 8/62 (12%), Positives = 20/62 (32%), Gaps = 1/62 (1%)

Query: 13  IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYR 72
            +L     + + F F+ +        A+    G  F  + + + +         +   + 
Sbjct: 41  PVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFI 99

Query: 73  GG 74
           GG
Sbjct: 100 GG 101

>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 = 64.2 bits (157), Expect = 1e-13
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          K+M   + GR +GFGF+ ++       A+ EM+GR    + + V  AQ K
Sbjct: 46 KVM--MEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK 93

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 13/52 (25%), Positives = 26/52 (50%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +L   ++  + +P+GF F+T+        A  E+ G+ F  R++ V  +  K
Sbjct: 37 ELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIK 88

>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 = 63.8 bits (156), Expect = 2e-13
 Identities = 19/52 (36%), Positives = 25/52 (48%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D+ I  E  +  PRGF F+ + DRR   DA   M G E   R + V  A+  
Sbjct: 42 DVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG 93

>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 = 63.4 bits (155), Expect = 2e-13
 Identities = 17/52 (32%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          ++ ++ + +  RPRGFGFIT+ D +++D A+  MH  +   + + V +A+P+
Sbjct: 39 EVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPR 89

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 64.9 bits (158), Expect = 2e-13
 Identities = 9/52 (17%), Positives = 22/52 (42%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +LK    R +G+ +G+  +  A   ++   +  + G+      + V  A  +
Sbjct: 86  ELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.5 bits (155), Expect = 3e-13
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
           D++I+   +    +GFGF+T+ +    D A  ++HG     R I VN A  ++
Sbjct: 58  DVEII--FNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108

>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 = 3e-13
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          K++   D    +G+GF+ +  + A + AI +M+G    DR + V + + +
Sbjct: 36 KVV--CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 83

>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 = 63.0 bits (154), Expect = 3e-13
 Identities = 12/52 (23%), Positives = 27/52 (51%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           + +  ++ +G+ +GF FI++  R     AI  + G  +   +++V  A+P 
Sbjct: 44 RIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95

>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 = 63.5 bits (155), Expect = 3e-13
 Identities = 14/75 (18%), Positives = 32/75 (42%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           ++ + L+R +G  +G+  + Y   +    A+  ++G++   + ISV+    +   +    
Sbjct: 51  NIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRR 110

Query: 70  GYRGGGYSSGGRGSY 84
           G R    S   R   
Sbjct: 111 GGRRRSRSPDRRRRL 125

>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 = 63.1 bits (154), Expect = 4e-13
 Identities = 11/52 (21%), Positives = 24/52 (46%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              I     +GR RG  FIT+ ++     A+  ++G +   +++ +   + K
Sbjct: 54  GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 105

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 62.7 bits (153), Expect = 7e-13
 Identities = 12/50 (24%), Positives = 28/50 (56%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           K+ +++ +   + FGF++Y +  +   AI+ M+G + G + + V   + K
Sbjct: 56  KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK 105

>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 = 61.7 bits (150), Expect = 1e-12
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 6   THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
           T    + I L++++G+P+G   ++Y D      A+    G++F    + V+ A+ K 
Sbjct: 48  TGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104

>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 = 62.9 bits (154), Expect = 1e-12
 Identities = 12/48 (25%), Positives = 26/48 (54%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
            +M +  +G  RG+GF+++  +    +A+  M G++   R + +N A 
Sbjct: 118 HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 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 = 50.2 bits (121), Expect = 5e-08
 Identities = 10/59 (16%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHG 70
          KIM+++ + +   + F+ Y      + A++ ++G++  + ++ +N A         D  
Sbjct: 31 KIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTF 88

>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 = 61.7 bits (150), Expect = 2e-12
 Identities = 15/52 (28%), Positives = 26/52 (50%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           D+ I+ ++ S R RGF F+ + +     +A    +G E   R I V+ +  K
Sbjct: 75  DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +I L    G+ +G  +I +      +  + E  G E   R +S+     K
Sbjct: 125 EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 = 50.3 bits (121), Expect = 6e-08
 Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
          DL ++ +  +G  R FG++ +     ++ A+ E+ G +     I + K + +   +V   
Sbjct: 42 DLAVV-DVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAA 99

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 10/48 (20%), Positives = 27/48 (56%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
           K+ +++ +   + FGF+++ +  +   AI+ M+G + G + + V   +
Sbjct: 71  KVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 60.8 bits (148), Expect = 4e-12
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP--KMGGEVS 67
           +  ++ +R +G+ RG+GF+T ADR A + A ++ +      R  +VN A    K     +
Sbjct: 46  EAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSLQT 104

Query: 68  DHGYRGGGYSSG 79
                  G SSG
Sbjct: 105 GFAIGVSGPSSG 116

>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 = 63.8 bits (156), Expect = 4e-12
 Identities = 11/63 (17%), Positives = 24/63 (38%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
              ++    +G+ +G+GF  Y  + +   A  ++ G+  G R + V+            H
Sbjct: 124 RCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLH 183

Query: 70  GYR 72
              
Sbjct: 184 SRC 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 = 58.5 bits (142), Expect = 3e-10
 Identities = 9/50 (18%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           ++      G+ +GF  + Y      ++A ++  G   G   + V+   P 
Sbjct: 216 QLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264

>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 = 51.1 bits (123), Expect = 7e-08
 Identities = 9/48 (18%), Positives = 17/48 (35%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +      + +G  F+T  +    + AI   H     +R +SV      
Sbjct: 48 LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD 95

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 60.9 bits (148), Expect = 5e-12
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           D+ I  +R +   RGF F+ + D+R  +DA+  M G     R + V  A+  
Sbjct: 76  DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127

>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 = 61.4 bits (150), Expect = 5e-12
 Identities = 20/52 (38%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           D ++ML++D+G+ RGFGF+TY    A+D    +    +F DR I + +A+P+
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEPR 166

>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 = 56.4 bits (137), Expect = 3e-10
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
          DLKIM +  +GR RGFGF+++    ++D+ ++  H      +VI   +A P+ 
Sbjct: 32 DLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRD 82

>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 = 59.4 bits (145), Expect = 5e-12
 Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
          N + I+ ++ SG P+GF +I ++D+ ++  ++  +    F  R I V   +    G
Sbjct: 34 NRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTNRPG 88

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 59.6 bits (145), Expect = 5e-12
 Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          DL+++  R +G+P+G  ++ Y +      A+ +M G    + +I V  +   
Sbjct: 46 DLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSG 96

>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 = 59.6 bits (145), Expect = 8e-12
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 11/73 (15%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHG---REFGDRVISVNKAQPKMGGEV 66
           +L ++ +R +G  +G  F+TY +R +   A   +H        +R I V  A  +     
Sbjct: 42  ELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSE----- 96

Query: 67  SDHGYRGGGYSSG 79
                 G G SSG
Sbjct: 97  ---SRGGSGPSSG 106

>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 = 58.7 bits (143), Expect = 8e-12
 Identities = 7/48 (14%), Positives = 21/48 (43%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
          K +L++ + + +G+GF+ +    A   A+  +       ++   +   
Sbjct: 36 KAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS 83

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 58.2 bits (142), Expect = 9e-12
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          D  +M ++ + R RGFGF+T+     ++    E+H  E  ++++   KA
Sbjct: 28 DAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 8/56 (14%), Positives = 20/56 (35%), Gaps = 2/56 (3%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE 65
           +++  +  +G  +GFGF+ + +       + + H      R         K   +
Sbjct: 44 MVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQD 97

>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 = 60.7 bits (148), Expect = 1e-11
 Identities = 11/50 (22%), Positives = 25/50 (50%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +IM +  +G   G+ F+ +        AI+ ++G    ++ + V+ A+P 
Sbjct: 34 RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG 83

>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 = 58.0 bits (141), Expect = 8e-11
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF--GDRVISVNKA 58
              I+ ++ +GRPRG  F+ Y  R    +AI  ++      G + +SV  A
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>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 = 58.8 bits (143), Expect = 1e-11
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D++I+   +    +GFGF+T+ +    D A  ++HG     R I VN A  +
Sbjct: 44 DVEII--FNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 93

>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 = 60.2 bits (146), Expect = 1e-11
 Identities = 21/81 (25%), Positives = 33/81 (40%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
            + + L++      GF F+ Y  R   ++A+R ++G    DR+I  +       G     
Sbjct: 68  KIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGR 127

Query: 70  GYRGGGYSSGGRGSYGADRPG 90
           G  GG      R  Y A R G
Sbjct: 128 GRSGGQVRDEYRQDYDAGRGG 148

>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 = 58.4 bits (142), Expect = 2e-11
 Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 3/53 (5%)

Query: 12 KIMLERDSG---RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           I  +++        GFGF+ Y        A++++ G       + V  ++  
Sbjct: 36 TISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA 88

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 3/52 (5%)

Query: 12  KIMLERD-SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
           +I+  RD SG  RG GF         +  I   +G+            +P +
Sbjct: 56  RIL--RDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLL 105

>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 = 58.5 bits (142), Expect = 2e-11
 Identities = 12/53 (22%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 9   NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            D++I+ +R+S R +G  ++ + + +++  AI  + G+      I V  +Q +
Sbjct: 53  RDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAE 104

>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 = 58.1 bits (141), Expect = 2e-11
 Identities = 11/48 (22%), Positives = 23/48 (47%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          + +  +G+ +G+ FI +A      +A+   + RE   R I +    P+
Sbjct: 44 VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPR 91

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 57.6 bits (140), Expect = 3e-11
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR-EFGDRVISVNKAQPKMGGEVSDHG 70
          K+ L        G+ F+ Y D+     AI  + G+ E   +++ V+ +  K         
Sbjct: 33 KLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK--------K 84

Query: 71 YRGGGYSSG 79
           R  G SSG
Sbjct: 85 LRSSGPSSG 93

>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 = 57.6 bits (140), Expect = 4e-11
 Identities = 10/53 (18%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
          ++KI+ +R +G  +G+GF+++ +   +   +       F  + + +  A  K 
Sbjct: 38 EVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQI--NFHGKKLKLGPAIRKQ 87

>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 = 57.8 bits (140), Expect = 4e-11
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 9   NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
           N + I+ ++ SG P+G+ +I +A+R ++D A+  M    F  R I V   +  M G
Sbjct: 64  NRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG 118

>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 = 57.3 bits (139), Expect = 4e-11
 Identities = 14/52 (26%), Positives = 26/52 (50%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +  +  +R +G+ +G+GF+ +      D AI+ M   +   + I VNKA   
Sbjct: 44 NTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH 95

>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 = 59.1 bits (143), Expect = 4e-11
 Identities = 11/52 (21%), Positives = 24/52 (46%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           ++ + L+R +G  +G+  + Y   +    A   ++G E   + I V+    K
Sbjct: 101 NIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 56.8 bits (138), Expect = 4e-11
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 15 LERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE 65
          ++ ++G+ +G G + +      + A R M+G +   R I V   +   G  
Sbjct: 40 IKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGPS 90

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 59.7 bits (144), Expect = 7e-11
 Identities = 14/110 (12%), Positives = 27/110 (24%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
           ++K    R +G+ +GF  +      +    +  +  RE   +   V     +   +    
Sbjct: 99  EIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQ 158

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAG 119
             +                 G     F  G  G          G R    
Sbjct: 159 SRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGP 208

>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 = 58.4 bits (142), Expect = 7e-11
 Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 2/49 (4%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR--EFGDRVISVNKA 58
           +I++++ +G  RG GFI +  R   ++AI+ ++G+        I+V  A
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>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 = 57.2 bits (139), Expect = 2e-10
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          K++ ++ +G+  G+GF+ Y D +  + AI  ++G     + I V+ A+P 
Sbjct: 33 KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS 82

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH------GREFGDRVISVNKAQPK 61
            ++++L  D+   +G  F  +  + A    +          G +   R + V+ A  +
Sbjct: 44  YVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR 101

>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 = 55.7 bits (135), Expect = 1e-10
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
           I  +R+ G+P+ FGF+ +    ++  AI  ++G     R I+V+   
Sbjct: 47 TICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>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 = 58.8 bits (143), Expect = 2e-10
 Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 12  KIMLERDS-GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            I   +          F+ + ++ + + A+ +M+    G+R ISV+ A  K
Sbjct: 242 NIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291

>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 = 55.0 bits (133), Expect = 4e-09
 Identities = 5/49 (10%), Positives = 15/49 (30%)

Query: 13  IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +        R F +I    +      + +++G +     +    + P 
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL 197

>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 = 44.6 bits (106), Expect = 1e-05
 Identities = 9/51 (17%), Positives = 15/51 (29%), Gaps = 3/51 (5%)

Query: 9   NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
             + +       +   F  I +A       AI + H    G   I V+   
Sbjct: 69  IHVDVA--DSLKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLT 116

>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 = 58.1 bits (141), Expect = 2e-10
 Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           K++   D    +G+GF+ +  + A + AI +M+G    DR + V + + +
Sbjct: 134 KVV--CDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181

>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 = 51.1 bits (123), Expect = 5e-08
 Identities = 7/59 (11%), Positives = 22/59 (37%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHG 70
           ++  +  + R  G+ ++ +      + A+  M+      + + +  +Q       S  G
Sbjct: 46  RVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG 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 = 54.8 bits (133), Expect = 2e-10
 Identities = 9/49 (18%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           +++ ++  + + RGF FIT+ +   +   + E      G     +  A
Sbjct: 28 SIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNVGLSKCEIKVA 75

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 55.5 bits (134), Expect = 2e-10
 Identities = 6/52 (11%), Positives = 19/52 (36%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +++I+L   + +  G   + +   R   + ++ +H       +I        
Sbjct: 35 EVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG 86

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +  +M +  + R RGFGF+T+ D+  +D  +      E   + I    A P+
Sbjct: 54  ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVAFPR 104

>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 = 55.4 bits (134), Expect = 3e-10
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           I+ ++D G+ RG G +T+        AI   +G+   DR + V   +  
Sbjct: 46 DILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA 94

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           D  +M +  S R RGFGF+T++    +D A+          RV+   +A  +
Sbjct: 56  DCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAR 106

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 54.9 bits (133), Expect = 4e-10
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D  IM ++ + + RGFGF+ + D   +   +          R I      P+
Sbjct: 45 DCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-ASRPHTLDGRNIDPKPCTPR 95

>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 = 54.6 bits (132), Expect = 4e-10
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 22  PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK--MGGEVSDHGYRGGGYSSG 79
            + + FI + +R     A+ EM+G++     I +  A+P      E         G SSG
Sbjct: 44  LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>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 = 54.6 bits (132), Expect = 4e-10
 Identities = 9/49 (18%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +++  +G  R FG++ +     ++ A+ E+ G +     I + K + +
Sbjct: 48 AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGR 95

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 53.6 bits (130), Expect = 4e-10
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          +  +M +  + R RGFGF+T+ D+  +D  +      E   + I    A
Sbjct: 29 ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVA 76

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 56.5 bits (137), Expect = 4e-10
 Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            ++IM +R SG+ RGF F+T+ D  ++D  +              V KA  K
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSK 183

>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 = 51.5 bits (124), Expect = 3e-08
 Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D  +M + ++ R RGFGF+TYA    +D A+      +   RV+   +A  +
Sbjct: 42 DCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRAVSR 92

>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 = 53.3 bits (129), Expect = 8e-10
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
          D  I ++ ++GR RGFGFI + D  +++  + +        RVI   KA
Sbjct: 40 DCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLDGRVIDPKKA 87

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 10/40 (25%), Positives = 21/40 (52%)

Query: 22  PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             GF F+ + +  +   AI E+HG+ F ++ + V  ++  
Sbjct: 64  LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 10/53 (18%), Positives = 31/53 (58%), Gaps = 1/53 (1%)

Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            ++++ ++D+ + +GF ++ + +  ++ +A+    G   GDR + V+ A+ +
Sbjct: 42 RSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGR 93

>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 = 52.7 bits (127), Expect = 2e-09
 Identities = 9/41 (21%), Positives = 22/41 (53%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          + R + F+ +++R    +A++ ++G+      I V  A+P 
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV 89

>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 = 53.3 bits (128), Expect = 3e-09
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 17  RDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              GR +G  FI   + +A   A++E +G     + + V  A+  
Sbjct: 86  MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA 130

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D+ +     S + RG  F+ + +  +  +A+R M G  F D+ + +  A+  
Sbjct: 41 DILVS---RSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89

>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 = 52.8 bits (127), Expect = 3e-09
 Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +  +R SGR  G   + +  R     A+++  G     R + +     +
Sbjct: 66  AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114

>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 = 51.4 bits (124), Expect = 5e-09
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 8/57 (14%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSG 79
          + +GF+   D+ A +DAIR +H  +     I+V  ++ K             G SSG
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK--------ASSGPSSG 90

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 51.5 bits (124), Expect = 5e-09
 Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF-GDRVISVNKAQPK 61
          K++L++ +G  +G+GF+ + D      A+ E  G    G + + ++ A PK
Sbjct: 41 KVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPK 90

>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 = 51.5 bits (124), Expect = 5e-09
 Identities = 10/41 (24%), Positives = 16/41 (39%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          + +GFGFI    R   + A  E+       + + V  A   
Sbjct: 49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 89

>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 = 54.3 bits (131), Expect = 6e-09
 Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 5/56 (8%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF----GDRVISVNKAQPK 61
              ++++ D GR  G GF+ +A +     A+       F      R + V   +  
Sbjct: 125 KAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF 179

>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 = 48.1 bits (115), Expect = 6e-07
 Identities = 13/40 (32%), Positives = 17/40 (42%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          R RGFGFI    R   + A  E+ G     R + +  A  
Sbjct: 56 RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 51.3 bits (123), Expect = 7e-09
 Identities = 7/51 (13%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDR-VISVNKAQ 59
          +++  ++  +G+ +GF F+           I+  HG+    +  + +   +
Sbjct: 41 NMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91

>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 = 51.1 bits (123), Expect = 7e-09
 Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
               +  R +GFG+  + D  ++  A+  ++    G+R I V+ A   
Sbjct: 51 PREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDR-VISVNKA 58
                + G+ +G+ F+ YA      DA++   G +   +    VN  
Sbjct: 50 NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97

>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 = 50.8 bits (122), Expect = 1e-08
 Identities = 10/54 (18%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 10 DLKIMLERD-SGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQPK 61
           +++  +   +G  RGFGF+ +  ++    A   + H      R + +  A  +
Sbjct: 44 TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE 97

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 7/55 (12%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGRE----FGDRVISVNKAQP 60
          +++++ ++ + + RGF F+  +        ++ +           + I V+ A+ 
Sbjct: 40 NIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
               +  R +GFG+  + D  ++  A+  ++    G++ I V+ A   
Sbjct: 47 PREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQA 94

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 13/41 (31%), Positives = 20/41 (48%)

Query: 21  RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            P GF F+ + D R   DA+RE+ GR      + V  +  +
Sbjct: 108 NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE 148

>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 = 49.5 bits (119), Expect = 2e-08
 Identities = 7/39 (17%), Positives = 17/39 (43%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          + + F+          AI +++G+E   + I+V  +   
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81

>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 = 49.6 bits (119), Expect = 2e-08
 Identities = 12/42 (28%), Positives = 21/42 (50%)

Query: 20 GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            PR   F+TY    + D A+ E++G +     + VN A+ +
Sbjct: 46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 87

>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 = 49.8 bits (119), Expect = 2e-08
 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 17 RDSGRPRGFGFITYADRRAMDDAIREMHGREF--GDRVISVNKAQPK 61
           D  + RGF F+ Y   RA   A R++           I+V+ A+P+
Sbjct: 46 ADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE 92

>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 = 49.6 bits (119), Expect = 3e-08
 Identities = 8/48 (16%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
            +  +R SGR  G   + +  +     A+++ +G     R +++    
Sbjct: 60  AVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 10/46 (21%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDR-VISVN 56
                + G+ +G+ F+ YA      DA++   G +   +    VN
Sbjct: 36 NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 81

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
            FGFI + + +++ DAI          + + +  +      +  DHG  G
Sbjct: 45 NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQ-FDHGDHG 94

>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 = 48.8 bits (117), Expect = 4e-08
 Identities = 7/39 (17%), Positives = 16/39 (41%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          + + F+         +AIR +   EF  + + V  +  +
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR 82

>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 = 48.8 bits (117), Expect = 5e-08
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 2/50 (4%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          K++ E  S  P  + F+ + + R    A+  M+GR+   + + VN A   
Sbjct: 46 KMITEHTSNDP--YCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP 93

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 48.0 bits (115), Expect = 7e-08
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 7/52 (13%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D+ I   +     R F F+T+AD +       E          + ++ A+PK
Sbjct: 40 DVFIP--KPF---RAFAFVTFADDKVAQSLCGEDL--IIKGISVHISNAEPK 84

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 12/53 (22%), Positives = 20/53 (37%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
           P GF F+ + D R  +DA+R + G+      + V  +         D     
Sbjct: 35 NPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPAR 87

>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 = 49.9 bits (120), Expect = 8e-08
 Identities = 10/54 (18%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 10 DLKIMLERDSGRP--RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          ++ ++ +R    P  +G  F+T+  R+A  +A   +H  +    +    + +P 
Sbjct: 32 EINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPA 85

>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 = 49.1 bits (118), Expect = 2e-07
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 10  DLKIMLERDS-GRPRGFGFITYADRRAMDDAIREMHGREF---GDRVISVNKA 58
           + +I+  R   G  RG  F+T+  R     AI+ MH  +        + V  A
Sbjct: 124 ECRIL--RGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>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 = 51.0 bits (121), Expect = 8e-08
 Identities = 22/110 (20%), Positives = 36/110 (32%), Gaps = 6/110 (5%)

Query: 19  SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSD-HGYRGGGYS 77
           S + RG  F+ + +  +  +A+R M G  F D+ + +  A+       SD      G + 
Sbjct: 48  SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD-----SDIIAKMKGTFV 102

Query: 78  SGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSR 127
              R          +    K    G  A     AV G        +   R
Sbjct: 103 ERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPR 152

>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 = 48.5 bits (116), Expect = 9e-08
 Identities = 9/53 (16%), Positives = 18/53 (33%)

Query: 20 GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYR 72
             RG  ++ Y D     +A+  + G    +R + V         +  D   +
Sbjct: 44 PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKK 96

>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 = 46.9 bits (112), Expect = 2e-07
 Identities = 9/52 (17%), Positives = 19/52 (36%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
           +   + G P G   + +  R     A+ +++ R  G R + +        G
Sbjct: 47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>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 = 46.9 bits (112), Expect = 2e-07
 Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG----DRVISVNKAQPK 61
          KI+  R +G P G+ F+ +AD    +  + +++G+        +   +N A   
Sbjct: 41 KIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS 94

>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 = 46.9 bits (112), Expect = 2e-07
 Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 4/55 (7%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR---EFGDRVISVNKAQPK 61
          +  ++   D G  +G  F+ ++       AI  +HG          + V  A   
Sbjct: 44 ECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTD 97

>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 = 46.5 bits (111), Expect = 3e-07
 Identities = 7/39 (17%), Positives = 16/39 (41%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            FGFI + + +++ DAI          + + +  +   
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN 95

>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 = 46.1 bits (110), Expect = 3e-07
 Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 2/44 (4%)

Query: 20 GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG 63
             R F F+T+AD +       E          + ++ A+PK  
Sbjct: 39 KPFRAFAFVTFADDQIAQSLCGEDL--IIKGISVHISNAEPKHN 80

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 8/51 (15%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 11  LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           L I+++  S    G  +I +A + +    +    G  F    + +  ++  
Sbjct: 61  LDIVVDL-SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110

>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 = 46.4 bits (110), Expect = 5e-07
 Identities = 8/50 (16%), Positives = 15/50 (30%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                  S  P    ++TY        AI+ ++      R +  +    K
Sbjct: 52  NSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTK 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 45.8 bits (109), Expect = 6e-07
 Identities = 7/42 (16%), Positives = 12/42 (28%)

Query: 20  GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              +G  FI Y         I  +    F  R +     + +
Sbjct: 60  YPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101

>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 = 45.4 bits (108), Expect = 8e-07
 Identities = 9/40 (22%), Positives = 19/40 (47%)

Query: 22  PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +G+ F+ Y++ R    A+   +GR    + + +N A   
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100

>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 = 45.0 bits (107), Expect = 9e-07
 Identities = 8/46 (17%), Positives = 19/46 (41%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
           +   + G P G   + +  R     A+ +++ R  G R + ++  
Sbjct: 47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 44.1 bits (104), Expect = 2e-06
 Identities = 11/41 (26%), Positives = 17/41 (41%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           PR   F+ Y D  A   A+  + G   G   + V  A+ +
Sbjct: 54 GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>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 = 43.8 bits (104), Expect = 3e-06
 Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 8/60 (13%)

Query: 20  GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSG 79
                F F+ + D R  +DA+    G ++    + V   +   G         G G SSG
Sbjct: 58  RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG--------TGSGPSSG 109

>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 = 43.6 bits (103), Expect = 3e-06
 Identities = 8/44 (18%), Positives = 15/44 (34%)

Query: 18 DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             R +   F+T  +     +AI+  H   F  + + V      
Sbjct: 35 YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 44.5 bits (105), Expect = 7e-06
 Identities = 10/91 (10%), Positives = 28/91 (30%), Gaps = 8/91 (8%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA---QPKMGGEV 66
            +KI+  +     +    +  AD      A+  ++G +   + I +  +     ++  E 
Sbjct: 33  RVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREG 87

Query: 67  SDHGYRGGGYSSGGRGSYGADRPGGQDDCFK 97
            +       Y +     +         + F 
Sbjct: 88  QEDQGLTKDYGNSPLHRFKKPGSKNFQNIFP 118

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 1/50 (2%)

Query: 12  KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +  +R SGR  G   + +  R     A+++  G     R + +     +
Sbjct: 119 AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167

>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 = 43.9 bits (103), Expect = 1e-05
 Identities = 1/47 (2%), Positives = 12/47 (25%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
              + +          G + +  +    + +  ++  +  +      
Sbjct: 152 PTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198

>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 = 40.1 bits (93), Expect = 3e-04
 Identities = 16/101 (15%), Positives = 31/101 (30%), Gaps = 12/101 (11%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
            +K M  +      G   +  AD  A+D AI  ++      + ++V  ++         +
Sbjct: 34  KVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSY 88

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPS 110
           G   G  S         D    +++ F         R    
Sbjct: 89  GLEDGSCSY-------KDFSESRNNRFSTPEQAAKNRIQHP 122

>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 = 41.9 bits (99), Expect = 2e-05
 Identities = 6/39 (15%), Positives = 16/39 (41%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +G+ F+ ++   +   AI  ++G      V+     +  
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 40.7 bits (95), Expect = 2e-05
 Identities = 10/36 (27%), Positives = 15/36 (41%)

Query: 81  RGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRG 116
             ++    P     C +C R  HWA +C S    +G
Sbjct: 19  EHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQG 54

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 40.7 bits (95), Expect = 2e-05
 Identities = 9/27 (33%), Positives = 13/27 (48%)

Query: 95  CFKCGRPGHWARDCPSAVGGRGGAGGS 121
           CFKCG+ GH+A++C             
Sbjct: 4   CFKCGKKGHFAKNCHEHAHNNAEPKVP 30

>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 = 40.7 bits (96), Expect = 4e-05
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 2/43 (4%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFG--DRVISVNKAQPK 61
          +   F +I Y    A   A  +M G   G  DR + V+ A+  
Sbjct: 51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG 93

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 39.5 bits (92), Expect = 5e-05
 Identities = 9/35 (25%), Positives = 13/35 (37%)

Query: 88  RPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSF 122
               ++ C  C   GH A+ C    G +G   G  
Sbjct: 26  SGNSRERCQLCNGMGHNAKQCRKRDGNQGQRPGKG 60

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 8/33 (24%), Positives = 11/33 (33%)

Query: 90  GGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSF 122
             +  C+ CG PGH+   CP             
Sbjct: 2   RARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQ 34

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 40.1 bits (94), Expect = 5e-05
 Identities = 5/41 (12%), Positives = 16/41 (39%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                 +TY+ +     A+ +++G +  +  + V     +
Sbjct: 52 SETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92

>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 = 42.5 bits (99), Expect = 6e-05
 Identities = 39/241 (16%), Positives = 62/241 (25%)

Query: 11  LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHG 70
           + ++  + SG+PRG+ FI Y   R M  A +   G++   R + V+  + +         
Sbjct: 132 IHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRR 191

Query: 71  YRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCPSAVGGRGGAGGSFSSRSRFGG 130
             GG   +   G+    R  G+DD  +       +                  SR R   
Sbjct: 192 LGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKE 251

Query: 131 VGVRGDYLGGGRDRYIDDRYDGGRYGDRDRYDSKDSKYGSRDRYVSDRYPPAGDRLAGDR 190
              R       R R      +  R       D    +     R           +     
Sbjct: 252 RERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRG 311

Query: 191 YGGSDRYPVNGYGKERGYERDVGARAGSDRYASGGPARDDGRGYRSRAAPYDRPSRGDRP 250
            GG    P                               D    RS  +  +R    DR 
Sbjct: 312 GGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRD 371

Query: 251 S 251
            
Sbjct: 372 R 372

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 40.5 bits (94), Expect = 7e-05
 Identities = 9/42 (21%), Positives = 13/42 (30%)

Query: 68  DHGYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGHWARDCP 109
              +R          +     P     C+ CG  GH+  DC 
Sbjct: 81  PSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCK 122

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 9/26 (34%), Positives = 12/26 (46%)

Query: 95  CFKCGRPGHWARDCPSAVGGRGGAGG 120
           C  C + GH  +DCP  +    GA  
Sbjct: 7   CNNCSQRGHLKKDCPHIICSYCGATD 32

>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 = 39.9 bits (93), Expect = 7e-05
 Identities = 5/40 (12%), Positives = 15/40 (37%)

Query: 16  ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
           +       G  ++ +      + A+ +++ R F  + I  
Sbjct: 61  DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 14  MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
           +L+   GR  G G + +   +   +A+ + +      R + V+ A  +    V+  G+  
Sbjct: 47  LLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER--QWVAAGGHIT 103

Query: 74  GGYSSG 79
            G SSG
Sbjct: 104 SGPSSG 109

>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 = 38.5 bits (90), Expect = 3e-04
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 2/52 (3%)

Query: 4  CLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
          C  H   + I ++++S   +G  ++      A   A+  +HGR F  ++I+ 
Sbjct: 38 CNKHGGVIHIYVDKNS--AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITA 87

>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 = 37.9 bits (88), Expect = 4e-04
 Identities = 5/46 (10%), Positives = 13/46 (28%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSD 68
               + + +      A R +   +F    + +  A   + G    
Sbjct: 46 GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQ 91

>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 = 37.8 bits (88), Expect = 4e-04
 Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +     GR  G  F+ +A +   + A+ + H    G R I + K+   
Sbjct: 47 TLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRA 94

>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 = 37.8 bits (88), Expect = 4e-04
 Identities = 9/70 (12%), Positives = 25/70 (35%), Gaps = 4/70 (5%)

Query: 14  MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
           +L  ++G+  G   + + +      + R +H ++   R   V+    +   ++ +     
Sbjct: 48  VLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLE---DMREIEKNP 103

Query: 74  GGYSSGGRGS 83
                 G  S
Sbjct: 104 PAQGKSGPSS 113

>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 = 39.2 bits (91), Expect = 5e-04
 Identities = 11/94 (11%), Positives = 28/94 (29%), Gaps = 5/94 (5%)

Query: 10  DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDH 69
            +KI+  +     +    +  AD      A+  ++G +   + I +  ++ +      + 
Sbjct: 64  RVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREG 118

Query: 70  GYRGGGYSSGGRGSYGADRPGGQDDCFKCGRPGH 103
               G     G       +  G  +      P  
Sbjct: 119 QEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152

>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 = 37.9 bits (88), Expect = 5e-04
 Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 1/67 (1%)

Query: 14  MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
           +    +G+  G GF+ + +      A+   H +  G+R I V+    K   E  D   + 
Sbjct: 58  IAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKR 116

Query: 74  GGYSSGG 80
                  
Sbjct: 117 LQSGPSS 123

>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 Length = 105

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 4/59 (6%)

Query: 1  MQQCLTHNNDLKIMLERDSG----RPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
            +C  +     I + R          G  F+ +        A++ + GR+F +RV+  
Sbjct: 33 RDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91

>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 = 6e-04
 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 14  MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRG 73
            +    GRP G  F+ +A      +A+   H    G R I + ++      +V +     
Sbjct: 59  FVTYPDGRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAAEVQQVLNRFSSA 117

Query: 74  GGYSSG 79
            G SSG
Sbjct: 118 SGPSSG 123

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	255
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.63
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.61
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.61
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.6
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.6
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.57
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.57
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.57
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.57
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.56
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.56
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.56
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.55
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.55
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.55
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.55
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.55
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.55
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.54
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.54
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.54
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.54
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.54
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.53
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.53
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.53
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.53
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.53
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.53
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.52
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.52
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.52
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.52
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.52
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.52
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.52
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.51
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.51
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.51
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.51
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.51
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.5
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.5
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.49
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.49
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.49
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.49
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.49
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.49
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.49
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.48
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.48
2div_A	99	TRNA selenocysteine associated protein; structural	99.48
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.48
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.48
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.48
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.47
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.47
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.47
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.47
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.46
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.46
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.46
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.46
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.46
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.46
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.45
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.45
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.45
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.45
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.44
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.44
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.44
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.44
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.44
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.43
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.43
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.43
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.43
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.43
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.43
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.43
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.42
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.42
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.42
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.42
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.41
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.41
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.4
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.39
1x5p_A	97	Negative elongation factor E; structure genomics,	99.38
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.38
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.38
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.38
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.38
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.37
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.37
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.37
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.37
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.37
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.36
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.36
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.35
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.35
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.34
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.34
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.34
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.34
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.34
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.34
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.34
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.33
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.33
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.33
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.33
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.33
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.33
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.33
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.33
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.32
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.32
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.32
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.31
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.31
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.31
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.3
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.3
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.3
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.3
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.29
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.29
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.29
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.29
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.29
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.28
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.28
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.28
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.28
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.28
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.28
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.27
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.27
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.27
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.27
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.26
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.26
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.26
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.26
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.25
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.25
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.24
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.24
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.23
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.23
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.23
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.23
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.23
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.23
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.22
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.22
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.21
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.21
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.21
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.21
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.21
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.2
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.18
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.18
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.17
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.17
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.17
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.14
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.12
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.06
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.04
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.02
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.0
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.97
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.94
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.92
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.92
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.89
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.85
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.82
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.77
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.74
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.71
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.6
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.6
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.22
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	97.95
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	97.4
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.2
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.93
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	96.01
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.0
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.9
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	95.63
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	95.23
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.54
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	94.53
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	94.2
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	93.1
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	91.99
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	88.96
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	87.9
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	87.44
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	86.95
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	86.51
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	85.58
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	85.37
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	85.3
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	84.86
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	83.73
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	82.89
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	82.71
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	82.64
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	80.83
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	80.68
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	80.36

>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=99.63  E-value=3e-16  Score=120.01  Aligned_cols=60  Identities=22%  Similarity=0.521  Sum_probs=58.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||++||+++|.+++|.|++|+|
T Consensus        39 ~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           39 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             HHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             HHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            589999999999999999999999999999999999999999999999999999999987

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

Probab=99.61  E-value=7.1e-16  Score=120.29  Aligned_cols=62  Identities=11%  Similarity=0.244  Sum_probs=59.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++|+.|++++|||||+|++.++|++||++||+++|.+++|.|++|..+.
T Consensus        26 ~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~~   87 (110)
T 3s8s_A           26 MCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQ   87 (110)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTTH
T ss_pred             HHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            58999999999999999999999999999999999999999999999999999999997543

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

Probab=99.61  E-value=7.6e-16  Score=125.86  Aligned_cols=65  Identities=20%  Similarity=0.339  Sum_probs=61.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|+++++|++||++||+++|++++|+|++|+++....
T Consensus        59 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  123 (156)
T 1h2v_Z           59 LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGR  123 (156)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCTTC
T ss_pred             HHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCcC
Confidence            58999999999999999999999999999999999999999999999999999999999866543

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

Probab=99.60  E-value=3.1e-15  Score=113.74  Aligned_cols=65  Identities=18%  Similarity=0.417  Sum_probs=61.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|.+++|+|++|+++....
T Consensus        35 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   99 (103)
T 2cq0_A           35 LFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG   99 (103)
T ss_dssp             TSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCSC
T ss_pred             HHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCCC
Confidence            79999999999999999999999999999999999999999999999999999999999876553

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

Probab=99.60  E-value=2.5e-15  Score=112.39  Aligned_cols=65  Identities=25%  Similarity=0.587  Sum_probs=61.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|++++|.|++|+++....
T Consensus        25 ~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   89 (95)
T 2dnz_A           25 IFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDGG   89 (95)
T ss_dssp             HHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCCC
T ss_pred             HHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCCC
Confidence            58999999999999999999999999999999999999999999999999999999999876553

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

Probab=99.57  E-value=3.4e-15  Score=113.21  Aligned_cols=66  Identities=27%  Similarity=0.356  Sum_probs=62.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|.+++|+|++|+++.....
T Consensus        32 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   97 (102)
T 2cqb_A           32 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES   97 (102)
T ss_dssp             HHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCCC
T ss_pred             HhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999998776543

>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=99.57  E-value=4.1e-15  Score=112.17  Aligned_cols=66  Identities=20%  Similarity=0.325  Sum_probs=61.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|.+++|.|++|+++.....
T Consensus        28 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   93 (99)
T 1whw_A           28 LFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQ   93 (99)
T ss_dssp             HHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTTCC
T ss_pred             HHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccccc
Confidence            589999999999999999999999999999999999999999999999999999999998876543

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

Probab=99.57  E-value=6e-15  Score=111.39  Aligned_cols=65  Identities=26%  Similarity=0.557  Sum_probs=61.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+ ||+++|++++|+|++|+++.....
T Consensus        30 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~~~   94 (99)
T 2dgs_A           30 YFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSKSS   94 (99)
T ss_dssp             HHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCCCC
T ss_pred             HHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcccCC
Confidence            58999999999999999999999999999999999999998 999999999999999998776543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.57  E-value=9e-16  Score=117.03  Aligned_cols=62  Identities=11%  Similarity=0.275  Sum_probs=59.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC-eEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD-RVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G-r~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||++||+++|.+ ++|.|++|.++.
T Consensus        32 ~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~~   94 (100)
T 3ns6_A           32 LFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVE   94 (100)
T ss_dssp             HHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHHH
T ss_pred             HHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchhh
Confidence            58999999999999999999999999999999999999999999999999 999999998753

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

Probab=99.57  E-value=3.4e-15  Score=111.79  Aligned_cols=65  Identities=31%  Similarity=0.409  Sum_probs=61.4

Q ss_pred             CCCCCccceEE-EEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDL-KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V-~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++| +|++++.|+++++||||+|.++++|++||+.||+++|.+++|.|++|.++....
T Consensus        25 ~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   90 (96)
T 1x5t_A           25 TFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKG   90 (96)
T ss_dssp             HHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCCC
T ss_pred             HHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCCC
Confidence            58999999999 999999999999999999999999999999999999999999999999877554

>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=99.56  E-value=3.1e-15  Score=109.90  Aligned_cols=62  Identities=24%  Similarity=0.490  Sum_probs=57.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||+.||+++|.+++|.|++|++++
T Consensus        26 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~kp   87 (87)
T 3bs9_A           26 AFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP   87 (87)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC---
T ss_pred             HHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCCC
Confidence            58999999999999999999999999999999999999999999999999999999998763

>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=99.56  E-value=6.3e-15  Score=107.35  Aligned_cols=62  Identities=19%  Similarity=0.432  Sum_probs=59.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      +|++||+|++|.|+.++.|+++++||||+|.++++|++||+.||+.+|.+++|.|++|++++
T Consensus        21 ~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           21 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             HHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             HHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            58999999999999999999999999999999999999999999999999999999999875

>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=99.56  E-value=5.3e-15  Score=114.75  Aligned_cols=66  Identities=20%  Similarity=0.393  Sum_probs=61.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|.+++|+|++|+++.....
T Consensus        45 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~  110 (115)
T 2cpz_A           45 MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKS  110 (115)
T ss_dssp             HHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCCCC
T ss_pred             HHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcCCC
Confidence            589999999999999999999999999999999999999999999999999999999998766543

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

Probab=99.55  E-value=9.7e-16  Score=115.18  Aligned_cols=64  Identities=19%  Similarity=0.357  Sum_probs=58.7

Q ss_pred             CCCCCc-cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLT-HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG-~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~l-nG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|| +|++|+|++|+.|++++|||||+|.++++|++||+.| |+.+|.+++|.|++|++++..
T Consensus        21 ~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~~   86 (91)
T 2lxi_A           21 QLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPKI   86 (91)
T ss_dssp             HHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCCC
T ss_pred             HHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCCC
Confidence            588999 8999999999999999999999999999999999987 456899999999999987654

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

Probab=99.55  E-value=3.9e-15  Score=112.88  Aligned_cols=65  Identities=25%  Similarity=0.488  Sum_probs=61.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|++++|+|++|+++....
T Consensus        32 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   96 (102)
T 1x5s_A           32 VFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR   96 (102)
T ss_dssp             HHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCCC
T ss_pred             HHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            58899999999999999999999999999999999999999999999999999999999876553

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

Probab=99.55  E-value=4e-15  Score=113.17  Aligned_cols=65  Identities=29%  Similarity=0.408  Sum_probs=61.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|++++|.|++|+++....
T Consensus        33 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dnm_A           33 VFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL   97 (103)
T ss_dssp             HHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCSCC
T ss_pred             HHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCCCC
Confidence            58999999999999999999999999999999999999999999999999999999999766554

>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=99.55  E-value=5e-15  Score=112.82  Aligned_cols=65  Identities=22%  Similarity=0.280  Sum_probs=61.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|.+++|+|++|+++....
T Consensus        35 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   99 (105)
T 1x5u_A           35 LFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL   99 (105)
T ss_dssp             HHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcCC
Confidence            58999999999999999999999999999999999999999999999999999999999876553

>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=99.55  E-value=1.4e-15  Score=113.43  Aligned_cols=64  Identities=14%  Similarity=0.221  Sum_probs=55.6

Q ss_pred             CCCCCc--cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLT--HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG--~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||  +|++|+|+.|+.|++++|||||+|.+.++|++||++||+++|++++|+|+++.++...
T Consensus        21 ~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~~   86 (90)
T 3p5t_L           21 AVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHH   86 (90)
T ss_dssp             HHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC------
T ss_pred             HHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCccc
Confidence            589999  9999999999999999999999999999999999999999999999999999987644

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

Probab=99.55  E-value=5.6e-15  Score=118.15  Aligned_cols=65  Identities=18%  Similarity=0.369  Sum_probs=61.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|.+++|+|++|+++....
T Consensus        62 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  126 (139)
T 1u6f_A           62 LFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRP  126 (139)
T ss_dssp             HHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCCC
T ss_pred             HHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            58899999999999999999999999999999999999999999999999999999999876654

>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=99.54  E-value=3.8e-15  Score=117.22  Aligned_cols=65  Identities=15%  Similarity=0.296  Sum_probs=61.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|++++|.|++|+++....
T Consensus        42 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  106 (126)
T 3ex7_B           42 KFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK  106 (126)
T ss_dssp             HHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSCC
T ss_pred             HHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCCC
Confidence            58999999999999999999999999999999999999999999999999999999999876554

>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=99.54  E-value=2.4e-14  Score=110.93  Aligned_cols=63  Identities=13%  Similarity=0.115  Sum_probs=58.2

Q ss_pred             CCCCCccceEEEEeecCCCC---CCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSG---RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg---~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|+   +++|||||+|+++++|++||+.||+++|++++|.|++|+++..
T Consensus        38 ~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           38 YFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC  103 (111)
T ss_dssp             TTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCSC
T ss_pred             HhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEecccccc
Confidence            69999999999999998754   5669999999999999999999999999999999999998764

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

Probab=99.54  E-value=5.8e-15  Score=112.63  Aligned_cols=63  Identities=16%  Similarity=0.308  Sum_probs=60.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||++||+++|.+++|.|++|+++..
T Consensus        43 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  105 (106)
T 1p27_B           43 KFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  105 (106)
T ss_dssp             HHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESSC
T ss_pred             HHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCCC
Confidence            589999999999999999999999999999999999999999999999999999999998754

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

Probab=99.54  E-value=9.6e-15  Score=113.14  Aligned_cols=65  Identities=23%  Similarity=0.459  Sum_probs=61.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|.++.|.|++|+++....
T Consensus        35 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           35 AFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP   99 (115)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCCS
T ss_pred             HHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCCC
Confidence            58999999999999999999999999999999999999999999999999999999999876554

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

Probab=99.54  E-value=1.1e-14  Score=110.08  Aligned_cols=63  Identities=19%  Similarity=0.483  Sum_probs=59.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++ ++++++||||+|.++++|++||++||+++|.+++|+|++|+++...
T Consensus        37 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   99 (100)
T 2do4_A           37 ICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSS   99 (100)
T ss_dssp             HHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSCC
T ss_pred             HHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            58999999999999997 9999999999999999999999999999999999999999987643

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

Probab=99.53  E-value=6e-15  Score=112.48  Aligned_cols=60  Identities=13%  Similarity=0.348  Sum_probs=55.9

Q ss_pred             CCCCCcc--ceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCC----eeCCeEEEEEeccc
Q 025249            1 MQQCLTH--NNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR----EFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~--I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~----~i~Gr~I~V~~A~~   60 (255)
                      ||++||+  |++|+|++|+.|+++||||||+|.++++|++||+.||+.    .|++++|.|++|+.
T Consensus        29 ~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           29 ALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             HSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             HHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            5899995  679999999999999999999999999999999999997    49999999999975

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

Probab=99.53  E-value=2.4e-14  Score=108.84  Aligned_cols=64  Identities=28%  Similarity=0.468  Sum_probs=60.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+.+  ++++++||||+|.++++|++||++||+++|.+++|.|++|+++.....
T Consensus        35 ~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   98 (103)
T 2d9p_A           35 AFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQS   98 (103)
T ss_dssp             TTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCCCC
T ss_pred             HHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccCCC
Confidence            7999999999999998  899999999999999999999999999999999999999998776544

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

Probab=99.53  E-value=1.4e-14  Score=108.06  Aligned_cols=59  Identities=20%  Similarity=0.399  Sum_probs=57.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||+.||+++|.+++|+|++|+
T Consensus        36 ~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           36 IFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             HTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             HHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            58999999999999999999999999999999999999999999999999999999985

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

Probab=99.53  E-value=1.4e-14  Score=111.92  Aligned_cols=65  Identities=20%  Similarity=0.361  Sum_probs=61.2

Q ss_pred             CCCCCccce--------EEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNN--------DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~--------~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|+        .|+|++++.|+++++||||+|.++++|++||+.||+++|.+++|.|++|+++....
T Consensus        35 ~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           35 FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             HHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCST
T ss_pred             HHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCCCC
Confidence            589999999        69999999999999999999999999999999999999999999999999877654

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

Probab=99.53  E-value=1.3e-14  Score=110.62  Aligned_cols=66  Identities=15%  Similarity=0.357  Sum_probs=61.7

Q ss_pred             CCCCCccceEEEEeec-CCCCCCCcEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLE-RDSGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~D-k~Tg~srGfaFVtF~~~e~a~~AI~~l-nG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+++ +.++++++||||+|.++++|++||+.| |+++|.+++|.|++|+++.....
T Consensus        35 ~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~~~~  102 (107)
T 2cph_A           35 LFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQS  102 (107)
T ss_dssp             HHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCCCCC
T ss_pred             HHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCCCCC
Confidence            5899999999999999 889999999999999999999999999 99999999999999998776543

>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=99.53  E-value=1.6e-14  Score=110.92  Aligned_cols=66  Identities=15%  Similarity=0.299  Sum_probs=61.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc------CCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH------GREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln------G~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||      +++|++++|.|++|.++.....
T Consensus        35 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~~~  106 (111)
T 1x4h_A           35 VLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS  106 (111)
T ss_dssp             HHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccCCC
Confidence            58999999999999999999999999999999999999999999      9999999999999998776543

>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=99.52  E-value=1.2e-14  Score=109.32  Aligned_cols=63  Identities=22%  Similarity=0.479  Sum_probs=60.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.+.++|++||++||+.+|.++.|.|++|+++..
T Consensus        22 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           22 LCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             HHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             HHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999998654

>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=99.52  E-value=2e-14  Score=109.60  Aligned_cols=64  Identities=19%  Similarity=0.391  Sum_probs=59.9

Q ss_pred             CCCCCccceEEEEeecCCC-CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDS-GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~T-g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++|| |++|+|++++.| +++++||||+|.++++|++|| +||+++|.+++|.|++|+++.....
T Consensus        35 ~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~~~   99 (104)
T 1wi8_A           35 FFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDS   99 (104)
T ss_dssp             HTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCCCC
T ss_pred             HHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCCCC
Confidence            589999 999999999998 999999999999999999999 8999999999999999998876543

>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=99.52  E-value=2.2e-14  Score=136.54  Aligned_cols=66  Identities=21%  Similarity=0.434  Sum_probs=62.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|+.|+||+++.|++++|||||+|.++++|++||++||+++|.+++|.|++|+++....+
T Consensus       122 ~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~~~~  187 (437)
T 3pgw_S          122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGW  187 (437)
T ss_pred             HHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCCCC
Confidence            699999999999999999999999999999999999999999999999999999999998776544

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

Probab=99.52  E-value=2.5e-14  Score=111.10  Aligned_cols=64  Identities=25%  Similarity=0.394  Sum_probs=59.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||+ +|.+++|+|++|.++....
T Consensus        37 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~~~~~  100 (116)
T 2cqd_A           37 YFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPR  100 (116)
T ss_dssp             HHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTCCCC
T ss_pred             HHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccCCCcc
Confidence            589999999999999999999999999999999999999999998 8999999999998765443

>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=99.52  E-value=1e-14  Score=111.29  Aligned_cols=65  Identities=23%  Similarity=0.390  Sum_probs=60.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee---CCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF---GDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i---~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|   .+++|.|++|.++....
T Consensus        33 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~~~  100 (106)
T 2dgp_A           33 LFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGG  100 (106)
T ss_dssp             HHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSCCC
T ss_pred             HHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCcccccC
Confidence            589999999999999999999999999999999999999999999988   89999999999876553

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

Probab=99.52  E-value=1.3e-14  Score=108.27  Aligned_cols=60  Identities=23%  Similarity=0.400  Sum_probs=57.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|++++|+|++|++
T Consensus        35 ~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           35 VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             HHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             HHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            589999999999999999999999999999999999999999999999999999999874

>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=99.52  E-value=1.3e-14  Score=111.50  Aligned_cols=63  Identities=17%  Similarity=0.266  Sum_probs=60.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.+.++|++||+.||+++|++++|.|++|+++..
T Consensus        46 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  108 (110)
T 1oo0_B           46 KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  108 (110)
T ss_dssp             HHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESSC
T ss_pred             HHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCCC
Confidence            589999999999999999999999999999999999999999999999999999999998764

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

Probab=99.51  E-value=1.3e-14  Score=109.21  Aligned_cols=65  Identities=14%  Similarity=0.268  Sum_probs=60.2

Q ss_pred             CCCCCccceEEEEeecCC---CCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERD---SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~---Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.   |+++++||||+|.++++|++||++||+++|++++|.|++|+++....
T Consensus        25 ~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   92 (98)
T 2cpf_A           25 VFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKPA   92 (98)
T ss_dssp             HHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCCC
Confidence            589999999999999987   77999999999999999999999999999999999999999876554

>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=99.51  E-value=1.3e-14  Score=116.09  Aligned_cols=63  Identities=24%  Similarity=0.367  Sum_probs=60.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|+++++||||+|+++++|++||++||+.+|++++|.|++|+++..
T Consensus        66 ~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~p  128 (129)
T 2kxn_B           66 VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP  128 (129)
T ss_dssp             HHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSSC
T ss_pred             HHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            589999999999999999999999999999999999999999999999999999999988653

>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=99.51  E-value=2.3e-14  Score=109.11  Aligned_cols=64  Identities=16%  Similarity=0.289  Sum_probs=59.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC---eEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD---RVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G---r~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++++ ++++++||||+|.++++|++||++||+++|.+   ++|.|++|+++....
T Consensus        35 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~~~  101 (105)
T 2dnh_A           35 LFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESG  101 (105)
T ss_dssp             HHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCCCS
T ss_pred             HHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCcccC
Confidence            58999999999999997 89999999999999999999999999999998   999999999877654

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

Probab=99.51  E-value=3.4e-14  Score=108.11  Aligned_cols=63  Identities=17%  Similarity=0.474  Sum_probs=58.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++|+ |++|+|++++.|++++|||||+|+++++|++|| +||+++|.+++|.|++|+++....
T Consensus        35 ~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2dng_A           35 IFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDK   97 (103)
T ss_dssp             HTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCCC
T ss_pred             HHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCCC
Confidence            589996 999999999999999999999999999999999 899999999999999999876553

>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=99.51  E-value=1.3e-14  Score=106.06  Aligned_cols=59  Identities=27%  Similarity=0.390  Sum_probs=56.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|.+++|.|++|+
T Consensus        27 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~ak   85 (85)
T 3mdf_A           27 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   85 (85)
T ss_dssp             HHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            58999999999999999999999999999999999999999999999999999999985

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

Probab=99.50  E-value=3e-14  Score=110.65  Aligned_cols=65  Identities=23%  Similarity=0.381  Sum_probs=60.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||+. |+++|++++|.|++|+++.....
T Consensus        47 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~~~~  111 (116)
T 1x4b_A           47 YYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGS  111 (116)
T ss_dssp             HHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCCCCC
T ss_pred             HHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCccCCC
Confidence            589999999999999999999999999999999999999997 99999999999999998876543

>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=99.50  E-value=4.1e-14  Score=110.78  Aligned_cols=63  Identities=21%  Similarity=0.411  Sum_probs=59.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++ |+++++||||+|.+.++|++||++||+++|++++|+|++|+++...
T Consensus        27 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           27 VFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ   89 (116)
T ss_dssp             HHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSCS
T ss_pred             HHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCCC
Confidence            58999999999999997 9999999999999999999999999999999999999999976644

>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=99.49  E-value=7.6e-14  Score=106.00  Aligned_cols=64  Identities=27%  Similarity=0.466  Sum_probs=58.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+.++.+  +++||||+|.++++|++||++||+++|++++|.|++|+++.....
T Consensus        35 ~f~~~G~v~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~   98 (103)
T 2cq3_A           35 MFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS   98 (103)
T ss_dssp             HGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCCCC
T ss_pred             HHHhcCCeEEEEEEecCCC--CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCCCC
Confidence            5899999999999998654  899999999999999999999999999999999999998776543

>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=99.49  E-value=2.1e-14  Score=108.35  Aligned_cols=61  Identities=13%  Similarity=0.115  Sum_probs=56.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|++|+.|   ++||||+|.++++|++||++||+++|.+++|+|++|+++...
T Consensus        33 ~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~   93 (96)
T 2dgx_A           33 AFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASGP   93 (96)
T ss_dssp             HHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSSCC
T ss_pred             hccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            5889999999999999877   789999999999999999999999999999999999887644

>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=99.49  E-value=2e-14  Score=111.20  Aligned_cols=62  Identities=23%  Similarity=0.592  Sum_probs=59.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||+.||+.+|.+++|.|++|+++.
T Consensus        46 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           46 IFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             HHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             HHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            58999999999999999999999999999999999999999999999999999999999875

>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=99.49  E-value=3.1e-14  Score=104.93  Aligned_cols=61  Identities=21%  Similarity=0.428  Sum_probs=58.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++|| +||+++|.+++|.|++|+++.
T Consensus        26 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~~   86 (89)
T 3ucg_A           26 HFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTNR   86 (89)
T ss_dssp             HHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTTS
T ss_pred             HHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCCC
Confidence            5899999999999999999999999999999999999999 899999999999999998754

>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=99.49  E-value=1.9e-14  Score=108.23  Aligned_cols=62  Identities=13%  Similarity=0.210  Sum_probs=58.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.++.|+++++||||+|.++++|++||++||+++|.+++|+|+++..+.
T Consensus        35 ~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (98)
T 2cqp_A           35 FFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS   96 (98)
T ss_dssp             HTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCSS
T ss_pred             HHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCCC
Confidence            58999999999999999999999999999999999999999999999999999999998653

>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=99.49  E-value=2.8e-14  Score=111.38  Aligned_cols=62  Identities=19%  Similarity=0.417  Sum_probs=56.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|++|+.  .+||||||+|+++++|++||++||+++|.+++|.|++|+++...
T Consensus        25 ~F~~~G~v~~v~i~~d~~--~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~   86 (115)
T 4f25_A           25 TFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKER   86 (115)
T ss_dssp             HHGGGSCEEEEEEEEETT--EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC-
T ss_pred             HHhccCCEEEEEEeecCC--CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCcccc
Confidence            689999999999999854  47999999999999999999999999999999999999887654

>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=99.49  E-value=1.9e-14  Score=105.71  Aligned_cols=63  Identities=11%  Similarity=0.307  Sum_probs=58.6

Q ss_pred             CCCCCccceEEEEeecCCCCC-CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGR-PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~-srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++.|+. +++||||+|.++++|++||++||+.+|.++.|.|++|.++..
T Consensus        24 ~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   87 (88)
T 4a8x_A           24 IFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWP   87 (88)
T ss_dssp             HHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCCC
T ss_pred             HHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCCC
Confidence            589999999999999988866 999999999999999999999999999999999999987653

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

Probab=99.48  E-value=2.1e-14  Score=109.43  Aligned_cols=65  Identities=18%  Similarity=0.329  Sum_probs=60.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+.++.|+++++||||+|+++++|++||+. |+++|++++|.|++|+++.....
T Consensus        36 ~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~~~~  100 (105)
T 2dh8_A           36 YFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPS  100 (105)
T ss_dssp             HHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSCCTT
T ss_pred             HHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCCCCC
Confidence            589999999999999999999999999999999999999997 99999999999999998776543

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

Probab=99.48  E-value=3.3e-14  Score=107.40  Aligned_cols=59  Identities=20%  Similarity=0.364  Sum_probs=56.9

Q ss_pred             CCCCCccceE--------EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNND--------LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~--------V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++        |+|++++.|++++|||||+|.+.++|++||+.||+++|.+++|+|++|+
T Consensus        33 ~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           33 YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             HHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            5899999999        9999999999999999999999999999999999999999999999985

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

Probab=99.48  E-value=2.1e-14  Score=108.25  Aligned_cols=63  Identities=19%  Similarity=0.367  Sum_probs=59.3

Q ss_pred             CCCCCccce-EEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeE----EEEEecccCCC
Q 025249            1 MQQCLTHNN-DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRV----ISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~-~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~----I~V~~A~~k~~   63 (255)
                      ||++||+|+ +|+|++++.|+++++||||+|.++++|++||+.||+++|.++.    |+|++|++...
T Consensus        29 ~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~~~   96 (99)
T 2div_A           29 AFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGP   96 (99)
T ss_dssp             HHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCCSS
T ss_pred             HHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCCCC
Confidence            588999999 9999999999999999999999999999999999999999999    99999987643

>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=99.48  E-value=3.7e-14  Score=108.30  Aligned_cols=58  Identities=14%  Similarity=0.263  Sum_probs=55.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|++++ |+++++||||+|.++++|++||++||+++|.+++|+|++|.
T Consensus        49 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           49 LFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             HHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            58999999999999998 99999999999999999999999999999999999999986

>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=99.48  E-value=2.2e-14  Score=108.88  Aligned_cols=64  Identities=27%  Similarity=0.626  Sum_probs=60.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.+.++|++||+.||+++|.++.|.|++|.++...
T Consensus        28 ~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   91 (104)
T 1p1t_A           28 IFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNK   91 (104)
T ss_dssp             HHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTHH
T ss_pred             HHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCccch
Confidence            5899999999999999999999999999999999999999999999999999999999976543

>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=99.48  E-value=2.3e-14  Score=107.00  Aligned_cols=60  Identities=13%  Similarity=0.261  Sum_probs=57.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|.|+.++.++++++||||+|.++++|++||++||+++|.+++|+|+++.+
T Consensus        35 ~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~s   94 (95)
T 2ek1_A           35 FFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPSS   94 (95)
T ss_dssp             HTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC-
T ss_pred             HHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEeccC
Confidence            589999999999999999999999999999999999999999999999999999999864

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.47  E-value=6.2e-14  Score=108.68  Aligned_cols=60  Identities=15%  Similarity=0.128  Sum_probs=56.3

Q ss_pred             CCCCCccceEEEEeecCCC-CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDS-GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~T-g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|++|+|++++.+ ++++|||||+|.++++|++||++||+..|++++|.|+++.+
T Consensus        33 ~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           33 ECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             HGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             HHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            4899999999999999765 68999999999999999999999999999999999999975

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

Probab=99.47  E-value=7.5e-14  Score=107.73  Aligned_cols=63  Identities=19%  Similarity=0.283  Sum_probs=58.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|++++ ++++++||||+|.++++|++||++||+++|++++|.|++|++....
T Consensus        35 ~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   97 (114)
T 2do0_A           35 VFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPK   97 (114)
T ss_dssp             HHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCCCC
T ss_pred             HHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCCCC
Confidence            58999999999999997 6899999999999999999999999999999999999999865444

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

Probab=99.47  E-value=3.4e-14  Score=110.51  Aligned_cols=59  Identities=17%  Similarity=0.390  Sum_probs=56.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||+++|++++|+|++++
T Consensus        60 ~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~ak  118 (118)
T 2khc_A           60 TFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK  118 (118)
T ss_dssp             HTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC-
T ss_pred             HHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            58999999999999999999999999999999999999999999999999999999874

>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=99.47  E-value=8.8e-14  Score=105.64  Aligned_cols=63  Identities=19%  Similarity=0.306  Sum_probs=57.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.+  +++||||+|.++++|++||+.||+++|.+++|.|++|+++....
T Consensus        35 ~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   97 (103)
T 2cqi_A           35 LFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQK   97 (103)
T ss_dssp             HHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTCCC
T ss_pred             HHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCcccc
Confidence            5889999999999998655  68999999999999999999999999999999999999866543

>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=99.46  E-value=2.6e-14  Score=110.68  Aligned_cols=62  Identities=19%  Similarity=0.397  Sum_probs=58.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++|| +||+++|.++.|.|++|+++..
T Consensus        45 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~  106 (114)
T 2cq4_A           45 FFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN  106 (114)
T ss_dssp             HHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHHHH
T ss_pred             HHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCCcc
Confidence            5899999999999999999999999999999999999999 8999999999999999987543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.46  E-value=8.6e-14  Score=107.67  Aligned_cols=63  Identities=22%  Similarity=0.417  Sum_probs=58.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||+.|+ ++|+++.|.|++|.++...
T Consensus        45 ~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~~a~~~~~~  107 (109)
T 2rs2_A           45 YFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAFPRRAQ  107 (109)
T ss_dssp             HHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEEECCCCCCC
T ss_pred             HHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEEEccCCCCC
Confidence            58999999999999999999999999999999999999999775 9999999999999987654

>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=99.46  E-value=2e-14  Score=106.46  Aligned_cols=63  Identities=25%  Similarity=0.564  Sum_probs=55.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.+++ |++||++||+.+|.+++|.|++|.++...
T Consensus        21 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~~   83 (90)
T 2ki2_A           21 LFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKSL   83 (90)
T ss_dssp             THHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC------
T ss_pred             HHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            6889999999999999999999999999999999 99999999999999999999999876544

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

Probab=99.46  E-value=4.6e-14  Score=107.25  Aligned_cols=64  Identities=22%  Similarity=0.446  Sum_probs=59.6

Q ss_pred             CCCC-CccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCe-eCCeEEEEEecccCCCCC
Q 025249            1 MQQC-LTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGRE-FGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfek-FG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~-i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++ ||+|++|+|++++ |+++++||||+|.++++|++||++||++. |++++|.|++|.++....
T Consensus        29 ~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           29 FFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRV   94 (104)
T ss_dssp             HHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSCC
T ss_pred             HHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcCC
Confidence            5788 9999999999998 99999999999999999999999999999 999999999998876554

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.46  E-value=3.4e-14  Score=117.38  Aligned_cols=61  Identities=15%  Similarity=0.332  Sum_probs=58.5

Q ss_pred             CCCCCc--cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLT--HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG--~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||  +|++|+|++|+.|++++|||||+|.+.++|++||+.||+++|.++.|.|++|.++
T Consensus        75 ~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           75 VIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             HHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             HHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            589999  9999999999999999999999999999999999999999999999999999764

>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=99.46  E-value=6.1e-14  Score=115.88  Aligned_cols=65  Identities=17%  Similarity=0.255  Sum_probs=59.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|+.|.|++++.|+++++||||+|.+.++|++||++||+++|.+++|.|.+|.++....
T Consensus        92 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           92 KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            58999999999999999999999999999999999999999999999999999999999876543

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

Probab=99.45  E-value=1.2e-13  Score=104.47  Aligned_cols=60  Identities=23%  Similarity=0.509  Sum_probs=55.0

Q ss_pred             CccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            5 LTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         5 FG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      |..+++|+|++++.|+++++||||+|.++++|++||+.||+++|.+++|+|++|+++...
T Consensus        36 F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   95 (102)
T 2fc8_A           36 FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG   95 (102)
T ss_dssp             STTCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSS
T ss_pred             hcCCeEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCC
Confidence            334568999999999999999999999999999999999999999999999999987755

>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=99.45  E-value=6.8e-14  Score=104.47  Aligned_cols=59  Identities=22%  Similarity=0.417  Sum_probs=55.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|+.++. +++++||||+|.++++|++||+.||+++|++++|.|++|+.
T Consensus        36 ~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   94 (95)
T 2ywk_A           36 LFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS   94 (95)
T ss_dssp             HHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             HHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcCC
Confidence            589999999999999975 89999999999999999999999999999999999999864

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.45  E-value=1.2e-13  Score=108.33  Aligned_cols=63  Identities=29%  Similarity=0.529  Sum_probs=59.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++|| +||+++|.++.|.|+++++....
T Consensus        56 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~  118 (124)
T 2jwn_A           56 HFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPG  118 (124)
T ss_dssp             HHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCCSS
T ss_pred             HHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCCCC
Confidence            5899999999999999999999999999999999999999 79999999999999999875543

>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=99.45  E-value=1.3e-13  Score=105.89  Aligned_cols=62  Identities=16%  Similarity=0.252  Sum_probs=55.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.+   .++++||||+|+++++|++||++||+++|++++|+|++|+++....
T Consensus        42 ~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~  103 (109)
T 1x4a_A           42 VFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTG  103 (109)
T ss_dssp             HHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCCCCC
T ss_pred             HHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCCCCC
Confidence            5899999999999664   4589999999999999999999999999999999999999876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.17  E-value=7.1e-15  Score=114.37  Aligned_cols=65  Identities=18%  Similarity=0.314  Sum_probs=61.4

Q ss_pred             CCCCCccceE--------EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNND--------LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~--------V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++        |+|++++.|+++++||||+|.++++|++||++||+++|.+++|.|++|+++....
T Consensus        27 ~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           27 YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN   99 (116)
Confidence            6999999999        9999999999999999999999999999999999999999999999999877653

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

Probab=99.44  E-value=3.3e-14  Score=104.24  Aligned_cols=59  Identities=14%  Similarity=0.318  Sum_probs=55.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|+.++.|+++++||||+|.++++|++||++||+++|.++.|+|+++.
T Consensus        25 ~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A           25 LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             TSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            69999999999999999999999999999999999999999999999999998876654

>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=99.44  E-value=3e-14  Score=124.55  Aligned_cols=61  Identities=15%  Similarity=0.272  Sum_probs=58.5

Q ss_pred             CCCCCc--cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLT--HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG--~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||  +|++|+|++|+.|+++||||||+|+++++|++||++||+++|++++|+|++|+++
T Consensus        88 ~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C           88 AVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             HHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHH
T ss_pred             HHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCC
Confidence            689999  9999999999999999999999999999999999999999999999999999754

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

Probab=99.44  E-value=1.5e-13  Score=102.11  Aligned_cols=60  Identities=17%  Similarity=0.366  Sum_probs=56.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++| +|++|+|+++ .+++++|||||+|.++++|++||+ ||+++|.++.|+|.+|++++.
T Consensus        30 ~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~~   89 (91)
T 2dgw_A           30 FLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGPS   89 (91)
T ss_dssp             HHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCCC
T ss_pred             HHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCCC
Confidence            58999 9999999999 899999999999999999999999 999999999999999998754

>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=99.44  E-value=7.5e-14  Score=113.69  Aligned_cols=65  Identities=25%  Similarity=0.401  Sum_probs=61.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.+.++|++||++||+++|.+++|.|++|+++....
T Consensus        90 ~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  154 (158)
T 2kn4_A           90 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  154 (158)
T ss_dssp             HHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCCC
T ss_pred             HHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCCC
Confidence            58999999999999999999999999999999999999999999999999999999999876543

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

Probab=99.44  E-value=1.6e-13  Score=107.78  Aligned_cols=63  Identities=14%  Similarity=0.238  Sum_probs=59.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++ |+++++||||+|.++++|++||+.||+++|.+++|+|++|.+....
T Consensus        55 ~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  117 (124)
T 2kt5_A           55 LFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDL  117 (124)
T ss_dssp             HHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTTCC
T ss_pred             HHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCC
Confidence            58999999999999998 9999999999999999999999999999999999999999876544

>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=99.43  E-value=2e-13  Score=105.52  Aligned_cols=61  Identities=18%  Similarity=0.308  Sum_probs=57.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee--------CCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF--------GDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i--------~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++++ |+++++||||+|.++++|++||+.||+++|        .+++|.|++|.|+.
T Consensus        45 ~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~~  113 (114)
T 1x5o_A           45 MLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPSS  113 (114)
T ss_dssp             TTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCSC
T ss_pred             HHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCCC
Confidence            79999999999999998 999999999999999999999999999999        57889999999753

>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=99.43  E-value=7.6e-14  Score=106.01  Aligned_cols=60  Identities=22%  Similarity=0.431  Sum_probs=56.9

Q ss_pred             CCCCCccceEEEEeecC-CCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLER-DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk-~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++|| |++|+|++++ .|++++|||||+|.+.++|++|| +||+.+|.++.|.|++|+++.
T Consensus        39 ~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           39 FFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             HSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCSC
T ss_pred             HHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCCC
Confidence            589999 9999999998 69999999999999999999999 899999999999999998764

>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=99.43  E-value=1.7e-13  Score=105.10  Aligned_cols=59  Identities=14%  Similarity=0.124  Sum_probs=54.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++|| |++|+|++|+ |++++|||||+|+++++|++||+ ||+++|.++.|+|.++.+..
T Consensus        35 ~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           35 FFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             SSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCC
T ss_pred             HHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCCCC
Confidence            699999 5599999997 99999999999999999999995 89999999999999988765

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

Probab=99.43  E-value=4.1e-14  Score=101.37  Aligned_cols=57  Identities=23%  Similarity=0.538  Sum_probs=54.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||+ ||+++|++++|.|++|
T Consensus        19 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           19 YFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             HHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58899999999999999999999999999999999999998 9999999999999876

>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=99.43  E-value=2.3e-13  Score=103.32  Aligned_cols=64  Identities=11%  Similarity=0.251  Sum_probs=58.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||++  +++|+++.|.|++|.++.....
T Consensus        35 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~l~v~~a~~~~~~~~   98 (103)
T 2cqg_A           35 YFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQSQDS   98 (103)
T ss_dssp             HHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTCCCCC
T ss_pred             HHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCeEEEEEecCCCCcCCC
Confidence            589999999999999999999999999999999999999984  5699999999999998776543

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

Probab=99.43  E-value=5.6e-14  Score=113.06  Aligned_cols=65  Identities=25%  Similarity=0.401  Sum_probs=61.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||++||+++|.+++|+|++|+++....
T Consensus        67 ~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             HHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCT
T ss_pred             HHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCCc
Confidence            58999999999999999999999999999999999999999999999999999999999866543

>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=99.43  E-value=1.6e-13  Score=100.92  Aligned_cols=57  Identities=28%  Similarity=0.514  Sum_probs=53.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||+ +++++|++++|.|++|
T Consensus        31 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           31 YFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             HHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999999999997 5888999999999986

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

Probab=99.42  E-value=1.3e-13  Score=102.32  Aligned_cols=62  Identities=23%  Similarity=0.344  Sum_probs=57.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+++  ++++++||||+|.++++|++||++||+++|++++|+|++|+++...
T Consensus        28 ~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~   89 (92)
T 2dgv_A           28 KFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASGP   89 (92)
T ss_dssp             HHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCSSC
T ss_pred             HHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCCC
Confidence            5899999999999984  8899999999999999999999999999999999999999987654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.42  E-value=7.8e-14  Score=100.06  Aligned_cols=58  Identities=22%  Similarity=0.406  Sum_probs=55.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|++|.|+.++.|++++|||||+|.++++|++||+.|| ++|++++|.|++|.
T Consensus        20 ~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a~   77 (77)
T 1uaw_A           20 YFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAF   77 (77)
T ss_dssp             HHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEECC
T ss_pred             HHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEecC
Confidence            58999999999999999999999999999999999999999999 99999999999873

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.42  E-value=3.2e-14  Score=113.28  Aligned_cols=63  Identities=13%  Similarity=0.235  Sum_probs=58.9

Q ss_pred             CCCCCccceE--EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCC----eeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNND--LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR----EFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~--V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~----~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+.  |+|++|+.|+++||||||+|.++ +|++||+.||++    +|++++|.|++|+++...
T Consensus        43 ~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           43 ALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKRD  111 (131)
T ss_dssp             HHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCCC
T ss_pred             HHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCCC
Confidence            5899999977  99999999999999999999999 999999999999    999999999999986544

>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=99.42  E-value=9.2e-14  Score=106.42  Aligned_cols=65  Identities=25%  Similarity=0.340  Sum_probs=59.6

Q ss_pred             CCCCCcc-ceEEEEe-ecCCCCCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTH-NNDLKIM-LERDSGRPRGFGFITYADRRAMDDAIREMH--GREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~-I~~V~Iv-~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln--G~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+ |++|.|+ .++.|+++++||||+|.++++|++||+.||  +++|.+++|.|++|+++....
T Consensus        28 ~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~~~   96 (109)
T 2dis_A           28 EIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVD   96 (109)
T ss_dssp             HHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCSTT
T ss_pred             HHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCCcC
Confidence            5889998 9999999 899999999999999999999999999996  589999999999999876643

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

Probab=99.41  E-value=1.3e-13  Score=109.55  Aligned_cols=58  Identities=28%  Similarity=0.388  Sum_probs=55.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||+++|.+++|+|++|
T Consensus        83 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           83 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             HHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             HHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            5899999999999999999999999999999999999999999999999999999986

>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=99.41  E-value=1.8e-13  Score=105.94  Aligned_cols=60  Identities=18%  Similarity=0.253  Sum_probs=55.4

Q ss_pred             CCCCCccceEEEEeecCCC--CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~T--g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|++|+|++++.+  .+++||+||+|+++++|++||++||++.|++++|.|+++.+
T Consensus        35 ~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           35 ECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   96 (105)
T ss_dssp             HHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCH
Confidence            4789999999999999765  47899999999999999999999999999999999999864

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

Probab=99.40  E-value=2.6e-13  Score=104.81  Aligned_cols=60  Identities=28%  Similarity=0.515  Sum_probs=55.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.++.  .+++||||+|.+.++|++||++||+++|++++|.|++|+++.
T Consensus        49 ~F~~~G~i~~v~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  108 (109)
T 2err_A           49 MFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV  108 (109)
T ss_dssp             HGGGTCCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCSC
T ss_pred             HHHhcCCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCc
Confidence            589999999999999854  489999999999999999999999999999999999998763

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.39  E-value=1.4e-13  Score=105.53  Aligned_cols=60  Identities=17%  Similarity=0.257  Sum_probs=55.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCe-EEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDR-VISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr-~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+  +.|++++|||||+|.++++|++||+.||+++|.++ +|.|++|....
T Consensus        41 ~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           41 IFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             HHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCCC
T ss_pred             HHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchHh
Confidence            58999999999998  47899999999999999999999999999999998 99999998654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.38  E-value=1.1e-12  Score=98.78  Aligned_cols=59  Identities=24%  Similarity=0.328  Sum_probs=53.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+      ++++||||+|.++++|++||++||+++|.+++|+|++|+++....
T Consensus        33 ~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~   91 (97)
T 1x5p_A           33 AFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLD   91 (97)
T ss_dssp             HHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCCC
T ss_pred             HHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCCC
Confidence            58999999999995      468999999999999999999999999999999999999876554

>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=99.38  E-value=5.9e-13  Score=102.40  Aligned_cols=58  Identities=16%  Similarity=0.256  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC-----eEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD-----RVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G-----r~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+++       +||||+|+++++|++||++||+++|.+     ++|+|++|+++....
T Consensus        35 ~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~~~   97 (108)
T 1x4c_A           35 HMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSY   97 (108)
T ss_dssp             HHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSCCC
T ss_pred             HHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCCCC
Confidence            5899999999999987       899999999999999999999999999     999999999876543

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

Probab=99.38  E-value=8.2e-13  Score=99.88  Aligned_cols=61  Identities=21%  Similarity=0.396  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|   +|+.+ .++++++||||+|.++++|++||+.||+++|.+++|+|++|+++....
T Consensus        35 ~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   95 (101)
T 2fc9_A           35 VFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN   95 (101)
T ss_dssp             HCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCCC
T ss_pred             HHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCCC
Confidence            47777765   67777 789999999999999999999999999999999999999999876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.38  E-value=3e-13  Score=102.37  Aligned_cols=53  Identities=11%  Similarity=0.150  Sum_probs=50.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|+.      +||||||+|.++++|++||+.||+.+|.+++|.|++|.
T Consensus        27 lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           27 LCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             HHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             HHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            689999999999976      68999999999999999999999999999999999994

>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=99.38  E-value=3.1e-13  Score=104.38  Aligned_cols=55  Identities=9%  Similarity=0.207  Sum_probs=52.1

Q ss_pred             CCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            3 QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         3 ekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ++||+|++|+|++++. ++++|||||+|.++++|++||++||++.|++++|.|+++
T Consensus        49 ~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           49 EKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             ccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            8999999999999854 789999999999999999999999999999999999986

>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=99.37  E-value=2.1e-13  Score=106.10  Aligned_cols=60  Identities=12%  Similarity=0.281  Sum_probs=56.4

Q ss_pred             CCCCCccc-eEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHN-NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I-~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||.| ++|+|++|+ |++++|||||+|.++++|++||+. |+++|.++.|.|.+|.++.
T Consensus        35 ~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~~   95 (114)
T 2cpy_A           35 FLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLED   95 (114)
T ss_dssp             HTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHHH
T ss_pred             HHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHHH
Confidence            58999999 899999998 999999999999999999999986 9999999999999998655

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=2.5e-13  Score=104.66  Aligned_cols=58  Identities=5%  Similarity=0.076  Sum_probs=54.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|++|.|++|+. ++++|||||+|+++++|++||+ ||+++|+++.|.|.++..
T Consensus        31 ~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           31 WLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             HHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             HHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            589999999999999987 9999999999999999999999 999999999999998764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.37  E-value=2.6e-13  Score=108.67  Aligned_cols=60  Identities=13%  Similarity=0.255  Sum_probs=54.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|.|+.   |++++|||||+|.+.++|++||++||+++|.+++|.|++|+++..
T Consensus        53 ~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           53 LASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS  112 (127)
T ss_dssp             HHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCCH
T ss_pred             HhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcch
Confidence            589999999998854   678999999999999999999999999999999999999987653

>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=99.37  E-value=8.8e-14  Score=109.62  Aligned_cols=61  Identities=21%  Similarity=0.315  Sum_probs=56.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.+|.++.|++++|||||+|.++++|++||+ ||+++|.++.|.|.+|.++.
T Consensus        45 ~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~~  105 (124)
T 1wel_A           45 FFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKG  105 (124)
T ss_dssp             HSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHHH
T ss_pred             HHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCHHH
Confidence            59999999998888888999999999999999999999999 99999999999999998643

>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=99.37  E-value=1.4e-12  Score=101.24  Aligned_cols=61  Identities=21%  Similarity=0.360  Sum_probs=54.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      +|++||+|++|.| .++.   ++|||||+|.++++|++||+.||++.|++++|.|++|.++....
T Consensus        46 ~f~~~G~v~~v~i-~~~~---~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           46 ECSKFGQIRKLLL-FDRH---PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             HGGGTSCCSEEEE-ETTC---TTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCCSS
T ss_pred             HHHccCCEeEEEE-ecCC---CCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCcc
Confidence            5899999999955 5543   79999999999999999999999999999999999999876543

>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=99.36  E-value=1.7e-13  Score=105.88  Aligned_cols=66  Identities=17%  Similarity=0.284  Sum_probs=56.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|+.|.|..+..|+++++||||+|.++++|++||+.||+++|.+++|.|++|+++.....
T Consensus        45 ~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~  110 (115)
T 2cpx_A           45 LFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSS  110 (115)
T ss_dssp             HTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCCCC
T ss_pred             HHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCCCC
Confidence            588999996554444444889999999999999999999999999999999999999998766543

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

Probab=99.36  E-value=1.2e-12  Score=97.08  Aligned_cols=57  Identities=23%  Similarity=0.407  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+        ++||||+|.++++|++||++||+++|++++|.|++|+++....
T Consensus        28 ~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   84 (90)
T 2dnq_A           28 LFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKAS   84 (90)
T ss_dssp             HHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCCC
T ss_pred             HHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCCC
Confidence            58999999999998        4799999999999999999999999999999999999877654

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

Probab=99.35  E-value=1.1e-12  Score=105.52  Aligned_cols=60  Identities=20%  Similarity=0.469  Sum_probs=57.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|.|+.++.|++++|||||+|.++++|++||++||+.+|.+++|.|++|++
T Consensus       107 ~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             HHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            589999999999999999999999999999999999999999999999999999999974

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

Probab=99.35  E-value=9.5e-13  Score=110.80  Aligned_cols=64  Identities=20%  Similarity=0.395  Sum_probs=60.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+.|+|+.++.|+++++||||+|.++++|++||++||+++|.++.|.|++|.++...
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            5899999999999999999999999999999999999999999999999999999999987544

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.34  E-value=9.8e-13  Score=102.60  Aligned_cols=58  Identities=16%  Similarity=0.293  Sum_probs=53.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++| +|++|+|++|+. ++++|||||+|.++++|++|| +||+++|.++.|+|..|.++
T Consensus        36 ~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           36 FFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             HhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            58999 999999999975 999999999999999999999 59999999999999998764

>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=99.34  E-value=9.1e-13  Score=99.06  Aligned_cols=57  Identities=21%  Similarity=0.286  Sum_probs=52.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC--CeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG--DRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~--Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+++      ++||||+|.++++|++||++||+++|.  +++|.|++|+++..
T Consensus        37 ~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~~   95 (97)
T 1why_A           37 EFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS   95 (97)
T ss_dssp             HHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCC
T ss_pred             HHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCCC
Confidence            5899999999999864      689999999999999999999999999  99999999998754

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.34  E-value=4.6e-13  Score=105.05  Aligned_cols=60  Identities=20%  Similarity=0.307  Sum_probs=55.7

Q ss_pred             CCCCCcc---ceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTH---NNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~---I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+   |++|+|++++. ++++|||||+|.++++|++||+ ||+++|.++.|+|.+|+++.
T Consensus        37 ~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~~   99 (118)
T 2db1_A           37 FLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRTE   99 (118)
T ss_dssp             HTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECHHH
T ss_pred             HHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCHHH
Confidence            5899999   89999999977 9999999999999999999999 99999999999999987543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.34  E-value=1.6e-13  Score=100.01  Aligned_cols=54  Identities=19%  Similarity=0.355  Sum_probs=50.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCe-EEEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDR-VISVN   56 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr-~I~V~   56 (255)
                      ||++||+|++|.|+  +.|++++|||||+|.++++|++||++||+++|.++ +|+|+
T Consensus        27 ~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V~   81 (81)
T 2krb_A           27 IFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN   81 (81)
T ss_dssp             HHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCCC
T ss_pred             HHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEeC
Confidence            58999999999988  47899999999999999999999999999999999 88773

>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=99.34  E-value=6.6e-13  Score=101.58  Aligned_cols=61  Identities=20%  Similarity=0.364  Sum_probs=56.1

Q ss_pred             CCCCCccceE-EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNND-LKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~-V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++ |.|+++ .|++++|||||+|+++++|++||+. |+++|.++.|+|.++.++.-
T Consensus        35 ~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~~   96 (104)
T 1wg5_A           35 FFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAEV   96 (104)
T ss_dssp             HTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTTS
T ss_pred             HHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHHH
Confidence            5899999998 889998 8999999999999999999999996 99999999999999986543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.34  E-value=7.8e-14  Score=105.56  Aligned_cols=62  Identities=19%  Similarity=0.387  Sum_probs=57.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+. .||.++.|++++|||||+|.++++|++||+ ||+++|.+++|.|++|+++...
T Consensus        37 ~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~~~   98 (101)
T 1fj7_A           37 AISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGT   98 (101)
T ss_dssp             HHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCCCS
T ss_pred             HHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCCCC
Confidence            5889999999 788888899999999999999999999998 9999999999999999987654

>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=99.34  E-value=1.8e-13  Score=111.44  Aligned_cols=61  Identities=16%  Similarity=0.162  Sum_probs=55.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|| |++|+|++|++ ++++|||||+|+++++|++|| +||+++|.++.|+|.++.++...
T Consensus        66 ~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~~  126 (139)
T 2hgn_A           66 FFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS  126 (139)
T ss_dssp             HHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC-
T ss_pred             HHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCCC
Confidence            589999 78999999976 999999999999999999999 69999999999999999876543

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

Probab=99.33  E-value=2.5e-12  Score=95.72  Aligned_cols=57  Identities=14%  Similarity=0.248  Sum_probs=52.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+++        ||||+|.++++|++||++||+++|.+++|+|++|+++....
T Consensus        30 ~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   86 (92)
T 2dgt_A           30 KFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA   86 (92)
T ss_dssp             HHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCSCC
T ss_pred             HHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCCCC
Confidence            5899999999999864        99999999999999999999999999999999999876553

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

Probab=99.33  E-value=5.6e-13  Score=112.10  Aligned_cols=61  Identities=15%  Similarity=0.269  Sum_probs=57.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.++ |+++++||||+|+++++|++||++||+++|++++|+|++|.+..
T Consensus       108 ~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          108 LFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             HHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             HHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            58999999999999998 99999999999999999999999999999999999999998654

>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=99.33  E-value=7.7e-13  Score=104.78  Aligned_cols=60  Identities=17%  Similarity=0.163  Sum_probs=55.0

Q ss_pred             CCCCCccceEEEEeecCC----CCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERD----SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~----Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|++|+|++++.    |++++||+||+|.++++|++||++||+..|++++|.|+++..
T Consensus        45 ef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           45 ECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  108 (118)
T ss_dssp             HHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCh
Confidence            378999999999999865    457889999999999999999999999999999999999864

>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=99.33  E-value=1.8e-12  Score=100.21  Aligned_cols=58  Identities=12%  Similarity=0.006  Sum_probs=51.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHG--REFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG--~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+++      ++||||+|+++++|++||+.||+  .+|.+++|.|++|++++.-
T Consensus        36 lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~   95 (102)
T 1x4d_A           36 LVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRI   95 (102)
T ss_dssp             TTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTTS
T ss_pred             HHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCCC
Confidence            7999999999999976      47999999999999999999986  4599999999999976544

>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=99.33  E-value=2.6e-12  Score=97.71  Aligned_cols=58  Identities=19%  Similarity=0.318  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++        +||||+|.++++|++||++||+++|++++|.|++|+++.....
T Consensus        31 ~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~   88 (103)
T 2dgu_A           31 AFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRK   88 (103)
T ss_dssp             HHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCCC
T ss_pred             HHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcccch
Confidence            588999999999985        4999999999999999999999999999999999998766543

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

Probab=99.33  E-value=6.2e-13  Score=100.54  Aligned_cols=59  Identities=20%  Similarity=0.331  Sum_probs=55.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.+     +++||||+|.++++|++||++||+.+|.+++|.|++|+++...
T Consensus        20 ~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   78 (101)
T 2hvz_A           20 AFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRR   78 (101)
T ss_dssp             HHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCS
T ss_pred             HHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCc
Confidence            5889999999999987     7899999999999999999999999999999999999987644

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.33  E-value=7e-13  Score=107.27  Aligned_cols=61  Identities=33%  Similarity=0.601  Sum_probs=58.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.++.|++++|||||+|.++++|++||+ ||++.|.+++|+|++|+|+.
T Consensus       107 ~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             HHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCCC
T ss_pred             HHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCCC
Confidence            58899999999999999999999999999999999999998 89999999999999999863

>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=99.33  E-value=2.5e-12  Score=96.99  Aligned_cols=59  Identities=19%  Similarity=0.235  Sum_probs=54.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+++      ++||||+|.++++|++||++||+++|.+++|.|++|+++....
T Consensus        35 ~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~~~~   93 (99)
T 2cpj_A           35 LFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLT   93 (99)
T ss_dssp             HTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCSCCC
T ss_pred             HHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCCCCC
Confidence            6899999999999864      6899999999999999999999999999999999999876543

>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=99.32  E-value=1.6e-12  Score=99.82  Aligned_cols=59  Identities=12%  Similarity=0.282  Sum_probs=54.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.+      ++||||+|.++++|++||+.||+++|.+++|.|++|+++....
T Consensus        45 ~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~  103 (109)
T 1x4g_A           45 TFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMT  103 (109)
T ss_dssp             HHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCSSC
T ss_pred             HHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCCCC
Confidence            5889999999999986      6899999999999999999999999999999999999876554

>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=99.32  E-value=4.1e-12  Score=97.76  Aligned_cols=59  Identities=8%  Similarity=0.087  Sum_probs=52.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH--GREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln--G~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|.|+++      |+||||+|+++++|++||+.|+  +.+|.+++|.|++|+++....
T Consensus        35 ~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           35 LGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             TTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCCC
T ss_pred             HHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCcC
Confidence            7999999999999875      7899999999999999999774  678999999999999766543

>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=99.32  E-value=2.4e-13  Score=97.13  Aligned_cols=57  Identities=14%  Similarity=0.313  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||++||+|++|.|++++.|++++|||||+|.++++|++||+ +++.+|.+++|.|++|
T Consensus        19 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           19 YFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             HHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58899999999999999999999999999999999999998 5889999999999876

>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=99.31  E-value=6.6e-13  Score=107.60  Aligned_cols=59  Identities=20%  Similarity=0.343  Sum_probs=55.6

Q ss_pred             CCCCCcc---ceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTH---NNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~---I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+   |++|+|++|+. ++++|||||+|+++++|++||+ ||+++|.++.|+|.+|.++
T Consensus        64 ~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           64 FLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             HTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHH
T ss_pred             HHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChH
Confidence            5899999   89999999987 9999999999999999999999 9999999999999998754

>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=99.31  E-value=1.8e-12  Score=107.44  Aligned_cols=65  Identities=25%  Similarity=0.368  Sum_probs=55.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|+.|+|+.++.|++++|||||+|.++++|++||+. ++++|+++.|.|.+|.++.....
T Consensus       124 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC-------
T ss_pred             HHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhHhcc
Confidence            589999999999999999999999999999999999999985 79999999999999999877654

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

Probab=99.31  E-value=1.7e-12  Score=107.82  Aligned_cols=63  Identities=21%  Similarity=0.444  Sum_probs=60.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|.|+.+++|+++++||||+|.++++|++||++||+.+|++++|.|++|+++..
T Consensus       134 ~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          134 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             HHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             HHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            588999999999999999999999999999999999999999999999999999999998754

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.30  E-value=9.8e-13  Score=102.42  Aligned_cols=59  Identities=10%  Similarity=0.086  Sum_probs=52.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH--GREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln--G~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+++      ||||||+|+++++|++||+.|+  +.+|.+++|.|++|+++....
T Consensus        36 lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           36 LGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             HHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             HHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence            6899999999999985      6899999999999999999886  478999999999999876553

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

Probab=99.30  E-value=1.4e-12  Score=98.18  Aligned_cols=58  Identities=22%  Similarity=0.374  Sum_probs=52.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|+ |.|+.+    ++++||||+|.++++|++||++||+++|.+++|.|++|+++..
T Consensus        39 ~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   96 (97)
T 2e5j_A           39 ALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD   96 (97)
T ss_dssp             HHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCCC
T ss_pred             HHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            588999997 777765    6789999999999999999999999999999999999998754

>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=99.30  E-value=2.4e-12  Score=100.37  Aligned_cols=57  Identities=16%  Similarity=0.279  Sum_probs=48.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeE-----EEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRV-----ISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~-----I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+++       +||||+|+++++|++||++||+++|++++     |+|+.+.++...
T Consensus        36 ~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~~~~   97 (115)
T 3beg_B           36 HMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS   97 (115)
T ss_dssp             HHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC----C
T ss_pred             HHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCCCCC
Confidence            5899999999999886       89999999999999999999999999988     788877765543

>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=99.30  E-value=7.1e-13  Score=99.22  Aligned_cols=60  Identities=20%  Similarity=0.324  Sum_probs=54.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|.|+.   |+++++||||+|.++++|++||+.||+.+|.++.|.|++|+++..
T Consensus        32 ~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           32 IFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   91 (97)
T ss_dssp             HHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             HHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCCc
Confidence            589999999999874   567889999999999999999999999999999999999998654

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

Probab=99.29  E-value=3.1e-12  Score=94.81  Aligned_cols=56  Identities=13%  Similarity=0.247  Sum_probs=51.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+++        ||||+|.++++|++||+.||+++|++++|.|++|+++...
T Consensus        29 ~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   84 (90)
T 2dnp_A           29 LFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK   84 (90)
T ss_dssp             HHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCCC
T ss_pred             HHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCCC
Confidence            5889999999999864        9999999999999999999999999999999999987544

>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=99.29  E-value=3.8e-12  Score=102.37  Aligned_cols=63  Identities=22%  Similarity=0.498  Sum_probs=59.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||+..|.+++|.|.++.++..
T Consensus        22 ~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~   84 (167)
T 1fxl_A           22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA   84 (167)
T ss_dssp             HHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG
T ss_pred             HHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc
Confidence            589999999999999999999999999999999999999999999999999999999987653

>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=99.29  E-value=2.3e-12  Score=104.70  Aligned_cols=59  Identities=22%  Similarity=0.501  Sum_probs=56.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|+.|.|+.++.|++++|||||+|.++++|++||++||+++|.+++|.|++|.
T Consensus       114 ~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          114 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            58899999999999999999999999999999999999999999999999999999884

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

Probab=99.29  E-value=1.8e-12  Score=98.01  Aligned_cols=55  Identities=18%  Similarity=0.230  Sum_probs=51.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|++|+|+      ++++||||+|.+.++|++||+.||+++|++++|.|++|+++
T Consensus        47 ~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           47 LFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             HHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             HHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            58999999999998      36799999999999999999999999999999999999874

>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=99.28  E-value=3.5e-12  Score=101.37  Aligned_cols=59  Identities=10%  Similarity=0.086  Sum_probs=53.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH--GREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln--G~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+++      |+||||+|+++++|++||+.|+  +.+|.+++|.|++|+++....
T Consensus        51 lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           51 LGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             HHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             HHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            6899999999999986      6899999999999999999887  468999999999999876554

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.28  E-value=3e-12  Score=98.83  Aligned_cols=56  Identities=11%  Similarity=0.081  Sum_probs=50.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCe--eCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGRE--FGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~--i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|++      .|+||||+|+++++|++||+.||+..  |.+++|.|++|+++.
T Consensus        41 lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           41 ALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             HHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             HHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            689999999999986      46899999999999999999999875  789999999998764

>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=99.28  E-value=2.9e-12  Score=103.55  Aligned_cols=63  Identities=19%  Similarity=0.382  Sum_probs=59.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|++++|||||+|.++++|++||+.||+..|.+++|.|.++.++..
T Consensus        23 ~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~   85 (168)
T 1b7f_A           23 LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE   85 (168)
T ss_dssp             HHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS
T ss_pred             HHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc
Confidence            589999999999999999999999999999999999999999999999999999999987654

>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=99.28  E-value=7.9e-13  Score=101.65  Aligned_cols=60  Identities=22%  Similarity=0.369  Sum_probs=55.7

Q ss_pred             CCCCCcc---ceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTH---NNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~---I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||.   |++|+|++++. ++++|||||+|.++++|++||+ ||++.|.++.|+|.+|.++.
T Consensus        31 ~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~~   93 (107)
T 2lmi_A           31 FFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNED   93 (107)
T ss_dssp             HTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHHH
T ss_pred             HHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHHH
Confidence            5889888   99999999987 9999999999999999999999 99999999999999998643

>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=99.28  E-value=3.8e-12  Score=97.86  Aligned_cols=56  Identities=16%  Similarity=0.332  Sum_probs=50.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|        +++||||+|+++++|++||++||+++|++++|.|++|+++...
T Consensus        48 ~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~  103 (110)
T 1wf1_A           48 IFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPD  103 (110)
T ss_dssp             HHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCCSC
T ss_pred             HHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCCCC
Confidence            5899999999999        4689999999999999999999999999999999999865433

>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=99.28  E-value=4.1e-12  Score=99.92  Aligned_cols=59  Identities=12%  Similarity=0.094  Sum_probs=52.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH--GREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln--G~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|++      +|+||||+|+++++|++||+.||  ..+|.+++|.|++|+++....
T Consensus        46 lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~~~  106 (112)
T 1x4f_A           46 LAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLV  106 (112)
T ss_dssp             TTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSSSS
T ss_pred             HHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccccc
Confidence            799999999999985      47999999999999999999886  456999999999998776543

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

Probab=99.27  E-value=4.7e-12  Score=97.85  Aligned_cols=56  Identities=21%  Similarity=0.461  Sum_probs=51.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+        ++||||+|.+.++|++||+.||+.+|++++|.|++|+++...
T Consensus        51 ~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~r  106 (108)
T 2jvo_A           51 IFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKR  106 (108)
T ss_dssp             HHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC--
T ss_pred             HHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCCCC
Confidence            58999999999998        589999999999999999999999999999999999987644

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

Probab=99.27  E-value=1.9e-12  Score=101.42  Aligned_cols=58  Identities=14%  Similarity=0.232  Sum_probs=51.4

Q ss_pred             CCCCCc-cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLT-HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG-~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++|| +|+.|+|+.+    +++|||||+|+++++|++||++||+++|++++|+|++|+..+
T Consensus        48 ~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~p  106 (111)
T 2jvr_A           48 LARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPP  106 (111)
T ss_dssp             HHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC--
T ss_pred             HHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            588999 8999998653    488999999999999999999999999999999999998654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.27  E-value=2.5e-12  Score=109.79  Aligned_cols=61  Identities=20%  Similarity=0.429  Sum_probs=55.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++|+.  .++|||||+|.++++|++||++||+++|++++|.|++|+++.+
T Consensus       123 ~F~~~G~i~~~~i~~d~~--~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          123 TFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             HHGGGSCEEEEEEEEETT--EEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCHHH
T ss_pred             HHhhcCCeEEEEeeccCC--CCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCCcc
Confidence            589999999999999853  4799999999999999999999999999999999999987653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.27  E-value=4.8e-12  Score=108.01  Aligned_cols=62  Identities=8%  Similarity=0.122  Sum_probs=58.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||++||++.|.++.|.|.++....
T Consensus        35 ~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~   96 (213)
T 4f02_A           35 KFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDP   96 (213)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCT
T ss_pred             HHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccc
Confidence            58999999999999999999999999999999999999999999999999999999987544

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.26  E-value=1.4e-12  Score=98.79  Aligned_cols=61  Identities=16%  Similarity=0.372  Sum_probs=55.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++ |++++|||||+|.++++|++||+  |+++|+++.|.|.++.++...
T Consensus        29 ~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~~~~   89 (102)
T 2xs2_A           29 FFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRKQNL   89 (102)
T ss_dssp             HHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEECC--
T ss_pred             HHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcCcch
Confidence            58999999999999998 99999999999999999999998  899999999999999876654

>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=99.26  E-value=4e-12  Score=98.22  Aligned_cols=58  Identities=5%  Similarity=-0.031  Sum_probs=51.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCC--eeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR--EFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~--~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|.|+++      |+||||+|+++++|++||+.||+.  +|.+++|.|++|+++...
T Consensus        35 ~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           35 ALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             HHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             HHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            6899999999999874      689999999999999999988754  599999999999876644

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.26  E-value=2.3e-12  Score=104.12  Aligned_cols=59  Identities=17%  Similarity=0.089  Sum_probs=52.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCC----HHH----HHHHHH--HhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYAD----RRA----MDDAIR--EMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~----~e~----a~~AI~--~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|.+|.|++|++|++++|||||+|.+    +++    |.+||+  +||+..|++++|+|++..
T Consensus        26 ~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           26 YFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             HHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECC
T ss_pred             HHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECc
Confidence            58999999999999999999999999999996    322    788988  789999999999999865

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

Probab=99.26  E-value=4.2e-12  Score=95.46  Aligned_cols=57  Identities=16%  Similarity=0.229  Sum_probs=51.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+        ++||||+|.+.++|++||++||+++|.+++|.|++|+++....
T Consensus        31 ~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   87 (96)
T 2kvi_A           31 IFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQ   87 (96)
T ss_dssp             HHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCCC--
T ss_pred             HHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCCCCC
Confidence            58999999999995        5899999999999999999999999999999999998766543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.25  E-value=9.3e-12  Score=100.41  Aligned_cols=59  Identities=10%  Similarity=0.151  Sum_probs=53.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcE-EEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGF-GFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGf-aFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.+     +++| |||+|++.++|++||++||+++|.+  ++|+|++|+++.-.
T Consensus        48 lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l~  109 (130)
T 3zzy_A           48 IFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN  109 (130)
T ss_dssp             HHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSCC
T ss_pred             HHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCcee
Confidence            6999999999998874     3688 9999999999999999999999998  89999999986543

>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=99.25  E-value=4.8e-12  Score=97.78  Aligned_cols=59  Identities=14%  Similarity=0.211  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+++.   .+++||||+|.+.++|++||+.||+.+|.++.|.|++|+++.
T Consensus        28 ~F~~~G~v~~v~i~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (115)
T 3lqv_A           28 IFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANR   86 (115)
T ss_dssp             HHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHH
T ss_pred             HHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCh
Confidence            58999999999999864   458999999999999999999999999999999999998643

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

Probab=99.24  E-value=4e-12  Score=95.07  Aligned_cols=58  Identities=10%  Similarity=0.186  Sum_probs=53.2

Q ss_pred             CCCCCccceEE-EEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDL-KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V-~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++| .|+.++.+++    |||+|.++++|++||+.||+++|.+++|.|++|+++.
T Consensus        35 ~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   93 (96)
T 2e44_A           35 LLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEM   93 (96)
T ss_dssp             HHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCC
T ss_pred             HHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCccc
Confidence            58899999999 5899877654    9999999999999999999999999999999999874

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=8.7e-12  Score=93.23  Aligned_cols=59  Identities=14%  Similarity=0.239  Sum_probs=52.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|  +.++.|++   ||||+|.++++|++||+ ||+++|++++|.|++|.++....
T Consensus        28 ~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~~~   86 (94)
T 2e5g_A           28 YFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEFQS   86 (94)
T ss_dssp             HGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCCCC
T ss_pred             HHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCCCC
Confidence            58999999987  77777776   99999999999999999 99999999999999998766543

>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=99.23  E-value=5e-12  Score=102.39  Aligned_cols=57  Identities=23%  Similarity=0.394  Sum_probs=53.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.+     ++|||||+|.++++|++||+.||+++|.+++|.|++|+++.
T Consensus        93 ~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           93 AFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            5899999999999987     68999999999999999999999999999999999998864

>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=99.23  E-value=8.3e-12  Score=100.81  Aligned_cols=58  Identities=24%  Similarity=0.367  Sum_probs=55.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A   58 (255)
                      ||++||+|+.|.|+.++.++++++||||+|.++++|++||++||+..|.+  ++|+|++|
T Consensus       109 ~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          109 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             hhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            58999999999999999999999999999999999999999999999988  99999986

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

Probab=99.23  E-value=3.8e-12  Score=95.19  Aligned_cols=59  Identities=17%  Similarity=0.325  Sum_probs=51.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|..|     +.+++++|||||+|.++++|++||+.||+++|.+++|.|++|.++...
T Consensus        36 ~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (96)
T 1fjc_A           36 VFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT   94 (96)
T ss_dssp             HHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCCC
T ss_pred             HHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            47777776655     467889999999999999999999999999999999999999887543

>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=99.23  E-value=1.9e-12  Score=104.12  Aligned_cols=64  Identities=20%  Similarity=0.248  Sum_probs=53.8

Q ss_pred             CCCCCccceEEE--Eee---cCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLK--IML---ERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~--Iv~---Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+.|.  ++.   ...|++++|||||+|.+.++|++||+.||+++|.++.|.|++|++....
T Consensus        65 ~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~  133 (143)
T 3egn_A           65 IFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPK  133 (143)
T ss_dssp             HHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCSCC-
T ss_pred             HHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCc
Confidence            589999998851  222   2357899999999999999999999999999999999999999875544

>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=99.23  E-value=1.3e-11  Score=93.37  Aligned_cols=54  Identities=17%  Similarity=0.268  Sum_probs=50.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+        ++||||+|.+.++|++||++||+.+|.+++|.|++|+++.
T Consensus        43 ~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (97)
T 2xnq_A           43 IFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA   96 (97)
T ss_dssp             HHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCCC
T ss_pred             HHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCCC
Confidence            58999999999984        6899999999999999999999999999999999998754

>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=99.23  E-value=8.6e-12  Score=98.21  Aligned_cols=56  Identities=14%  Similarity=0.141  Sum_probs=51.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      +|++||+|++|.|+++.    ++||+||+|.+.++|++||++||+..|++++|.|+++..
T Consensus        37 ~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           37 ECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL   92 (114)
T ss_dssp             HHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcH
Confidence            47999999999997763    589999999999999999999999999999999999863

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=1.3e-11  Score=94.99  Aligned_cols=58  Identities=12%  Similarity=0.130  Sum_probs=50.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|.|+.     +++|||||+|+++++|++||+.++  .+.+++|.|++|+++....
T Consensus        37 ~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           37 LLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQPQDA   94 (100)
T ss_dssp             HHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCCCCC
T ss_pred             HHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCCCCC
Confidence            589999999999983     689999999999999999999865  5789999999998776443

>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=99.22  E-value=6.5e-12  Score=93.50  Aligned_cols=58  Identities=17%  Similarity=0.264  Sum_probs=50.2

Q ss_pred             CCCCCcc-ceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcC-CeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTH-NNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHG-REFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~-I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG-~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+ |..|.|+       +++||||+|.++++|++||++||+ ++|++++|.|++|+++....
T Consensus        28 ~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   87 (93)
T 2cqh_A           28 LFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRS   87 (93)
T ss_dssp             HHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCCC
T ss_pred             HHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCccccC
Confidence            5889999 5555553       478999999999999999999999 99999999999999876553

>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=99.22  E-value=8.2e-12  Score=91.15  Aligned_cols=53  Identities=15%  Similarity=0.193  Sum_probs=49.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~l-nG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|+++      ++||||+|.++++|++||++| |+++|++++|.|++|+
T Consensus        32 ~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A           32 HFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             HHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             HHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            5899999999999974      689999999999999999999 9999999999999985

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

Probab=99.22  E-value=2.1e-11  Score=91.82  Aligned_cols=56  Identities=18%  Similarity=0.373  Sum_probs=50.9

Q ss_pred             CCCCC--ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCL--THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekF--G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|  |+|++|+|+        ++||||+|.+.++|++||+.||+++|.+++|.|++|+++...
T Consensus        35 ~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   92 (99)
T 2cpd_A           35 EFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKD   92 (99)
T ss_dssp             HHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCCC
T ss_pred             HHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCC
Confidence            58899  999999875        469999999999999999999999999999999999987654

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

Probab=99.21  E-value=9.7e-12  Score=104.57  Aligned_cols=62  Identities=18%  Similarity=0.267  Sum_probs=55.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||++.|.++.|.|.++..+.
T Consensus        48 ~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  109 (216)
T 2qfj_A           48 AFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG  109 (216)
T ss_dssp             HHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCG
T ss_pred             HHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCcc
Confidence            58999999999999999999999999999999999999999999999999999998887543

>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=99.21  E-value=6.6e-12  Score=97.40  Aligned_cols=56  Identities=7%  Similarity=-0.009  Sum_probs=51.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.      +++||||+|.+.++|++||+.||+++|.+++|.|++|....
T Consensus        30 ~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A           30 TFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             HHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            689999999999875      57899999999999999999999999999999999997543

>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=99.21  E-value=8.1e-12  Score=104.55  Aligned_cols=59  Identities=8%  Similarity=0.079  Sum_probs=52.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.+    ++++||||+|++.++|++||++||+++|.+  ++|+|++|+++..
T Consensus        66 ~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           66 IFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             HHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             HHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            6899999999999754    257899999999999999999999999976  9999999998753

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.21  E-value=1.8e-11  Score=97.82  Aligned_cols=57  Identities=12%  Similarity=0.226  Sum_probs=50.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcE-EEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGF-GFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGf-aFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+. +     .|| |||+|++.++|++||++||+.+|.+  ++|.|++|+++..
T Consensus        45 ~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           45 VCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             HHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             HHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            699999999999975 2     276 9999999999999999999999988  6899999998753

>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=99.21  E-value=1.6e-11  Score=90.83  Aligned_cols=55  Identities=15%  Similarity=0.182  Sum_probs=50.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++| +|++|+|+      +++|||||+|.++++|++||++||+++|.+++|+|++|..+.
T Consensus        25 ~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A           25 LLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             HTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             HHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            58999 99999985      578999999999999999999999999999999999997654

>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=99.20  E-value=1.2e-11  Score=99.44  Aligned_cols=58  Identities=24%  Similarity=0.441  Sum_probs=54.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeE--EEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRV--ISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~--I~V~~A   58 (255)
                      ||++||+|++|+|+.++.++++++||||+|.++++|++||++||+++|.++.  |.|++|
T Consensus       108 ~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          108 LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            5899999999999999999999999999999999999999999999999965  888876

>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=99.18  E-value=2e-11  Score=101.07  Aligned_cols=62  Identities=26%  Similarity=0.434  Sum_probs=56.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|++++|||||+|.++++|++||+. ++.+|.++.|.|.++.++..
T Consensus        33 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~   94 (196)
T 1l3k_A           33 HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSRED   94 (196)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC---
T ss_pred             HHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCccc
Confidence            589999999999999999999999999999999999999985 88999999999999987644

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=3.8e-12  Score=101.44  Aligned_cols=59  Identities=20%  Similarity=0.324  Sum_probs=53.3

Q ss_pred             CCCCCccc----eEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHN----NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I----~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++|++|    +.|+|++| .|++++|||||+|+++++|++||+. |+++|.++.|+|..|.++
T Consensus        43 ~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~~  105 (123)
T 2dha_A           43 FFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTAA  105 (123)
T ss_dssp             HHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECHH
T ss_pred             HHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCHH
Confidence            58899875    68999999 5899999999999999999999985 999999999999988754

>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=99.17  E-value=1.3e-11  Score=97.52  Aligned_cols=57  Identities=12%  Similarity=0.148  Sum_probs=50.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee-----CCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF-----GDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i-----~Gr~I~V~~A~~k~~   63 (255)
                      +|++||+|++|.|+.+      |+||||+|+++++|++||++||+++|     .+++|.|++|+..+.
T Consensus        47 ~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~p~  108 (114)
T 2cq2_A           47 VLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQW  108 (114)
T ss_dssp             HHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCCCC
T ss_pred             HHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccCcc
Confidence            5899999999988753      68999999999999999999999998     689999999986543

>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=99.17  E-value=1.8e-11  Score=108.38  Aligned_cols=61  Identities=18%  Similarity=0.276  Sum_probs=56.1

Q ss_pred             CCCCCccceEEEEeecCC-CCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERD-SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~-Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|+.|+|+.++. |+++++||||+|.++++|++|| +||++.|.+++|.|++|++++
T Consensus       231 ~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          231 SFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             HHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             HHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            589999999999999977 7999999999999999999999 999999999999999999874

>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=99.17  E-value=2.4e-11  Score=104.07  Aligned_cols=57  Identities=18%  Similarity=0.185  Sum_probs=52.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+++     ++|||||+|+++++|++||+.||+++|.+++|.|.+|+.+.
T Consensus        25 ~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A           25 VFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             HHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             HHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            6899999999999986     47999999999999999999999999999999999997543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.17  E-value=1.9e-11  Score=94.85  Aligned_cols=57  Identities=11%  Similarity=0.165  Sum_probs=49.1

Q ss_pred             CCCCCccceEEEEeecCCC---CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDS---GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~T---g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|+ |.|+.++.|   ++++|||||+|+++++|++||++|+  .|+++.|.|..+.+
T Consensus        28 ~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~~~   87 (114)
T 2dnl_A           28 SFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVSSPT   87 (114)
T ss_dssp             HTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEECCSS
T ss_pred             HHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEeccCCC
Confidence            599999999 999999888   7999999999999999999999995  57777777665543

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

Probab=99.17  E-value=3.9e-11  Score=96.29  Aligned_cols=62  Identities=16%  Similarity=0.381  Sum_probs=56.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++. +++++||||+|.++++|++||+.||+.+|.++.|.|.++.++..
T Consensus        20 ~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~   81 (166)
T 3md3_A           20 YFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQ   81 (166)
T ss_dssp             HHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCC
T ss_pred             HHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCC
Confidence            589999999999999964 67999999999999999999999999999999999999987654

>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=99.16  E-value=7e-12  Score=100.41  Aligned_cols=58  Identities=21%  Similarity=0.389  Sum_probs=52.7

Q ss_pred             CCCCCccce--EEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNN--DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~--~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++| .|+  +|+|++|+. ++++|||||+|+++++|++||+ +++++|.++.|+|..+.++
T Consensus        62 ~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~~a~~~  121 (126)
T 2hgm_A           62 FFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVFKSSQE  121 (126)
T ss_dssp             HTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCEEECHH
T ss_pred             HHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCHH
Confidence            58999 788  899999977 9999999999999999999998 4779999999999998754

>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=99.15  E-value=5.2e-11  Score=104.98  Aligned_cols=62  Identities=15%  Similarity=0.294  Sum_probs=58.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++ ++++++||||+|.++++|++||++||+.+|.+++|.|++|.++..
T Consensus       205 ~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          205 ALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            58999999999999985 899999999999999999999999999999999999999998765

>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=99.14  E-value=3.3e-11  Score=97.67  Aligned_cols=58  Identities=24%  Similarity=0.389  Sum_probs=53.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC---eEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD---RVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G---r~I~V~~A~   59 (255)
                      ||++||+|++|+|+.++ +++++|||||+|.++++|++||++||+.+|..   ++|.|++|.
T Consensus       115 ~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          115 MFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            58999999999999995 68999999999999999999999999988874   999999984

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.13  E-value=2.7e-11  Score=92.69  Aligned_cols=55  Identities=9%  Similarity=0.094  Sum_probs=49.5

Q ss_pred             CCCCC-ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCL-THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekF-G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++| |+|++|       |+   |||||+|.+.++|++||++||+++|.+++|+|++|+.+..--
T Consensus        33 lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd~~   88 (96)
T 2diu_A           33 LSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELC   88 (96)
T ss_dssp             HHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCCCC
T ss_pred             HHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCccee
Confidence            68999 599998       33   999999999999999999999999999999999999876543

>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=99.12  E-value=6.5e-11  Score=104.23  Aligned_cols=60  Identities=20%  Similarity=0.323  Sum_probs=55.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++   +++++|||||+|.+.++|++||+.||+++|.++.|.|++++.+..
T Consensus        33 ~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   92 (282)
T 3pgw_A           33 IFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   92 (282)
T ss_pred             HHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCcc
Confidence            589999999999986   678999999999999999999999999999999999999976553

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.08  E-value=6.5e-11  Score=104.63  Aligned_cols=58  Identities=12%  Similarity=0.160  Sum_probs=50.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee------------CCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF------------GDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i------------~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.      +||||||+|.+.++|++||++||++.|            .++.|.|++|+..+..
T Consensus       163 ~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          163 VFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             HHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             HHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence            589999999999996      479999999999999999999999999            8999999999876543

>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=99.07  E-value=9.1e-11  Score=95.07  Aligned_cols=63  Identities=16%  Similarity=0.311  Sum_probs=56.5

Q ss_pred             CCCCCccceEEEEeecCCCC--CCCcEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSG--RPRGFGFITYADRRAMDDAIREMHGREFG---DRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg--~srGfaFVtF~~~e~a~~AI~~lnG~~i~---Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.++  ++++||||+|.++++|++||+.||+..|.   .+.|.|..+.++..
T Consensus        23 ~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~   90 (175)
T 3nmr_A           23 LFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKN   90 (175)
T ss_dssp             HHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCC
T ss_pred             HHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEcccccccc
Confidence            58999999999999999887  89999999999999999999999998876   67888888876554

>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=99.06  E-value=7.7e-11  Score=86.84  Aligned_cols=58  Identities=21%  Similarity=0.253  Sum_probs=48.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+++     +++||||+|+++++|++|+..  ...+.+++|.|++|.++....
T Consensus        25 ~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~~~~   82 (88)
T 1wf0_A           25 FFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKHNSN   82 (88)
T ss_dssp             HSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCCCCC
T ss_pred             HHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCCCCC
Confidence            5999999999999876     789999999999999866442  346689999999999877654

>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=99.06  E-value=1.7e-10  Score=101.72  Aligned_cols=64  Identities=16%  Similarity=0.346  Sum_probs=60.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++.|++++|||||+|.++++|++||+.||+..|.+++|.|.++.++...
T Consensus       115 ~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~  178 (284)
T 3smz_A          115 LVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT  178 (284)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCC
T ss_pred             HHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCC
Confidence            5889999999999999999999999999999999999999999999999999999999876543

>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=99.06  E-value=1.5e-10  Score=86.28  Aligned_cols=54  Identities=22%  Similarity=0.357  Sum_probs=43.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCe--eCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGRE--FGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~--i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+++     +||||||+|+++++|++    |++..  +.+++|.|++|.++..
T Consensus        31 ~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           31 FFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             HHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC----
T ss_pred             HHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCCc
Confidence            5899999999999985     88999999999999884    44444  5699999999998764

>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=99.04  E-value=1.2e-10  Score=93.90  Aligned_cols=60  Identities=28%  Similarity=0.550  Sum_probs=54.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++++.|++++|||||+|.++++|++||+.  .+.|+++.|.|.++.++.
T Consensus        23 ~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~~   82 (167)
T 2cjk_A           23 YFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPRD   82 (167)
T ss_dssp             HHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCHH
T ss_pred             HHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccchh
Confidence            589999999999999999999999999999999999999985  468999999999887543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=1.9e-10  Score=87.19  Aligned_cols=52  Identities=12%  Similarity=0.263  Sum_probs=48.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      +|++||+|+.|+|+.|        .+||||.+.++|.+||+ ||+++|.+++|+|++++|.
T Consensus        35 ~F~~~G~Vi~vr~~~d--------~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           35 QFASFGEVILIRFVED--------KMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             HHHTTCCEEEEEECSS--------SEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             HHHhCCCeEEEEEecC--------CEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            3789999999999998        38999999999999998 9999999999999999864

>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=99.02  E-value=2.7e-10  Score=96.78  Aligned_cols=58  Identities=3%  Similarity=0.023  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|.|++++ +++++|||||+|+++++|++||+.++ .+|+++.|.|.+++.
T Consensus       129 ~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          129 WLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETTT
T ss_pred             HHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhHH
Confidence            58999999999999985 58899999999999999999998665 699999999998865

>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=99.00  E-value=3.8e-10  Score=92.04  Aligned_cols=46  Identities=20%  Similarity=0.444  Sum_probs=43.5

Q ss_pred             CCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249           17 RDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus        17 k~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ..++++++||||+|.+.++|++||++||+++|.+++|.|++|++++
T Consensus       130 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          130 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCCC
Confidence            5788999999999999999999999999999999999999999864

>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=98.97  E-value=2.7e-10  Score=98.17  Aligned_cols=57  Identities=12%  Similarity=0.270  Sum_probs=53.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++++     ++||||+|.++++|++||+.||+.+|.++.|.|+++.++.
T Consensus        55 ~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~  111 (229)
T 2adc_A           55 LFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN  111 (229)
T ss_dssp             HHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             HHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCcc
Confidence            58899999999999984     7899999999999999999999999999999999998653

>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=98.96  E-value=3e-10  Score=82.93  Aligned_cols=44  Identities=14%  Similarity=0.357  Sum_probs=40.9

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK   57 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~   57 (255)
                      +|++|+|+++      ++||||+|.++++|++|| +||+++|.+++|+|+.
T Consensus        43 ~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           43 PVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             cceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            8999999865      689999999999999999 8999999999999974

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.94  E-value=3.1e-10  Score=94.64  Aligned_cols=57  Identities=12%  Similarity=0.270  Sum_probs=53.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.++     ++||||+|.++++|++||+.||+.+|.++.|.|.++.++.
T Consensus        24 ~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A           24 LFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             HHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             HHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            58999999999999984     7899999999999999999999999999999999998654

>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=98.92  E-value=6.7e-10  Score=98.17  Aligned_cols=63  Identities=11%  Similarity=0.209  Sum_probs=50.9

Q ss_pred             CCCCCc-cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLT-HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG-~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|| +|+.|+|+.++. +++++||||+|.++++|++||+.||++.|.++.|.|.++.++...
T Consensus       137 ~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  200 (292)
T 2ghp_A          137 LLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS  200 (292)
T ss_dssp             HHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---
T ss_pred             HHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCccc
Confidence            588999 999999999865 789999999999999999999999999999999999999876644

>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=98.92  E-value=1.2e-09  Score=93.70  Aligned_cols=58  Identities=17%  Similarity=0.181  Sum_probs=53.3

Q ss_pred             CCCCccceEEEEeecCC----CCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            2 QQCLTHNNDLKIMLERD----SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~----Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      |++||+|++|.|+++..    |+.++||+||+|.+.++|++||+.||+..|+|++|.|+++.
T Consensus       150 ~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          150 CGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            68999999999996644    55899999999999999999999999999999999999975

>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=98.89  E-value=1.1e-09  Score=96.07  Aligned_cols=62  Identities=16%  Similarity=0.233  Sum_probs=54.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcC-CeeC---CeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHG-REFG---DRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG-~~i~---Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|.|+.| .|++++|||||+|.+.++|++||+.||+ ..+.   +++|.|+++.+...
T Consensus       116 ~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          116 AFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             HHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             HHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeeccccCc
Confidence            5899999999999999 6899999999999999999999999954 4444   89999999987543

>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=98.85  E-value=2.9e-10  Score=92.72  Aligned_cols=61  Identities=18%  Similarity=0.366  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      +|++|++|.. .++.+..+++++|||||+|.++++|++||+ ||+++|.+++|.|.++.++..
T Consensus        33 ~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~   93 (175)
T 1fje_B           33 AISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDS   93 (175)
T ss_dssp             HHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCSSC
T ss_pred             HHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCccc
Confidence            3667888777 455666889999999999999999999995 999999999999999987654

>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=98.82  E-value=2e-09  Score=82.15  Aligned_cols=50  Identities=12%  Similarity=0.187  Sum_probs=46.3

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      |++||+|+.|+|+.|+        +||||.+.++|.+||+ ||+++|.++.|+|++..+
T Consensus        45 F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~~   94 (95)
T 1ufw_A           45 LGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccCC
Confidence            7789999999999983        9999999999999998 999999999999997654

>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=98.77  E-value=7.3e-09  Score=90.91  Aligned_cols=54  Identities=24%  Similarity=0.364  Sum_probs=50.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|+++      ++||||+|.++++|++||+.||++.|.++.|.|.++.+
T Consensus        42 ~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           42 LFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             HTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            5899999999999764      68999999999999999999999999999999999875

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

Probab=98.74  E-value=9.4e-10  Score=91.08  Aligned_cols=43  Identities=12%  Similarity=0.347  Sum_probs=38.8

Q ss_pred             CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249           20 GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus        20 g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      +++++||||+|.++++|++|| +||+++|.+++|.|.++.+...
T Consensus        48 ~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~~~   90 (198)
T 2yh0_A           48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQP   90 (198)
T ss_dssp             ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCCCC
T ss_pred             cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCCCC
Confidence            456899999999999999999 7999999999999999887543

>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=98.71  E-value=7.5e-09  Score=95.85  Aligned_cols=53  Identities=13%  Similarity=0.201  Sum_probs=45.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC---Ce--EEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG---DR--VISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~---Gr--~I~V~~A~   59 (255)
                      +|++||+|++|.|+.      +|+||||+|++.++|++||++||+++|.   ++  +|.|++++
T Consensus        40 ~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           40 VLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE   97 (345)
T ss_dssp             HHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECS
T ss_pred             HHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEee
Confidence            589999999987754      5799999999999999999999999983   34  57777774

>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=98.60  E-value=3.3e-08  Score=79.83  Aligned_cols=50  Identities=12%  Similarity=0.266  Sum_probs=42.4

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      .|++|++.+      +++||||+|.++++|++|| +||+++|.+++|.|.++.+...
T Consensus        41 ~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~   90 (172)
T 2g4b_A           41 PVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQP   90 (172)
T ss_dssp             SEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCCC
T ss_pred             ceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccCC
Confidence            566666554      5799999999999999999 7999999999999999876543

>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=98.60  E-value=2e-08  Score=85.80  Aligned_cols=52  Identities=6%  Similarity=0.129  Sum_probs=45.6

Q ss_pred             CCCCCccc--eEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 025249            1 MQQCLTHN--NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS   54 (255)
Q Consensus         1 lfekFG~I--~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~   54 (255)
                      ||++||+|  ++|+|+.++  +.+++||||+|+++++|++||++||+++|.+...+
T Consensus       143 ~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~  196 (205)
T 3tyt_A          143 ICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGP  196 (205)
T ss_dssp             HHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSS
T ss_pred             HHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCC
Confidence            58899999  899998875  45679999999999999999999999999886543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.22  E-value=1.1e-06  Score=69.82  Aligned_cols=53  Identities=4%  Similarity=0.085  Sum_probs=47.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCC-HHHHHHHHHHhc--CCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYAD-RRAMDDAIREMH--GREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~-~e~a~~AI~~ln--G~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|..|.|+.+..      .|||.|.+ +++|++||++||  +.+|++..|+|++..
T Consensus        39 ~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL~   94 (121)
T 1owx_A           39 LFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   94 (121)
T ss_dssp             HTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             HHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEECC
Confidence            589999999999999865      59999999 899999999995  788999988888765

>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=98.06  E-value=3.4e-06  Score=72.23  Aligned_cols=40  Identities=15%  Similarity=0.348  Sum_probs=38.1

Q ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecccC
Q 025249           22 PRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKAQPK   61 (255)
Q Consensus        22 srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A~~k   61 (255)
                      .++||||+|.+.++|++||++||+.+|. +++|+|++|+++
T Consensus       188 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          188 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            5799999999999999999999999999 999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.04  E-value=2.7e-06  Score=70.50  Aligned_cols=40  Identities=15%  Similarity=0.348  Sum_probs=37.9

Q ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecccC
Q 025249           22 PRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKAQPK   61 (255)
Q Consensus        22 srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A~~k   61 (255)
                      .++||||+|.++++|++||++||++.|. +++|.|++|+++
T Consensus       157 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            5799999999999999999999999999 999999999875

>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=97.95  E-value=7.9e-06  Score=71.46  Aligned_cols=38  Identities=11%  Similarity=0.296  Sum_probs=36.0

Q ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecc
Q 025249           22 PRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKAQ   59 (255)
Q Consensus        22 srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A~   59 (255)
                      .++||||+|.+.++|++||+.||+++|. ++.|+|++|+
T Consensus       243 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            3599999999999999999999999999 9999999986

>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=97.40  E-value=0.00014  Score=58.29  Aligned_cols=38  Identities=11%  Similarity=0.136  Sum_probs=31.8

Q ss_pred             eEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee
Q 025249            9 NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF   48 (255)
Q Consensus         9 ~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i   48 (255)
                      +.++|+++..  +++|||||+|.++++|++||+++++...
T Consensus         1 ~~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~   38 (158)
T 2kn4_A            1 MQYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNG   38 (158)
T ss_dssp             CEEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             CcEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCC
Confidence            3678888865  5899999999999999999998876433

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.20  E-value=0.0003  Score=54.95  Aligned_cols=46  Identities=13%  Similarity=0.257  Sum_probs=41.3

Q ss_pred             ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 025249            6 THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNK   57 (255)
Q Consensus         6 G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~   57 (255)
                      +.|++|.|+.|.      +=|+|+|.+...|.+|.-+||+.+|.+++|.|.-
T Consensus        51 g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           51 KDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             cceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            889999999883      3699999999999999888999999999998864

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=96.93  E-value=0.00058  Score=54.41  Aligned_cols=48  Identities=10%  Similarity=0.167  Sum_probs=40.9

Q ss_pred             EEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEecccC
Q 025249           11 LKIMLERDSGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQPK   61 (255)
Q Consensus        11 V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~l-nG~~i~Gr~I~V~~A~~k   61 (255)
                      ..|.++  ..+.+|+++|+|.+.++|++||++| |+.+|++ .|.|+++.++
T Consensus         3 ~al~l~--g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            3 YKLILN--GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             EEEEEC--CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             eEeeec--cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            345553  4578999999999999999999999 9999999 9999988753

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=96.00  E-value=0.0056  Score=39.12  Aligned_cols=23  Identities=43%  Similarity=1.067  Sum_probs=19.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC
Q 025249           90 GGQDDCFKCGRPGHWARDCPSAV  112 (255)
Q Consensus        90 ~g~~~~~~~g~~Gh~~~~cp~~~  112 (255)
                      .....||.|+..|||+++||...
T Consensus         8 ~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            8 LDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCCCeeeECCCCCcchhhCcCCc
Confidence            34578999999999999999764

>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=95.90  E-value=0.013  Score=46.17  Aligned_cols=50  Identities=18%  Similarity=0.214  Sum_probs=40.5

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC-eEEEEEec
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD-RVISVNKA   58 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G-r~I~V~~A   58 (255)
                      |++||+|+++....      ..-+-.|+|.+..+|++||. .|++.|.+ -.|-|...
T Consensus        44 F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           44 FAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             HHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             HHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            78999999987621      12389999999999999998 69999985 66777664

>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=95.63  E-value=0.011  Score=45.46  Aligned_cols=55  Identities=15%  Similarity=0.139  Sum_probs=46.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||.+|.++....+++.     . -=..|.|.++++|.+|-.+||+..|.++.|+|-++++-
T Consensus        30 Lf~~~~~~~tF~~lkS-----F-RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A           30 LFRTYDKDTTFQYFKS-----F-KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             HHHTTCSSCEEEEETT-----T-TEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             HHHhhCcCcceeecCc-----c-eEEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            4678888888777664     1 14589999999999999999999999999999999854

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=95.23  E-value=0.0068  Score=41.55  Aligned_cols=24  Identities=42%  Similarity=1.020  Sum_probs=20.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC
Q 025249           89 PGGQDDCFKCGRPGHWARDCPSAV  112 (255)
Q Consensus        89 ~~g~~~~~~~g~~Gh~~~~cp~~~  112 (255)
                      ......||.|+..|||+++||...
T Consensus        20 ~~~~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           20 QLDRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             TCCTTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCCCCcceeCCCCCcccccCcCCc
Confidence            345678999999999999999864

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.54  E-value=0.018  Score=46.13  Aligned_cols=57  Identities=18%  Similarity=0.167  Sum_probs=40.8

Q ss_pred             CCCCccceEE-EEeec--------CCCCC-----CCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            2 QQCLTHNNDL-KIMLE--------RDSGR-----PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         2 fekFG~I~~V-~Iv~D--------k~Tg~-----srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      |++||+|++- .+..+        +.+.+     ...+-.|+|+++.+|++||. .|+++|.+..|-|....
T Consensus        27 Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           27 FQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             HGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             HHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECC
Confidence            8899999883 22110        00111     13477999999999999998 79999999888887665

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=94.53  E-value=0.0017  Score=52.88  Aligned_cols=18  Identities=39%  Similarity=1.082  Sum_probs=11.9

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPS  110 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~  110 (255)
                      ..||+|+..||++++||.
T Consensus        98 ~~C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKL  115 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCS
T ss_pred             CcccEeCCccchhhhCCC
Confidence            456777766777666665

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.20  E-value=0.025  Score=38.52  Aligned_cols=20  Identities=45%  Similarity=1.446  Sum_probs=17.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCC
Q 025249           92 QDDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        92 ~~~~~~~g~~Gh~~~~cp~~  111 (255)
                      ...||.|+..|||+++||..
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            45799999999999999954

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=93.10  E-value=0.032  Score=32.80  Aligned_cols=19  Identities=42%  Similarity=1.076  Sum_probs=17.0

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~  111 (255)
                      ..||+|+..||++++|+..
T Consensus         7 ~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            7 IRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSS
T ss_pred             CEEEECCccccCHhHCccc
Confidence            4699999999999999865

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.99  E-value=0.33  Score=37.16  Aligned_cols=48  Identities=13%  Similarity=0.184  Sum_probs=37.6

Q ss_pred             ccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            6 THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         6 G~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      |+|+.|+...        .-|+|+|.+.+.|++.|++ ..++|++..|.|....++.
T Consensus        38 G~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P~~~~~   85 (104)
T 2dhx_A           38 GPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRPAPPRA   85 (104)
T ss_dssp             CCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEECCCCC
T ss_pred             ceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEcCCCCC
Confidence            6777777644        3789999999999999874 3568999999997765544

>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=88.96  E-value=0.3  Score=37.10  Aligned_cols=36  Identities=6%  Similarity=0.155  Sum_probs=29.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH   44 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln   44 (255)
                      ||+.||. +.|+.|.|       --|||.|.+++.|..||+.|.
T Consensus        35 lFs~fgg-v~I~WidD-------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           35 LFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             HHTTTCS-CCCEEEET-------TEEEEECSCHHHHHHHHHHHH
T ss_pred             HhhccCC-EEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            6889984 45666776       289999999999999998764

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=87.90  E-value=0.34  Score=32.81  Aligned_cols=21  Identities=38%  Similarity=0.904  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC
Q 025249           92 QDDCFKCGRPGHWARDCPSAV  112 (255)
Q Consensus        92 ~~~~~~~g~~Gh~~~~cp~~~  112 (255)
                      ...||+|+..|||+++||...
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTT
T ss_pred             CcceeECCCCCCccCcCCCcc
Confidence            357999999999999999764

>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=87.44  E-value=0.32  Score=37.05  Aligned_cols=36  Identities=8%  Similarity=0.175  Sum_probs=29.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH   44 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln   44 (255)
                      ||+.|| -+.|+.|.|       --|||.|.+++.|..||..|.
T Consensus        25 lFs~fg-gv~I~WidD-------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A           25 LFSAFG-NIQISWIDD-------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             HTTTSE-EEEEEEEET-------TEEEEEEEEECHHHHHHHHHT
T ss_pred             HHhccC-CEEEEEEcC-------CeEEEEecCHHHHHHHHHhcc
Confidence            689998 455667776       279999999999999998764

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=86.95  E-value=0.48  Score=33.21  Aligned_cols=44  Identities=16%  Similarity=0.222  Sum_probs=31.0

Q ss_pred             cceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            7 HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         7 ~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      .|-.|+|..+        |.||+.... .++++++.|+...+.++.|.|+.++
T Consensus        32 ~IG~I~i~d~--------~s~v~v~~~-~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           32 DIGIITIMDN--------ASYVEILNG-KGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             GEEEEEECSS--------CEEEEECTT-CHHHHHHHHTTCCC---CCCEEECC
T ss_pred             hccEEEEeCC--------cEEEEECHH-HHHHHHHHhccccCcCceEEEEECC
Confidence            3455666554        889988775 4667888899999999999998775

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=86.51  E-value=0.36  Score=29.91  Aligned_cols=18  Identities=33%  Similarity=1.051  Sum_probs=15.5

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPS  110 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~  110 (255)
                      ..||.|+..||++++||.
T Consensus        22 ~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             SSCTTTCCSSSCTTTSCC
T ss_pred             CccccCCCCCCccCcCcC
Confidence            469999999999999984

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=85.58  E-value=0.33  Score=35.56  Aligned_cols=21  Identities=33%  Similarity=0.912  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSAVG  113 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~~g  113 (255)
                      -.||+|+..||++++||....
T Consensus        47 ~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B           47 IYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             CBCSSSSCBSSCGGGCSSCCS
T ss_pred             CeecccCCCCcCcccCCcccc
Confidence            359999999999999998753

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=85.37  E-value=0.32  Score=33.22  Aligned_cols=21  Identities=33%  Similarity=0.738  Sum_probs=17.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSAVG  113 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~~g  113 (255)
                      ..||.|+..||++++||....
T Consensus        31 ~~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A           31 ERCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             SBCTTTCCBSSCGGGCCCCC-
T ss_pred             CeeCCCCCCCCCcCCCcCCCc
Confidence            469999999999999997754

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=85.30  E-value=0.44  Score=29.51  Aligned_cols=18  Identities=56%  Similarity=1.331  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~~  111 (255)
                      .||+|+..||++++||..
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            489999999999999975

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=84.86  E-value=0.34  Score=29.68  Aligned_cols=18  Identities=50%  Similarity=1.341  Sum_probs=13.4

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPS  110 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~  110 (255)
                      ..||.|+..||++++||.
T Consensus        20 ~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             TTCSSCCCTTGGGGTTCC
T ss_pred             CeEccCCCcCCccCcCcC
Confidence            357888888888888763

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=83.73  E-value=0.5  Score=28.87  Aligned_cols=18  Identities=39%  Similarity=1.322  Sum_probs=16.2

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~~  111 (255)
                      .||+|+..||++++||..
T Consensus         2 ~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB
T ss_pred             cccccCCCCcchhhCcCc
Confidence            489999999999999864

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=82.89  E-value=0.24  Score=33.60  Aligned_cols=19  Identities=47%  Similarity=1.328  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPSAV  112 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~~~  112 (255)
                      .||+|+..|||+++||...
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             -------------------
T ss_pred             ccccCCCCCcCHhhCcCCC
Confidence            5999999999999999774

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=82.71  E-value=0.58  Score=31.89  Aligned_cols=21  Identities=38%  Similarity=1.164  Sum_probs=18.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCC
Q 025249           92 QDDCFKCGRPGHWARDCPSAV  112 (255)
Q Consensus        92 ~~~~~~~g~~Gh~~~~cp~~~  112 (255)
                      ...||+|+..||++++||...
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTT
T ss_pred             CCcccccCCCCeehhhCcCCc
Confidence            356999999999999999874

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=82.64  E-value=0.61  Score=30.38  Aligned_cols=19  Identities=42%  Similarity=1.076  Sum_probs=17.1

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~  111 (255)
                      ..||+|+..||++.+||..
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCS
T ss_pred             CeeeecCCCCcChhhCcCC
Confidence            4699999999999999975

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.83  E-value=1.4  Score=30.26  Aligned_cols=18  Identities=39%  Similarity=1.082  Sum_probs=11.8

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPS  110 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~  110 (255)
                      ..||+|+..||++++||.
T Consensus         8 ~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCS
T ss_pred             CcccccCCCCcChhhCCC
Confidence            346677777777776664

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.68  E-value=0.82  Score=31.40  Aligned_cols=20  Identities=25%  Similarity=0.644  Sum_probs=17.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCC
Q 025249           92 QDDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        92 ~~~~~~~g~~Gh~~~~cp~~  111 (255)
                      ...||.|+..||++++||..
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGG
T ss_pred             CCccCCcCCcCCccCcCCCc
Confidence            35799999999999999975

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=80.36  E-value=0.67  Score=30.18  Aligned_cols=19  Identities=42%  Similarity=1.193  Sum_probs=17.1

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~  111 (255)
                      ..||.|+..||++++||..
T Consensus        28 ~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCSS
T ss_pred             CeeCcCCCcCCccCCCcCC
Confidence            4699999999999999965

---

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	255
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-09
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-08
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-06
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-06
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-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	7e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-05
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-05
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-05
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	9e-05
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-04
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	2e-04
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.002
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	4e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-04
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	9e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	0.001
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.001
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	0.001
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	0.001
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.004
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.004
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	0.004

>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 = 50.0 bits (119), Expect = 5e-09
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                ++ +  +G  +G+ F  Y D    D AI  ++G + GD+ + V +A   
Sbjct: 27 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 81

>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 = 49.2 bits (117), Expect = 1e-08
 Identities = 10/62 (16%), Positives = 19/62 (30%), Gaps = 1/62 (1%)

Query: 1  MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQ 59
                            +G  RGFGF+ +  ++    A   + H      R + +  A 
Sbjct: 29 FSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD 88

Query: 60 PK 61
           +
Sbjct: 89 SE 90

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 9/61 (14%), Positives = 20/61 (32%)

Query: 1  MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          M         ++ +   ++   RG  ++ Y D     +A   + G    +R + V     
Sbjct: 24 MYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA 83

Query: 61 K 61
           
Sbjct: 84 N 84

>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 = 48.5 bits (115), Expect = 2e-08
 Identities = 9/42 (21%), Positives = 22/42 (52%)

Query: 20 GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           + R + F+ +++R    +A++ ++G+      I V  A+P 
Sbjct: 41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV 82

>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 = 47.6 bits (113), Expect = 3e-08
 Identities = 5/51 (9%), Positives = 21/51 (41%)

Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
            +++  +  + R  G+ ++ +      + A+  M+      + + +  +Q
Sbjct: 28 LSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ 78

>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 = 46.9 bits (111), Expect = 7e-08
 Identities = 8/55 (14%), Positives = 19/55 (34%), Gaps = 2/55 (3%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              +++  +  +G  +GFGF+ + +       + + H      R         K
Sbjct: 34 EVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSK 86

>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 = 46.8 bits (111), Expect = 9e-08
 Identities = 11/45 (24%), Positives = 17/45 (37%)

Query: 17 RDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
               P G   +++ D    D  I+ + GR FG R I+       
Sbjct: 51 LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT 95

>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 = 46.2 bits (109), Expect = 1e-07
 Identities = 8/44 (18%), Positives = 16/44 (36%)

Query: 18 DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                GFGF+ Y        A++++ G       + V  ++  
Sbjct: 38 GVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA 81

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 1  MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
                     KIM + D+G  +G+ FI +A   A D AI  M+G+   +R I+V+ A  
Sbjct: 19 FSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK 78

Query: 61 K 61
          K
Sbjct: 79 K 79

>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 = 46.2 bits (109), Expect = 1e-07
 Identities = 10/40 (25%), Positives = 20/40 (50%)

Query: 22 PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           RG  F+ + +  +  +A+R M G  F D+ + +  A+  
Sbjct: 45 MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 84

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 8/56 (14%), Positives = 18/56 (32%)

Query: 3  QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
                     +   + G P G   + +  R     A+ +++ R  G R + +   
Sbjct: 31 YGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.5 bits (107), Expect = 2e-07
 Identities = 10/61 (16%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 1  MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
           +   +         +++        F+ + ++ + + A+ +M+    G+R ISV+ A  
Sbjct: 26 FEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADK 84

Query: 61 K 61
          K
Sbjct: 85 K 85

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             D  +M +  S R RGFGF+T++    +D A+          RV+   +A  +
Sbjct: 46 KLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAR 99

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 13 IMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF--GDRVISVNKAQPK 61
               D  + RGF F+ Y   RA   A R++           I+V+ A+P+
Sbjct: 35 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE 85

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 3e-07
 Identities = 14/60 (23%), Positives = 31/60 (51%)

Query: 1  MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          +   +      K++ ++ +G+  G+GF+ Y D +  + AI  ++G     + I V+ A+P
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 81

>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 = 46.9 bits (110), Expect = 3e-07
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 9   NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             ++IM +R SG+ RGF F+T+ D  ++D  +              V KA  K
Sbjct: 125 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSK 176

>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 = 44.7 bits (105), Expect = 4e-07
 Identities = 16/59 (27%), Positives = 32/59 (54%)

Query: 3  QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                +++ ++ +R++ R RGFGF+T+ +     DA+  M+G+    R I V++A   
Sbjct: 27 SKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 85

>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 = 44.3 bits (104), Expect = 7e-07
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
           +  +    +GFGF+T+ +    D A  ++HG     R I VN A  ++
Sbjct: 42 EIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 90

>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 = 44.3 bits (104), Expect = 7e-07
 Identities = 10/47 (21%), Positives = 18/47 (38%)

Query: 18 DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
            G+ +G  +I +      +  + E  G E   R +S+     K G 
Sbjct: 48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 44.3 bits (104), Expect = 9e-07
 Identities = 12/59 (20%), Positives = 29/59 (49%)

Query: 3  QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
              +    K+ +++ +   + FGF++Y +  +   AI+ M+G + G + + V   + K
Sbjct: 40 MPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK 98

>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 = 43.9 bits (103), Expect = 9e-07
 Identities = 15/48 (31%), Positives = 23/48 (47%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           L+ ++ + RGF F+ +        AI  M+  E   R I VN A+P 
Sbjct: 38 PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM 85

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 12/48 (25%), Positives = 24/48 (50%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +++     PR   F+TY    + D A+ E++G +     + VN A+ +
Sbjct: 30 IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 77

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 10/60 (16%), Positives = 21/60 (35%)

Query: 2  QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          Q            +  +      + F+ + + R    A+  M+GR+   + + VN A   
Sbjct: 27 QLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP 86

>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 = 43.5 bits (102), Expect = 1e-06
 Identities = 12/55 (21%), Positives = 28/55 (50%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            + + +  ++ +G+ +GF FI++  R     AI  + G  +   +++V  A+P 
Sbjct: 34 SISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 88

>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 = 43.1 bits (101), Expect = 1e-06
 Identities = 12/52 (23%), Positives = 26/52 (50%)

Query: 9  NDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          N  +IM +  +G   G+ F+ +        AI+ ++G    ++ + V+ A+P
Sbjct: 30 NTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP 81

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 14/55 (25%), Positives = 26/55 (47%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             +  +  +R +G+ +G+GF+ +      D AI+ M   +   + I VNKA   
Sbjct: 35 PVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAH 89

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 13/51 (25%), Positives = 23/51 (45%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG 64
           L++      GF F+ Y  R   ++A+R ++G    DR+I  +       G
Sbjct: 40 GLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEG 90

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGR-EFGDRVISVNKAQPK 61
           L        G+ F+ Y D+     AI  + G+ E   +++ V+ +  K
Sbjct: 28 PLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK 76

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
             D  +M + ++ R RGFGF+TYA    +D A+      +   RV+   +A
Sbjct: 32 TLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVDGRVVEPKRA 82

>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 = 42.5 bits (100), Expect = 3e-06
 Identities = 11/39 (28%), Positives = 18/39 (46%)

Query: 23 RGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +GF F+ Y + R    A+    GR    +V+ +N A   
Sbjct: 50 KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.5 bits (97), Expect = 4e-06
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
             +  +M +  + R RGFGF+T+ D+  +D  +      E   + I    A
Sbjct: 26 EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVA 76

>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 = 42.1 bits (98), Expect = 4e-06
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 5  LTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           T    + I L++++G+P+G   ++Y D      A+    G++F    + V+ A+ K
Sbjct: 40 RTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 41.9 bits (98), Expect = 5e-06
 Identities = 5/43 (11%), Positives = 16/43 (37%)

Query: 14  MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVN 56
           + +       G  ++ +      + A+ +++ R F  + I   
Sbjct: 59  VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 41.1 bits (96), Expect = 6e-06
 Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
             D  + L+  +GR RGFGF+ + +  ++D  + +    +   +VI   +A
Sbjct: 25 EVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQKEHKLNGKVIDPKRA 75

>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 = 41.5 bits (97), Expect = 6e-06
 Identities = 9/37 (24%), Positives = 13/37 (35%)

Query: 25 FGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          FGFI    R   + A  E+       + + V  A   
Sbjct: 46 FGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 82

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.1 bits (96), Expect = 7e-06
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREF--GDRVISVNKA 58
          + ++ +GRPRG  F+ Y  R    +AI  ++      G + +SV  A
Sbjct: 39 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 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 = 40.7 bits (95), Expect = 1e-05
 Identities = 6/41 (14%), Positives = 16/41 (39%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +G+ F+ ++   +   AI  ++G      V+     +  
Sbjct: 52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 14/55 (25%), Positives = 27/55 (49%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            N L   +  D    +G+GF+ +  + A + AI +M+G    DR + V + + +
Sbjct: 32 FGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 86

>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 = 40.9 bits (95), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 34/59 (57%)

Query: 3  QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            +      +++ +R++G+P+G+GF  Y D+     A+R ++GREF  R + V+ A  +
Sbjct: 30 SEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE 88

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 9/43 (20%), Positives = 17/43 (39%)

Query: 19 SGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
               G  F+ +        A++ + GR+F +RV+      P 
Sbjct: 54 EVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPD 96

>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 = 39.7 bits (92), Expect = 2e-05
 Identities = 11/55 (20%), Positives = 24/55 (43%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             ++ + L+R +G  +G+  + Y   +    A   ++G E   + I V+    K
Sbjct: 33 EIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 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 = 40.2 bits (93), Expect = 2e-05
 Identities = 10/60 (16%), Positives = 16/60 (26%)

Query: 3  QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
                     +L   SG  RG GF         +  I   +G+            +P +
Sbjct: 39 LKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLL 98

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 2/58 (3%)

Query: 5  LTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRV-ISVNKAQPK 61
          L        +L+        +  I Y  +     A+    GR FG+ + I V     K
Sbjct: 21 LLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SKDGRIFGESIMIGVKPCIDK 77

>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 = 39.5 bits (92), Expect = 3e-05
 Identities = 3/35 (8%), Positives = 13/35 (37%)

Query: 25 FGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ 59
             + +  +     A+++ +G     R +++    
Sbjct: 43 TADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 77

>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 = 39.3 bits (91), Expect = 3e-05
 Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG--DRVISVNKA 58
               +I++++ +G  RG GFI +  R   ++AI+ ++G++       I+V  A
Sbjct: 32 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 39.3 bits (91), Expect = 4e-05
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 3   QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM 62
           +      +  ++ +R +G+ RG+GF+T ADR A + A ++ +      R  +VN A    
Sbjct: 32  EGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGA 90

Query: 63  GGEVSDHGYRGG 74
                  G+  G
Sbjct: 91  KPRSLQTGFAIG 102

>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 = 38.4 bits (89), Expect = 5e-05
 Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
              +++ ++  + + RGF FIT+ +   +   + E      G     +  A
Sbjct: 25 EVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNVGLSKCEIKVA 75

>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 = 37.8 bits (87), Expect = 9e-05
 Identities = 14/52 (26%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
            +D  +M ++ + R RGFGF+T+     ++    E+H  E  ++++   KA
Sbjct: 25 KVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 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 = 38.1 bits (88), Expect = 1e-04
 Identities = 10/52 (19%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 10 DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          D++I+ +R+S R +G  ++ + + +++      + G+      I V  +Q +
Sbjct: 47 DVRIISDRNSRRSKGIAYVEFCEIQSVP-LAIGLTGQRLLGVPIIVQASQAE 97

>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 = 38.2 bits (88), Expect = 1e-04
 Identities = 13/55 (23%), Positives = 27/55 (49%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
            ++L   ++  + +P+GF F+T+        A  E+ G+ F  R++ V  +  K
Sbjct: 34 PLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIK 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 = 37.8 bits (87), Expect = 1e-04
 Identities = 11/59 (18%), Positives = 24/59 (40%)

Query: 3  QCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                    I     +GR RG  FIT+ ++     A+  ++G +   +++ +   + K
Sbjct: 40 ARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK 98

>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 = 37.4 bits (86), Expect = 1e-04
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
              ++IM +R SG+ RGF F+T+ D  ++D  +              V KA
Sbjct: 28 KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKA 78

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 8/41 (19%), Positives = 17/41 (41%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +      I +++  +  DA   +H  EF  + + +  AQ  
Sbjct: 44 KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL 84

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 36.0 bits (83), Expect = 2e-04
 Identities = 9/22 (40%), Positives = 12/22 (54%)

Query: 95  CFKCGRPGHWARDCPSAVGGRG 116
           CF CG+ GH AR+C +      
Sbjct: 4   CFNCGKEGHTARNCRAPRKKGC 25

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 32.9 bits (75), Expect = 0.002
 Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 76  YSSGGRGSYGADRPGGQDD-CFKCGRPGHWARDCP 109
           ++ G  G    +    +   C+KCG+ GH  +DC 
Sbjct: 5   FNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39

>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 = 36.7 bits (84), Expect = 2e-04
 Identities = 5/40 (12%), Positives = 14/40 (35%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
            R F +I    +      + +++G +     +    + P
Sbjct: 41 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 80

>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 = 37.6 bits (86), Expect = 3e-04
 Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 7/60 (11%)

Query: 25  FGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEVSDHGYRGGGYSSGGRGSY 84
           +GF+ +    +   AI  ++G    ++ + V  A          H   G   + G    Y
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG-------HQRPGIAGAVGDGNGY 138

>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 = 36.6 bits (84), Expect = 3e-04
 Identities = 8/61 (13%), Positives = 23/61 (37%)

Query: 1  MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP 60
          ++        ++ +  ++      F F+ + D R  +DA+    G ++    + V   + 
Sbjct: 31 IEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 90

Query: 61 K 61
           
Sbjct: 91 G 91

>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 = 36.7 bits (84), Expect = 4e-04
 Identities = 5/37 (13%), Positives = 15/37 (40%)

Query: 25 FGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             +  AD      A+  ++G +   + I +  ++ +
Sbjct: 42 NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ 78

>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 = 35.9 bits (82), Expect = 6e-04
 Identities = 7/40 (17%), Positives = 14/40 (35%)

Query: 22 PRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
           +   F+T  +     +AI+  H   F  + + V      
Sbjct: 39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD 78

>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 = 35.4 bits (81), Expect = 9e-04
 Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 2/45 (4%)

Query: 17 RDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
                R F F+T+AD +       E          + ++ A+PK
Sbjct: 36 FIPKPFRAFAFVTFADDQIAQSLCGEDL--IIKGISVHISNAEPK 78

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 35.3 bits (80), Expect = 0.001
 Identities = 8/48 (16%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 14 MLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
          +++  +G  R FG++ +     ++ A+  + G +     I + K + +
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 5/43 (11%), Positives = 15/43 (34%), Gaps = 2/43 (4%)

Query: 21 RPRGFGFITYADRRAMDDAIREMHGREF--GDRVISVNKAQPK 61
            +    + YAD  +   A   + G+        + ++ ++  
Sbjct: 43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 85

>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 = 35.2 bits (80), Expect = 0.001
 Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 6/61 (9%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH------GREFGDRVISVNKAQP 60
              ++++L  D+   +G  F  +  + A    +          G +   R + V+ A  
Sbjct: 34 DLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

Query: 61 K 61
          +
Sbjct: 94 R 94

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.8 bits (79), Expect = 0.001
 Identities = 7/50 (14%), Positives = 13/50 (26%)

Query: 6  THNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
                       S  P    ++TY        AI+ ++      R +  
Sbjct: 39 HKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKA 88

>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 = 33.6 bits (76), Expect = 0.004
 Identities = 6/47 (12%), Positives = 16/47 (34%), Gaps = 1/47 (2%)

Query: 12 KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA 58
            +L     + + F F+ +        A+    G  F  + + + + 
Sbjct: 37 NPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRP 82

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.1 bits (77), Expect = 0.004
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK 61
             D   +    +G+  G GF+ + +      A+   H +  G+R I V+    K
Sbjct: 44 IVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKK 97

>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 = 33.1 bits (75), Expect = 0.004
 Identities = 14/49 (28%), Positives = 23/49 (46%)

Query: 7  HNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV 55
             D+ I+ ++ S R RGF F+ + +     +A    +G E   R I V
Sbjct: 35 PIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	255
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.65
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.62
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.62
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.6
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.59
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.59
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.58
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.58
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.57
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.57
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.55
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.54
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.54
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.53
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.53
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.53
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.52
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.52
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.52
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.51
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.51
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.51
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.51
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.5
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.5
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.5
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.47
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.46
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.46
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.46
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.45
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.44
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	99.43
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.43
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.43
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.41
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.39
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.38
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.38
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.38
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.37
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.37
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.34
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.34
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.34
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.33
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.31
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.31
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.29
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.29
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.28
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.27
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.27
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.26
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.25
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.25
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.25
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.25
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.25
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.23
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.23
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.22
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.22
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.21
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.2
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.2
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.19
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.19
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.18
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.17
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.15
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.14
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.1
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.1
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.08
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.05
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.92
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.89
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.78
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.78
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.67
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.56
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.87
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	90.95
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	88.26
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	85.55
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	85.27

>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=99.65  E-value=1.5e-16  Score=117.94  Aligned_cols=62  Identities=19%  Similarity=0.437  Sum_probs=60.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.+.++|++||++||+.+|.+++|.|++|+|+.
T Consensus        28 ~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          28 LFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             TSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             HHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            79999999999999999999999999999999999999999999999999999999999875

>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=99.63  E-value=2.4e-16  Score=118.66  Aligned_cols=66  Identities=20%  Similarity=0.325  Sum_probs=62.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||++||+++|++++|+|++|+++.+...
T Consensus        28 ~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~~~~   93 (99)
T d1whwa_          28 LFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQ   93 (99)
T ss_dssp             HHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTTCC
T ss_pred             HHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCccCC
Confidence            589999999999999999999999999999999999999999999999999999999998776543

>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=99.62  E-value=1.8e-16  Score=117.20  Aligned_cols=61  Identities=18%  Similarity=0.303  Sum_probs=59.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.+.++|++||++||+.+|.+++|.|++|.++
T Consensus        27 ~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          27 KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             HHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             HHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            5899999999999999999999999999999999999999999999999999999999876

>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=99.62  E-value=2.4e-16  Score=116.58  Aligned_cols=64  Identities=27%  Similarity=0.354  Sum_probs=60.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.|+.|++++|||||+|.++++|++||++||+..|.+++|.|++|+|+..+
T Consensus        25 ~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~~k   88 (89)
T d2cqba1          25 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   88 (89)
T ss_dssp             HHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCC
Confidence            5899999999999999999999999999999999999999999999999999999999987543

>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=99.60  E-value=4.2e-16  Score=114.54  Aligned_cols=63  Identities=21%  Similarity=0.444  Sum_probs=60.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++|+.|+++++||||+|.++++|++||+.||+++|.+++|.|++|.+...
T Consensus        21 ~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~~~   83 (85)
T d2u2fa_          21 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK   83 (85)
T ss_dssp             HHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCCCC
T ss_pred             HHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999987653

>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=99.60  E-value=3.1e-16  Score=113.87  Aligned_cols=60  Identities=20%  Similarity=0.431  Sum_probs=58.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|++++.|+++++||||+|.++++|++||+.||+.+|.+++|.|++|+|
T Consensus        22 ~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          22 LFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             HHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            589999999999999999999999999999999999999999999999999999999986

>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=99.59  E-value=4e-16  Score=116.52  Aligned_cols=63  Identities=22%  Similarity=0.301  Sum_probs=60.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.+.++|++||++||+++|.+++|+|++|+++..
T Consensus        29 ~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          29 LFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             HHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             HHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999998753

>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=99.59  E-value=7.7e-16  Score=111.56  Aligned_cols=60  Identities=23%  Similarity=0.527  Sum_probs=58.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|++|+.+++++|||||+|.++++|++||++||++.|.+++|.|++|+|
T Consensus        22 ~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             HHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            589999999999999999999999999999999999999999999999999999999987

>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=99.58  E-value=6.8e-16  Score=112.35  Aligned_cols=64  Identities=31%  Similarity=0.419  Sum_probs=59.4

Q ss_pred             CCCCCccceEE-EEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDL-KIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V-~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+++ .|++++.|++++|||||+|.++++|++||++||+++|.+++|.|++|.++..+
T Consensus        18 ~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          18 TFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   82 (83)
T ss_dssp             HHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             HHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCcC
Confidence            58999999875 78999999999999999999999999999999999999999999999987654

>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=99.58  E-value=5.9e-16  Score=112.27  Aligned_cols=60  Identities=8%  Similarity=0.136  Sum_probs=57.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|++|+.|+++++||||+|.++++|++||++||++.|.+++|+|++|+.
T Consensus        20 ~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1          20 KFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             HHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            589999999999999999999999999999999999999999999999999999999963

>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=99.58  E-value=9.4e-16  Score=116.29  Aligned_cols=64  Identities=20%  Similarity=0.404  Sum_probs=61.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+.++.|+++||||||+|.++++|++||++||+++|.+++|+|++|+++.+.
T Consensus        38 ~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~~  101 (102)
T d2cpza1          38 MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  101 (102)
T ss_dssp             HHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             HHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCCC
Confidence            5899999999999999999999999999999999999999999999999999999999988654

>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=99.57  E-value=1e-15  Score=121.69  Aligned_cols=65  Identities=18%  Similarity=0.369  Sum_probs=61.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|++|+|+.|+.|++++|||||+|.+.++|++||+.||+++|++++|+|++|+++..+.
T Consensus        62 ~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~~p  126 (139)
T d1u6fa1          62 LFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRP  126 (139)
T ss_dssp             HHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCCC
T ss_pred             HHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCCC
Confidence            68999999999999999999999999999999999999999999999999999999998776553

>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=99.57  E-value=1.5e-15  Score=113.29  Aligned_cols=63  Identities=19%  Similarity=0.313  Sum_probs=59.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|.|++++.|++++|||||+|.+.++|++||+.||+.+|++++|.|++|.+..+
T Consensus        27 ~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~~~   89 (93)
T d1h2vz_          27 LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE   89 (93)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             HHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999976543

>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=99.55  E-value=2.1e-15  Score=112.17  Aligned_cols=62  Identities=13%  Similarity=0.275  Sum_probs=57.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      +|++||+|++|+|++|+.|++++|||||+|.++++|++||+++|  .|+|+.|.|++|.+++..
T Consensus        28 ~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~--~l~Gr~i~v~~a~~k~~~   89 (90)
T d2cqga1          28 YFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ   89 (90)
T ss_dssp             HHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCE--EETTEEEEEECCCTTCCC
T ss_pred             HHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCC--ccCCEEeEEEeCCCCCCC
Confidence            58999999999999999999999999999999999999999655  899999999999987654

>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=99.55  E-value=2.4e-15  Score=110.12  Aligned_cols=58  Identities=24%  Similarity=0.367  Sum_probs=55.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A   58 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||+.||+..|.+  ++|.|++|
T Consensus        26 ~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          26 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             HHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            58999999999999999999999999999999999999999999999987  88999987

>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=99.54  E-value=1.4e-15  Score=115.30  Aligned_cols=63  Identities=27%  Similarity=0.642  Sum_probs=59.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|++++|||||+|.+.++|++||++||+++|.+++|+|++|.++..
T Consensus        28 ~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~~~   90 (104)
T d1p1ta_          28 IFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN   90 (104)
T ss_dssp             HHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTTH
T ss_pred             hhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999987643

>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=99.54  E-value=3.9e-15  Score=113.01  Aligned_cols=62  Identities=26%  Similarity=0.414  Sum_probs=57.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++|+.|++++|||||+|.++++|++||+.||. +|++++|.|++|.++..
T Consensus        30 ~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~~~   91 (103)
T d2cqda1          30 YFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAK   91 (103)
T ss_dssp             HHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTTCC
T ss_pred             HHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCCCC
Confidence            589999999999999999999999999999999999999998875 89999999999986544

>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=99.54  E-value=2.2e-15  Score=110.05  Aligned_cols=62  Identities=15%  Similarity=0.327  Sum_probs=56.9

Q ss_pred             CCCCCccceEEEEeecCCCC---CCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSG---RPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg---~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|++++.+.   ++||||||+|+++++|++||++||+++|++++|.|++|+++.
T Consensus        18 ~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~~   82 (85)
T d2cpfa1          18 VFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERAT   82 (85)
T ss_dssp             HHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSS
T ss_pred             HHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            58999999999999998775   468999999999999999999999999999999999997644

>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=99.53  E-value=1.6e-15  Score=109.56  Aligned_cols=57  Identities=23%  Similarity=0.410  Sum_probs=54.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      +|++||+|++|+|++|+.|+++||||||+|.++++|++||+ ||+++|++++|.|++|
T Consensus        20 ~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          20 YFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             HHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             HHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            58999999999999999999999999999999999999997 7999999999999987

>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=99.53  E-value=4.6e-15  Score=113.01  Aligned_cols=63  Identities=24%  Similarity=0.399  Sum_probs=59.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+.|.|++|+.|++++|||||+|.+.++|++||+ |++++|+++.|.|++|.++.+.
T Consensus        40 ~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          40 YYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES  102 (103)
T ss_dssp             HHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSCCCC
T ss_pred             HHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcccCCC
Confidence            58999999999999999999999999999999999999996 8999999999999999988754

>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=99.53  E-value=3.2e-15  Score=109.63  Aligned_cols=58  Identities=24%  Similarity=0.436  Sum_probs=54.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A   58 (255)
                      ||++||+|++|+|++|+.|+++++||||+|.++++|++||++||+++|.+  ++|+|++|
T Consensus        26 ~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          26 LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            58999999999999999999999999999999999999999999999997  55999886

>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=99.53  E-value=3.6e-15  Score=107.60  Aligned_cols=59  Identities=14%  Similarity=0.261  Sum_probs=55.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|++|+|+.++ +++++|||||+|.++++|++||++||+++|.+++|+|++|..
T Consensus        20 ~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_          20 LFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             HHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             HHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            58899999999999985 899999999999999999999999999999999999999863

>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=99.52  E-value=3.3e-15  Score=109.75  Aligned_cols=61  Identities=18%  Similarity=0.293  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeec-CCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLE-RDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~D-k~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.+ +++++++|||||+|.+.++|++||+ ||+++|.+++|.|++|++++
T Consensus        25 ~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~kP   86 (86)
T d2ghpa3          25 SFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKKP   86 (86)
T ss_dssp             HHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCCC
T ss_pred             HHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCCC
Confidence            5899999999999764 6789999999999999999999996 99999999999999999874

>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=99.52  E-value=3.6e-15  Score=109.99  Aligned_cols=64  Identities=25%  Similarity=0.494  Sum_probs=60.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+.|.++.++.+++++|||||+|.++++|++||+.||+++|.+++|.|++|.++...
T Consensus        25 ~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~~   88 (90)
T d1x5sa1          25 VFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN   88 (90)
T ss_dssp             HHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCCC
T ss_pred             hhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCCC
Confidence            5889999999999999999999999999999999999999999999999999999999887653

>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=99.52  E-value=6.8e-15  Score=109.85  Aligned_cols=63  Identities=16%  Similarity=0.380  Sum_probs=58.2

Q ss_pred             CCCCCccceEEEEeecCC-CCCCCcEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERD-SGRPRGFGFITYADRRAMDDAIREM-HGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~-Tg~srGfaFVtF~~~e~a~~AI~~l-nG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++. |++++|||||+|.++++|++||+.| |+.+|.+++|.|++|+++..
T Consensus        28 ~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          28 LFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             HHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             HHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCCC
Confidence            589999999999999854 8999999999999999999999998 89999999999999987654

>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=99.51  E-value=6.2e-15  Score=107.27  Aligned_cols=55  Identities=25%  Similarity=0.432  Sum_probs=53.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISV   55 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V   55 (255)
                      ||++||+|++|+|++|+.|+++++||||+|.++++|++||++||+++|++++|+|
T Consensus        29 ~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          29 VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             HHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             HHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            5899999999999999999999999999999999999999999999999999987

>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=99.51  E-value=3.5e-15  Score=110.19  Aligned_cols=61  Identities=20%  Similarity=0.437  Sum_probs=56.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++.+  ++|||||+|+++++|++||++||+++|.+++|.|++|+++.+
T Consensus        28 ~F~~~G~v~~~~i~~~~~~--~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~   88 (89)
T d1cvja2          28 TFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   88 (89)
T ss_dssp             HHHTTSCEEEEEECCBTTB--CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTT
T ss_pred             HHHhcCCceEEEEEeecCC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            5899999999999998654  789999999999999999999999999999999999998764

>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=99.51  E-value=4.6e-15  Score=107.37  Aligned_cols=60  Identities=10%  Similarity=0.156  Sum_probs=51.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|+.+.++.++.++++++||||+|.++++|++||+.||+++|.+++|.|++|+|
T Consensus        21 ~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          21 LLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             HHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            588999999999999999999999999999999999999999999999999999999987

>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=99.51  E-value=1.8e-14  Score=107.22  Aligned_cols=61  Identities=28%  Similarity=0.495  Sum_probs=56.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.++.+  +++||||+|.++++|++||+.||+.+|.+++|.|++|+++..
T Consensus        31 ~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~~   91 (93)
T d2cq3a1          31 MFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   91 (93)
T ss_dssp             HGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             HHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCCC
Confidence            6899999999999998654  789999999999999999999999999999999999998764

>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=99.50  E-value=3.8e-15  Score=113.02  Aligned_cols=60  Identities=20%  Similarity=0.414  Sum_probs=57.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|++|+|++|+.|+++||||||+|.++++|++||+ ||+++|.++.|.|++|+++
T Consensus        38 ~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          38 FFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             HHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHH
T ss_pred             HHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCC
Confidence            58999999999999999999999999999999999999995 9999999999999998764

>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=99.50  E-value=1.1e-14  Score=106.65  Aligned_cols=58  Identities=28%  Similarity=0.453  Sum_probs=55.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|++|+|++|+.|++++|||||+|.++++|++||+ ++++.|+|++|+|+.|.
T Consensus        26 ~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          26 HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             HHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            58999999999999999999999999999999999999997 68899999999999986

>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=99.50  E-value=5e-15  Score=106.20  Aligned_cols=57  Identities=23%  Similarity=0.473  Sum_probs=54.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      +|++||+|++|.|++|+.|++++|||||+|.++++|++||+ +++++|+|+.|.|+.|
T Consensus        19 ~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          19 YFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             HHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             HHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            58999999999999999999999999999999999999997 7999999999999765

>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=99.47  E-value=4.8e-14  Score=104.22  Aligned_cols=56  Identities=11%  Similarity=0.089  Sum_probs=51.9

Q ss_pred             CCCCCccceEEEEeecCCCCCC---CcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRP---RGFGFITYADRRAMDDAIREMHGREFGDRVISVN   56 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~s---rGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~   56 (255)
                      ||++||+|++|.|++++.|+.+   ++||||+|+++++|++||++||+++|.++.|+|+
T Consensus        31 ~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          31 YFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             TTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             HhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            5999999999999999887655   4999999999999999999999999999999985

>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=99.46  E-value=3.6e-14  Score=104.81  Aligned_cols=61  Identities=20%  Similarity=0.322  Sum_probs=56.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.|+.+.  ++||||+|.+.++|++||+.||+++|.++.|+|++|+++..
T Consensus        28 ~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~~   88 (90)
T d2cqia1          28 LFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   88 (90)
T ss_dssp             HHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             HHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            58999999999999997765  68999999999999999999999999999999999987654

>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=99.46  E-value=3.5e-14  Score=106.37  Aligned_cols=64  Identities=20%  Similarity=0.362  Sum_probs=58.6

Q ss_pred             CCCCCccce--------EEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNN--------DLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~--------~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|.        .+.++++++|+++++||||+|.++++|++||++||+++|++++|.|++|++++.+
T Consensus        28 ~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          28 FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPM   99 (101)
T ss_dssp             HHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCCS
T ss_pred             HHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            588999874        5788889999999999999999999999999999999999999999999987654

>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=99.46  E-value=5.5e-15  Score=106.38  Aligned_cols=57  Identities=14%  Similarity=0.313  Sum_probs=53.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      +|++||+|++|+|++|+.|++++|||||+|.++++|++||+ ++.++|+++.|+|++|
T Consensus        19 ~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          19 YFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             HHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             HHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            58899999999999999999999999999999999999997 5778999999999876

>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=99.45  E-value=9.7e-14  Score=104.47  Aligned_cols=56  Identities=20%  Similarity=0.335  Sum_probs=51.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|.        |+||||+|+++++|++||++||+++|.+++|.|++|.++...
T Consensus        36 ~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~   91 (98)
T d1wf2a_          36 IFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN   91 (98)
T ss_dssp             SSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCCCC
T ss_pred             HHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            79999999999983        589999999999999999999999999999999999865443

>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=99.44  E-value=6e-14  Score=104.37  Aligned_cols=64  Identities=16%  Similarity=0.314  Sum_probs=59.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhc------CCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMH------GREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~ln------G~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|.|+.++.+++++|||||+|.++++|++||+.||      +.+|.+++|+|++|.++.+.
T Consensus        28 ~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~~a   97 (98)
T d1x4ha1          28 VLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA   97 (98)
T ss_dssp             HHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCC
T ss_pred             HHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCCcC
Confidence            58999999999999999999999999999999999999999887      57789999999999987653

>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=99.43  E-value=3.6e-14  Score=108.22  Aligned_cols=57  Identities=11%  Similarity=0.226  Sum_probs=53.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||++||+|++|+|+++ .|++++|||||+|+++++|++||++||++.|++++|+|+++
T Consensus        47 ~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          47 MEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4789999999999877 68999999999999999999999999999999999999875

>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=99.43  E-value=7.5e-14  Score=100.24  Aligned_cols=57  Identities=26%  Similarity=0.429  Sum_probs=54.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      +|++||+|+.++|+.++.|++++|||||+|.+++++++||+ ||+++|+|++|+|+.|
T Consensus        22 ~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          22 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             HHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             HHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            58999999999999999999999999999999999999986 8999999999999987

>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=99.43  E-value=3.5e-14  Score=100.82  Aligned_cols=57  Identities=23%  Similarity=0.538  Sum_probs=54.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      +|++||+|+.|.|++++.|+++++||||+|.++++|++||+ ||+++|++++|+|++|
T Consensus        19 ~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          19 YFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             HHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             HHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            58999999999999999999999999999999999999997 9999999999999987

>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=99.41  E-value=1.6e-14  Score=108.57  Aligned_cols=64  Identities=17%  Similarity=0.297  Sum_probs=60.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|+.|.|+.++.++++++||||+|.+.++|++||+.||+.+|.+++|.|++|+++..+
T Consensus        38 ~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~r  101 (102)
T d2cpxa1          38 LFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  101 (102)
T ss_dssp             HTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             HHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCcccC
Confidence            5889999999999999899999999999999999999999999999999999999999987654

>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=99.39  E-value=1.4e-13  Score=99.23  Aligned_cols=56  Identities=23%  Similarity=0.320  Sum_probs=51.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|.++      ++||||+|++.++|++||++||+.+|++++|+|++|++++
T Consensus        23 ~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1          23 AFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             HHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             HHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            5899999999999764      5799999999999999999999999999999999998764

>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=99.38  E-value=3.5e-13  Score=101.64  Aligned_cols=64  Identities=19%  Similarity=0.397  Sum_probs=55.3

Q ss_pred             CCCCCccceEEEEeecC-CCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLER-DSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk-~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++|| |++|.|+.++ .+++++|||||+|.++++|++|| +||+++|++++|+|++|.++.....
T Consensus        35 ~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~~~~   99 (104)
T d1wi8a_          35 FFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDKDS   99 (104)
T ss_dssp             HTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCCCC
T ss_pred             HHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCCCCCC
Confidence            589998 7888888775 47899999999999999998777 4999999999999999998766543

>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=99.38  E-value=1.6e-13  Score=102.84  Aligned_cols=57  Identities=12%  Similarity=0.313  Sum_probs=53.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+.+      |+||||+|.++++|++||++||+++|.+++|+|++|++++.
T Consensus        38 ~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p~   94 (96)
T d1x4ga1          38 TFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD   94 (96)
T ss_dssp             HHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             HHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            5899999999999976      68999999999999999999999999999999999987654

>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=99.38  E-value=1e-13  Score=105.12  Aligned_cols=57  Identities=12%  Similarity=0.251  Sum_probs=52.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+++     ++|||||+|+++++|++||+.||++.|.+++|+|++|+.+.
T Consensus        23 ~F~~fG~I~~v~i~~~-----~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~~   79 (109)
T d2adca1          23 LFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             HHHHHTCEEEEEECCT-----TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             HHhhccccceEEEEec-----ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            6899999999999997     37899999999999999999999999999999999997543

>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=99.37  E-value=1.3e-13  Score=97.36  Aligned_cols=54  Identities=15%  Similarity=0.355  Sum_probs=51.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVIS   54 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~   54 (255)
                      ||++||+|+.++|++++.|+++++||||+|.++++|++||+.||+++|+++.|+
T Consensus        18 ~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          18 LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             TSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             HHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999999999999999999999999999998763

>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=99.37  E-value=2.8e-13  Score=103.69  Aligned_cols=58  Identities=14%  Similarity=0.183  Sum_probs=53.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|++|+|+.+   +.++|||||+|.+.++|++||++||+++|.++.|.|.+|.++
T Consensus        27 ~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1          27 IFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             HHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             HHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            6899999999999865   456899999999999999999999999999999999998754

>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=99.34  E-value=5.6e-13  Score=97.73  Aligned_cols=56  Identities=20%  Similarity=0.271  Sum_probs=52.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+++      ++||||+|++.++|++||++||+.+|.+++|+|++|.++.
T Consensus        28 ~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1          28 LFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             HTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             HHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            6999999999999875      5799999999999999999999999999999999998764

>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=99.34  E-value=4.6e-14  Score=104.84  Aligned_cols=59  Identities=20%  Similarity=0.399  Sum_probs=54.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|+.|+|+.+ .|++++|||||+|+++++|++||+ ||+++|.+++|.|++|++|
T Consensus        33 ~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          33 AISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             HHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCS
T ss_pred             HHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCCC
Confidence            5889999999998754 789999999999999999999996 9999999999999999864

>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=99.34  E-value=7.2e-13  Score=98.60  Aligned_cols=58  Identities=16%  Similarity=0.252  Sum_probs=52.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||++||+|+.|+|+.+   ..+++||||+|+++++|++||++||+++|.+++|+|++|++.
T Consensus        34 ~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          34 VFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             HHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             HHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            6899999999988654   357899999999999999999999999999999999999864

>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=99.33  E-value=3.3e-13  Score=101.69  Aligned_cols=59  Identities=19%  Similarity=0.306  Sum_probs=55.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|+.|.|+.+ .++++++||||+|.++++|++||++||+++|.+++|.|..++|
T Consensus        38 ~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          38 MLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             TTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             HHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            7999999999999988 5889999999999999999999999999999999998887765

>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=99.31  E-value=5.6e-13  Score=97.14  Aligned_cols=58  Identities=14%  Similarity=0.244  Sum_probs=52.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEec
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKA   58 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A   58 (255)
                      ||+.|+.|..+.++.+..+++++|||||+|.++++|++||++||+++|.+++|+|++|
T Consensus        29 ~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          29 FFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             HTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             HHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            5889999988655555688999999999999999999999999999999999999976

>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=99.31  E-value=3e-13  Score=99.96  Aligned_cols=60  Identities=20%  Similarity=0.324  Sum_probs=54.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      +|++||+|++|+|+.   |+++++||||+|++.++|++||++||+.+|.++.|.|.+|+++.+
T Consensus        27 ~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~~   86 (91)
T d1nu4a_          27 IFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD   86 (91)
T ss_dssp             HHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCCT
T ss_pred             HhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCch
Confidence            479999999998865   456789999999999999999999999999999999999987653

>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=99.29  E-value=7e-13  Score=98.74  Aligned_cols=65  Identities=25%  Similarity=0.343  Sum_probs=56.3

Q ss_pred             CCCCCcc-ceEEEEeecC-CCCCCCcEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTH-NNDLKIMLER-DSGRPRGFGFITYADRRAMDDAIREMHG--REFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~-I~~V~Iv~Dk-~Tg~srGfaFVtF~~~e~a~~AI~~lnG--~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+ |++|.|+++. .+++++|||||+|.++++|++||+.|+.  ..+.++.|.|++|+|+.+..
T Consensus        21 ~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~~   89 (96)
T d2disa1          21 EIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVD   89 (96)
T ss_dssp             HHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCSTT
T ss_pred             HHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCCC
Confidence            5889996 8999999985 4689999999999999999999999864  45679999999999877654

>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=99.29  E-value=1.4e-12  Score=95.42  Aligned_cols=57  Identities=5%  Similarity=0.068  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|++|+|+.+ .+++++|||||+|.++++|++||+ +++++|.+++|.|.++.
T Consensus        26 ~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2          26 WLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             HHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            5899999999999887 588999999999999999999996 79999999999998864

>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=99.28  E-value=1.1e-12  Score=99.74  Aligned_cols=58  Identities=16%  Similarity=0.141  Sum_probs=53.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|++++      +++||||+|+++++|++||++||+++|.++.|+|.+|+++...
T Consensus        30 lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~~   87 (104)
T d1weya_          30 LFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIG   87 (104)
T ss_dssp             HHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSCC
T ss_pred             HhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCCC
Confidence            689999999999985      4679999999999999999999999999999999999876544

>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=99.27  E-value=8.2e-13  Score=95.46  Aligned_cols=58  Identities=19%  Similarity=0.321  Sum_probs=51.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCC-eeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGR-EFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~-~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||.|+++++++.      ++||||+|.+.++|++||++||+. +|.+++|.|++|.|+..+
T Consensus        21 ~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1          21 LFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             HHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             HHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            5889999998888764      689999999999999999999985 699999999999987654

>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=99.27  E-value=5.4e-13  Score=97.82  Aligned_cols=57  Identities=14%  Similarity=0.226  Sum_probs=51.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|++|+|+++       |||||+|++.++|++||++||+.+|.++.|.|.+++++...
T Consensus        20 ~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~~   76 (87)
T d3begb1          20 HMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   76 (87)
T ss_dssp             HHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             HHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcCC
Confidence            6899999999999775       89999999999999999999999999999999888765544

>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=99.26  E-value=4.6e-12  Score=92.26  Aligned_cols=57  Identities=16%  Similarity=0.315  Sum_probs=51.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||.|..+.+..      +++||||+|.++++|++||++||+++|.+++|.|++|+|+..
T Consensus        28 ~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1          28 EFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             HHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             hhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            588999998887754      578999999999999999999999999999999999998654

>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=99.25  E-value=1.6e-12  Score=95.49  Aligned_cols=59  Identities=19%  Similarity=0.226  Sum_probs=51.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGEV   66 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~~   66 (255)
                      ||++||+|++|+++.+     +++||||+|+++++|++||+  ++++|++++|.|++|+++.....
T Consensus        25 ~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~~~   83 (88)
T d1wf0a_          25 FFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNSNS   83 (88)
T ss_dssp             HSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCCCS
T ss_pred             HHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCCCC
Confidence            6999999999987654     67899999999999999986  67899999999999998775543

>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=99.25  E-value=1.9e-12  Score=98.13  Aligned_cols=56  Identities=7%  Similarity=-0.009  Sum_probs=50.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.      +++||||+|.++++|++||++||+++|.+++|.|++|....
T Consensus        30 ~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_          30 TFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             HHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             hhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            689999999998854      57899999999999999999999999999999999987543

>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=99.25  E-value=2.8e-12  Score=97.47  Aligned_cols=59  Identities=8%  Similarity=0.049  Sum_probs=52.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC--CeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG--DRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~--Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|.|+.++    +++||||+|+++++|++||++||+++|.  +++|.|.+++++..
T Consensus        27 ~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~~   87 (108)
T d2adba1          27 IFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL   87 (108)
T ss_dssp             HHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCSC
T ss_pred             HHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCccc
Confidence            69999999999999874    5799999999999999999999999984  78899999887553

>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=99.25  E-value=4.2e-12  Score=95.64  Aligned_cols=61  Identities=13%  Similarity=0.117  Sum_probs=53.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|+ |++|.|+++ .+++++|||||+|.++++|++||+ ||+++|.++.|+|.++.++...
T Consensus        35 ~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~   95 (102)
T d1weza_          35 FFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTS   95 (102)
T ss_dssp             SSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCC
T ss_pred             HHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCC
Confidence            689996 668888887 467899999999999999999986 8999999999999999876544

>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=99.25  E-value=1.7e-12  Score=97.46  Aligned_cols=58  Identities=12%  Similarity=0.158  Sum_probs=52.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGGE   65 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~~   65 (255)
                      ||++||+|+.|+|++       ++||||+|.++++|++||++||+.+|+++.|+|.+++++....
T Consensus        35 ~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~~~   92 (98)
T d1wg4a_          35 HMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPERS   92 (98)
T ss_dssp             HHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECCCS
T ss_pred             HHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCCCC
Confidence            589999999999875       4899999999999999999999999999999999998766543

>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=99.23  E-value=6.4e-12  Score=94.83  Aligned_cols=63  Identities=19%  Similarity=0.250  Sum_probs=57.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|+.|+.+.++.++.+++++|||||+|.++++|++||+ ||++.|.++.|.|.++.+++..
T Consensus        35 ~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~   97 (104)
T d1wg5a_          35 FFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR   97 (104)
T ss_dssp             HTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTSC
T ss_pred             HHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHhc
Confidence            58999999998888888899999999999999999999996 9999999999999999877544

>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=99.23  E-value=3e-12  Score=95.31  Aligned_cols=59  Identities=17%  Similarity=0.327  Sum_probs=51.5

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++||+|..|+     .++++++||||+|.+.++|++||++||+++|.+++|.|++|.++...
T Consensus        36 ~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~~   94 (96)
T d1fjca_          36 VFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT   94 (96)
T ss_dssp             HHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCCC
T ss_pred             HHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCC
Confidence            578888776553     36678999999999999999999999999999999999999987653

>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=99.22  E-value=4.8e-12  Score=91.77  Aligned_cols=54  Identities=7%  Similarity=0.244  Sum_probs=49.2

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG-DRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~-Gr~I~V~~A~   59 (255)
                      ||++||+|++|+|+++     .++||||+|.+.++|++||+.||+.+|. ++.|.|++|+
T Consensus        28 ~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          28 LFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             HHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             hhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            5899999999999875     4689999999999999999999999985 6899999986

>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=99.22  E-value=1.1e-11  Score=93.18  Aligned_cols=58  Identities=21%  Similarity=0.339  Sum_probs=53.1

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      |++||+|++|+|+.+    .++|||||+|+++++|++||+.||+..|++++|.|+++.++..
T Consensus        40 ~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          40 CSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             GGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             hcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcCC
Confidence            789999999998776    3679999999999999999999999999999999999988754

>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=99.21  E-value=3.3e-12  Score=96.09  Aligned_cols=59  Identities=12%  Similarity=0.254  Sum_probs=53.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||+.||.|+.+.++.+..+++++|||||+|.++++|++||+ ||++.|+++.|.|..+..
T Consensus        28 ~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1          28 FLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             HTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             hhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            58999999886666666899999999999999999999996 999999999999998764

>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=99.20  E-value=8e-12  Score=91.33  Aligned_cols=57  Identities=9%  Similarity=0.139  Sum_probs=50.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCee-CCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREF-GDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i-~Gr~I~V~~A~~k   61 (255)
                      ||++||+|+++.++..    +.++||||+|+++++|++||++||+..| ++++|+|+++++.
T Consensus        30 ~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          30 LFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             HHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            5899999999887664    3578999999999999999999999998 5899999999864

>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=99.20  E-value=1.6e-11  Score=90.16  Aligned_cols=57  Identities=14%  Similarity=0.122  Sum_probs=47.7

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMGG   64 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~~   64 (255)
                      ||++|| |+.+.+.      ++|+||||+|.++++|++||++||+++|.+++|.|+++..+...
T Consensus        25 lF~~~G-~~~~~~~------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~~   81 (88)
T d1wg1a_          25 LLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALL   81 (88)
T ss_dssp             HTCSSC-CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             HHHhcC-ceeeeee------ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            689999 3334443      36789999999999999999999999999999999999766543

>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=99.19  E-value=9.5e-12  Score=88.81  Aligned_cols=56  Identities=14%  Similarity=0.046  Sum_probs=50.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      ||++||+|+.|+|+.++.+  .++||||+|+++++|++||+ ||+++|+++.|.|+.+.
T Consensus        20 ~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~T   75 (75)
T d2ghpa2          20 YFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHLT   75 (75)
T ss_dssp             HHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             HHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEECC
Confidence            5899999999999998664  34699999999999999996 89999999999999763

>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=99.19  E-value=6e-12  Score=102.43  Aligned_cols=62  Identities=26%  Similarity=0.395  Sum_probs=58.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|+.|.|+.++.|++++|||||+|.++++|++||+ |+++.|+|++|.|.+|.+|.+
T Consensus       117 ~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         117 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQE  178 (183)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCCHHH
T ss_pred             hhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCCccc
Confidence            58899999999999999999999999999999999999997 788999999999999988654

>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=99.18  E-value=1.1e-11  Score=92.34  Aligned_cols=57  Identities=19%  Similarity=0.260  Sum_probs=50.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGD--RVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~G--r~I~V~~A~~k~~   63 (255)
                      ||++||+|+.|+|+++      ++||||+|.+.++|++||++||+.+|.+  ++|+|++|++.+.
T Consensus        37 ~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~~   95 (97)
T d1whya_          37 EFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS   95 (97)
T ss_dssp             HHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCC
T ss_pred             HHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCCC
Confidence            5899999999999875      5799999999999999999999999986  5899999987553

>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=99.17  E-value=1.8e-11  Score=91.83  Aligned_cols=56  Identities=13%  Similarity=0.138  Sum_probs=50.8

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHH--HhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIR--EMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~--~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.+      ++||||+|+++++|++||+  ++|..+|.++.|.|++|+.++
T Consensus        39 ~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~~   96 (99)
T d1x4fa1          39 LAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK   96 (99)
T ss_dssp             TTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             hhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCcc
Confidence            7999999999999875      5799999999999999997  578889999999999998665

>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=99.15  E-value=3.3e-11  Score=85.92  Aligned_cols=55  Identities=16%  Similarity=0.242  Sum_probs=46.9

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++|| |+.+++      .++++||||+|.+.++|++||++||+.+|.+++|.|++|....
T Consensus        18 ~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1          18 LLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             HTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             HHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            588998 444444      3468999999999999999999999999999999999997643

>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=99.14  E-value=3.9e-11  Score=88.33  Aligned_cols=56  Identities=13%  Similarity=0.036  Sum_probs=50.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREM--HGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~l--nG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|.|+.+      +++|||+|++.++|++||+.|  +..+|.+++|.|++|++.+
T Consensus        29 lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~~   86 (89)
T d1x4da1          29 LVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   86 (89)
T ss_dssp             TTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             HHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCcc
Confidence            7999999999999876      359999999999999999865  6788999999999998644

>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=99.10  E-value=1e-10  Score=85.40  Aligned_cols=56  Identities=9%  Similarity=0.114  Sum_probs=50.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEEecccCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREM--HGREFGDRVISVNKAQPKM   62 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~l--nG~~i~Gr~I~V~~A~~k~   62 (255)
                      ||++||+|++|+|+.+      ++||||+|++.++|++||+.|  +...|.+++|.|++++.+.
T Consensus        28 ~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          28 LGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             TTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             HHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            7999999999999865      479999999999999999865  5789999999999998664

>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=99.10  E-value=4.1e-11  Score=90.61  Aligned_cols=59  Identities=19%  Similarity=0.269  Sum_probs=53.4

Q ss_pred             CCCCccceEEEEeecCCC--CCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            2 QQCLTHNNDLKIMLERDS--GRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~T--g~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      |++||+|++|+|++++.+  ....|++||+|.++++|++||++||+..|++++|.|.++.+
T Consensus        35 ~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          35 CSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDP   95 (104)
T ss_dssp             HTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECH
T ss_pred             hcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCH
Confidence            789999999999987665  34568999999999999999999999999999999999864

>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=99.08  E-value=6.4e-11  Score=89.25  Aligned_cols=57  Identities=5%  Similarity=-0.042  Sum_probs=49.6

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREM--HGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~l--nG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|+++      |+||||+|++.++|++||+.|  +...|.+++|+|++++.+..
T Consensus        35 ~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~   93 (104)
T d1wexa_          35 ALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             HHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             hhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCcc
Confidence            6899999999999763      689999999999999999877  45678899999999976543

>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=99.05  E-value=1.9e-11  Score=93.56  Aligned_cols=60  Identities=22%  Similarity=0.340  Sum_probs=54.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k   61 (255)
                      ||+.||.|+.+.++.+..+++++|||||+|.++++|++||+ ||++.|.++.|.|..+.++
T Consensus        38 ~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~~   97 (112)
T d1wela1          38 FFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKK   97 (112)
T ss_dssp             HSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECHH
T ss_pred             HHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcChH
Confidence            58999999887777777899999999999999999999996 9999999999999988653

>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=98.92  E-value=8.1e-12  Score=91.67  Aligned_cols=58  Identities=12%  Similarity=0.278  Sum_probs=49.0

Q ss_pred             CCCCCccceEEEEe-----ecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIM-----LERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv-----~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|++||+|..+.|+     .+..++++++||||+|.++++|++||+ ||+++|.++.|+|+.++
T Consensus        21 ~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          21 FFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             HHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBCTT
T ss_pred             HHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECCCC
Confidence            47778887776553     456788999999999999999999985 99999999999997554

>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=98.89  E-value=6.4e-10  Score=80.62  Aligned_cols=54  Identities=19%  Similarity=0.219  Sum_probs=46.4

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeE-EEEEecccC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRV-ISVNKAQPK   61 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~-I~V~~A~~k   61 (255)
                      +|++||+|++|++..      .++||||+|.++++|++||+ ||+++|+++. |.|..+..|
T Consensus        23 ~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1          23 QFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             HHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             HHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            388999999998764      46899999999999999996 9999999975 578877654

>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=98.78  E-value=1.2e-09  Score=83.47  Aligned_cols=54  Identities=7%  Similarity=0.026  Sum_probs=46.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCH-HHHHHHHHHhcCCeeCCeEEEEEeccc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADR-RAMDDAIREMHGREFGDRVISVNKAQP   60 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~-e~a~~AI~~lnG~~i~Gr~I~V~~A~~   60 (255)
                      ||++||+|+.|.|+++      ++||||+|.+. ++|.+||++||+..|..+.+.|.++..
T Consensus        31 ~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          31 LFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             HTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             HHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            6999999999999864      68999999985 789999999999988877777766654

>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=98.78  E-value=1e-09  Score=82.40  Aligned_cols=43  Identities=14%  Similarity=0.210  Sum_probs=39.1

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFG   49 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~   49 (255)
                      ||++||+|++|.|+.+      ++||||+|++.++|++||++||+++|.
T Consensus        40 ~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          40 VLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             HHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             HHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            5899999999998875      579999999999999999999999883

>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=98.67  E-value=1.2e-08  Score=82.29  Aligned_cols=62  Identities=26%  Similarity=0.431  Sum_probs=55.0

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecccCCC
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQPKMG   63 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~~k~~   63 (255)
                      ||++||+|++|+|++++.|+.+++||||+|.++++|++||+ ++...|..+.|.+....++..
T Consensus        26 ~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~~~   87 (183)
T d1u1qa_          26 HFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSRED   87 (183)
T ss_dssp             HHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCTTG
T ss_pred             HHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhccc
Confidence            58999999999999999999999999999999999999998 566788888888887765543

>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=97.56  E-value=3.3e-05  Score=56.36  Aligned_cols=49  Identities=12%  Similarity=0.160  Sum_probs=44.1

Q ss_pred             CCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            2 QQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         2 fekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      |++||+|+-|+++.|        -..|||.+-++|.+|++ |++++|.+++|+|....
T Consensus        45 l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          45 LGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            678999999999998        67899999999999998 99999999999997543

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.87  E-value=0.00069  Score=46.95  Aligned_cols=56  Identities=11%  Similarity=0.092  Sum_probs=47.3

Q ss_pred             CCCCCccceEEEEeecCCCCCCCcEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEecc
Q 025249            1 MQQCLTHNNDLKIMLERDSGRPRGFGFITYADRRAMDDAIREMHGREFGDRVISVNKAQ   59 (255)
Q Consensus         1 lfekFG~I~~V~Iv~Dk~Tg~srGfaFVtF~~~e~a~~AI~~lnG~~i~Gr~I~V~~A~   59 (255)
                      +|+++++|.+|.|..- ..+..  .|-|...+.++|..||..||-..|..++|.|+++.
T Consensus        16 ~f~~h~~V~sv~l~~~-~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          16 AFARHGKVKSVELSPH-TDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHSCEEEEEECSC-CSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHhheeEEEEEEEec-cCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3677899999888553 22333  68999999999999999999999999999999986

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=90.95  E-value=0.03  Score=31.34  Aligned_cols=19  Identities=42%  Similarity=1.076  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCCCCCCCCCC
Q 025249           93 DDCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        93 ~~~~~~g~~Gh~~~~cp~~  111 (255)
                      -.||+||..||.++.|--.
T Consensus         7 ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           7 IRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSS
T ss_pred             eEeecCCccchhhhhccCc
Confidence            4799999999999999543

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=88.26  E-value=0.1  Score=27.89  Aligned_cols=18  Identities=50%  Similarity=1.248  Sum_probs=16.0

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~~  111 (255)
                      -||.|+..||+.++|-..
T Consensus         4 vcfscgktghikkdck~e   21 (26)
T d1dsqa_           4 VCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             BCTTTCCBSSCTTTTTCC
T ss_pred             EEEecCCcccchhhhhhh
Confidence            599999999999999753

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=85.55  E-value=0.21  Score=30.30  Aligned_cols=18  Identities=44%  Similarity=1.230  Sum_probs=15.1

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~~  111 (255)
                      .||.|+..|||+.+||..
T Consensus        24 ~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1          24 GCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             SCSSSCCSSSCTTTCCSS
T ss_pred             ccccCCCCCeecccCCCC
Confidence            588999999999999853

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=85.27  E-value=0.21  Score=30.31  Aligned_cols=18  Identities=50%  Similarity=1.304  Sum_probs=16.6

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 025249           94 DCFKCGRPGHWARDCPSA  111 (255)
Q Consensus        94 ~~~~~g~~Gh~~~~cp~~  111 (255)
                      .||+|+..||++.+||..
T Consensus         3 ~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           3 KCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCTTTCCSSSCTTTCSSC
T ss_pred             ccccCCCcCcCcccCcCC
Confidence            699999999999999975