Citrus Sinensis ID: 033734

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110--
Protein Sequence
MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN
Secondary Structure (PSIPRED)
cHHHHHccccccccccccccccccccHHHHHHHHccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcccEEEEEEEEcccccccccHHHHHHccccEEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccEcccEEEEEEccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MLADAFSQFGQVTEDLVYFYfksqplfplhyfliSDSFLFAATIIMDkgknrskgygyvtFSTEEEAQKALADMNgklldgrvifvdnvrpsrryntdaplarqsaqspeen
Flexible Loop (DISEMBL)
MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDnvrpsrryntdaplarqsaqspeen
Low Complexity Region (SEG)
MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN
Disordered region (IsUnstruct)
*****FSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEE*AQKALADMNGKLLDGRVIFVDNV***********************
Disordered Region (DISOPRED)
******SQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIF***************************
Disordered Region (DISEMBL)
MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD**************
Disordered Region (DISPRO)
MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR**********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN
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	112	2.2.26 [Sep-21-2011]
Q99069	142	Glycine-rich RNA-binding	N/A	no	0.535	0.422	0.45	5e-08
P19682	276	28 kDa ribonucleoprotein,	N/A	no	0.482	0.195	0.389	3e-07
Q98SP8	629	Embryonic polyadenylate-b	N/A	no	0.616	0.109	0.375	3e-07
Q9LIS2	136	Glycine-rich RNA-binding	no	no	0.526	0.433	0.348	4e-07
Q6DEY7	629	Embryonic polyadenylate-b	yes	no	0.616	0.109	0.375	5e-07
Q6GR16	629	Embryonic polyadenylate-b	N/A	no	0.616	0.109	0.361	7e-07
Q43349	342	29 kDa ribonucleoprotein,	no	no	0.464	0.152	0.481	9e-07
P27476	414	Nuclear localization sequ	yes	no	0.419	0.113	0.448	1e-06
Q9PTX2	164	Cold-inducible RNA-bindin	N/A	no	0.437	0.298	0.469	2e-06
Q9H361	631	Polyadenylate-binding pro	yes	no	0.410	0.072	0.458	2e-06

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

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 38/60 (63%)

Query: 28 PLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           LH    +   +  + II+D+   RS+G+G+VTFSTEE  + A+  MNGK LDGR I V+
Sbjct: 2  SLHSAFSTYGEVLESKIILDRETQRSRGFGFVTFSTEEAMRSAIEGMNGKELDGRNITVN 61

Possibly has a role in RNA transcription or processing during stress.
Sorghum bicolor (taxid: 4558)

>sp|P19682|ROC3_NICSY 28 kDa ribonucleoprotein, chloroplastic OS=Nicotiana sylvestris PE=1 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 39/59 (66%)

Query: 39  LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNT 97
           + +A ++ D+   RS+G+G+VT S+E E  +A+A+++G+ LDGR I V+      R NT
Sbjct: 217 VVSARVVFDRESGRSRGFGFVTMSSEAEMSEAIANLDGQTLDGRTIRVNAAEERPRRNT 275

Probably involved in the 3'-end processing of chloroplast mRNA's.

Nicotiana sylvestris (taxid: 4096)

>sp|Q98SP8|EPABA_XENLA Embryonic polyadenylate-binding protein A OS=Xenopus laevis GN=epabp-a PE=1 SV=2

 Score = 53.5 bits (127), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 45/72 (62%), Gaps = 3/72 (4%)

Query: 40  FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA 99
            +  ++MD    RS+G+G+V +   EEAQKA+++MNGK ++GR+I+V   R  +R    +
Sbjct: 218 LSVKVMMDDS-GRSRGFGFVNYGNHEEAQKAVSEMNGKEVNGRMIYVG--RAQKRIERQS 274

Query: 100 PLARQSAQSPEE 111
            L R+  Q  +E
Sbjct: 275 ELKRKFEQIKQE 286

Binds and protects the poly(A) tail of mRNA with or without an AU-rich element (ARE) and prevents mRNA deadenylation. Stimulates the translation of mRNAs to which it is bound during early development.

Xenopus laevis (taxid: 8355)

>sp|Q9LIS2|RBG4_ARATH Glycine-rich RNA-binding protein 4, mitochondrial OS=Arabidopsis thaliana GN=RBG4 PE=2 SV=1

 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 44/86 (51%), Gaps = 27/86 (31%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L  AF+ FG+VTE                           AT+I D+   RS+G+G+V+F
Sbjct: 51  LKQAFTSFGEVTE---------------------------ATVIADRETGRSRGFGFVSF 83

Query: 62  STEEEAQKALADMNGKLLDGRVIFVD 87
           S E+ A  A+ +M+GK L+GR I V+
Sbjct: 84  SCEDSANNAIKEMDGKELNGRQIRVN 109

Possibly has a role in RNA transcription or processing during stress. Binds sequence non-specifically to RNAs and DNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6DEY7|EPAB_XENTR Embryonic polyadenylate-binding protein OS=Xenopus tropicalis GN=epabp PE=2 SV=1

 Score = 53.1 bits (126), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 3/72 (4%)

Query: 40  FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA 99
            +  ++MD    RS+G+G+V +   EEAQKA+++MNGK ++GR+I+V   R  +R     
Sbjct: 218 LSVKVMMDD-TGRSRGFGFVNYGNHEEAQKAVSEMNGKEVNGRMIYVG--RAQKRIERQG 274

Query: 100 PLARQSAQSPEE 111
            L R+  Q  +E
Sbjct: 275 ELKRKFEQIKQE 286

Binds and protects the poly(A) tail of mRNA with or without an AU-rich element (ARE) and prevents mRNA deadenylation. Stimulates the translation of mRNAs to which it is bound during early development.

Xenopus tropicalis (taxid: 8364)

>sp|Q6GR16|EPABB_XENLA Embryonic polyadenylate-binding protein B OS=Xenopus laevis GN=epabp-b PE=2 SV=1

 Score = 52.8 bits (125), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 43/72 (59%), Gaps = 3/72 (4%)

Query: 40  FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA 99
            +  ++MD    RS+G+G+V +   EEAQKA+ +MNGK ++GR+++V   R  +R     
Sbjct: 218 LSVKVMMDNS-GRSRGFGFVNYGNHEEAQKAVTEMNGKEVNGRMVYVG--RAQKRIERQG 274

Query: 100 PLARQSAQSPEE 111
            L R+  Q  +E
Sbjct: 275 ELKRKFEQIKQE 286

Binds and protects the poly(A) tail of mRNA with or without an AU-rich element (ARE) and prevents mRNA deadenylation. Stimulates the translation of mRNAs to which it is bound during early development.

Xenopus laevis (taxid: 8355)

>sp|Q43349|ROC2_ARATH 29 kDa ribonucleoprotein, chloroplastic OS=Arabidopsis thaliana GN=RBP29 PE=1 SV=2

 Score = 52.4 bits (124), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 26/54 (48%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 42  ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD--NVRPSR 93
           A +I D+   RSKG+G+VT S+ +E QKA+  +NG  LDGR I V     RP R
Sbjct: 286 ARVIYDRDSGRSKGFGFVTLSSSQEVQKAINSLNGADLDGRQIRVSEAEARPPR 339

Could be involved in splicing and/or processing of chloroplast RNA's.

Arabidopsis thaliana (taxid: 3702)

>sp|P27476|NSR1_YEAST Nuclear localization sequence-binding protein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NSR1 PE=1 SV=1

 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 33/49 (67%)

Query: 39  LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           +  A +I ++G +RS+GYGYV F  +  A+KA+ +M GK +DGR I  D
Sbjct: 194 VIGARVIYERGTDRSRGYGYVDFENKSYAEKAIQEMQGKEIDGRPINCD 242

Involved in pre-rRNA processing. Specifically binds nuclear localization sequences. Candidate for a receptor at the nucleus that may be involved in both RNA and protein transport. Binds telomeric sequences of the type (TG[1-3])n in vitro.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9PTX2|CIRBP_LITCT Cold-inducible RNA-binding protein OS=Lithobates catesbeiana GN=cirbp PE=2 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 33/49 (67%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          ++ D+   RS+G+G+VTF   E+A+ A+A MNGK +DGR I VD    S
Sbjct: 37 VVKDRETKRSRGFGFVTFENCEDAKDAMAGMNGKTVDGRQIRVDQAGKS 85

Cold-inducible mRNA binding protein. Acts cooperatively with elavl1/elrA to stabilize AU-rich element (ARE)-containing mRNAs by binding to them and inhibiting their deadenylation. Essential for embryonic gastrulation and neural development, acting to maintain the expression of a set of adhesion molecules, and cell movement during embryogenesis. Required for pronephros development (By similarity). May play a role in hibernation.

Lithobates catesbeiana (taxid: 8400)

>sp|Q9H361|PABP3_HUMAN Polyadenylate-binding protein 3 OS=Homo sapiens GN=PABPC3 PE=1 SV=2

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 33/48 (68%), Gaps = 2/48 (4%)

Query: 39  LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           + +  ++ D+  N SKGYG+V F T E A++A+  MNG LL+GR +FV
Sbjct: 125 ILSCNVVCDE--NGSKGYGFVHFETHEAAERAIKKMNGMLLNGRKVFV 170

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Binds poly(A) with a slightly lower affinity as compared to PABPC1.

Homo sapiens (taxid: 9606)

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	112
224091949	139	predicted protein [Populus trichocarpa]	0.669	0.539	0.401	9e-13
255579369	127	RNA binding protein, putative [Ricinus c	0.669	0.590	0.401	1e-12
359482021	133	PREDICTED: glycine-rich RNA-binding prot	0.669	0.563	0.401	2e-12
449500867	134	PREDICTED: glycine-rich RNA-binding prot	0.723	0.604	0.378	5e-12
449462934	134	PREDICTED: glycine-rich RNA-binding prot	0.723	0.604	0.378	6e-12
351724633	113	uncharacterized protein LOC100527061 [Gl	0.580	0.575	0.445	1e-11
388502672	140	unknown [Medicago truncatula]	0.669	0.535	0.372	1e-11
255565709	121	Cold-inducible RNA-binding protein, puta	0.544	0.504	0.431	2e-11
361067299	84	Pinus taeda anonymous locus 0_15424_01 g	0.642	0.857	0.363	3e-11
357167535	137	PREDICTED: 40S ribosomal protein S19, mi	0.660	0.540	0.411	5e-11

>gi|224091949|ref|XP_002309412.1| predicted protein [Populus trichocarpa] gi|222855388|gb|EEE92935.1| predicted protein [Populus trichocarpa]

 Score = 77.4 bits (189), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 41/102 (40%), Positives = 59/102 (57%), Gaps = 27/102 (26%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L++AFSQ+GQV E                           A I+MD+  +RSKG+G+VT+
Sbjct: 55  LSEAFSQYGQVVE---------------------------AKIVMDRALDRSKGFGFVTY 87

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLAR 103
           ++E+EAQKAL +MNGK L+GRVI+VD  +    +    P+AR
Sbjct: 88  ASEDEAQKALDEMNGKALNGRVIYVDYAKLKTNFGGGIPIAR 129

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579369|ref|XP_002530529.1| RNA binding protein, putative [Ricinus communis] gi|223529933|gb|EEF31861.1| RNA binding protein, putative [Ricinus communis]

 Score = 77.0 bits (188), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 41/102 (40%), Positives = 58/102 (56%), Gaps = 27/102 (26%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L +AFSQ+GQV E                           ATI+ D+  +RSKG+G+VTF
Sbjct: 47  LTEAFSQYGQVVE---------------------------ATIVSDRVLDRSKGFGFVTF 79

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLAR 103
           ++E+EA  AL++MNGK L+GRVI+VD  +P      + P+AR
Sbjct: 80  ASEDEAHNALSEMNGKTLNGRVIYVDYAKPRTDSRNEVPIAR 121

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482021|ref|XP_002276063.2| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Vitis vinifera] gi|297740158|emb|CBI30340.3| unnamed protein product [Vitis vinifera]

 Score = 76.3 bits (186), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/102 (40%), Positives = 57/102 (55%), Gaps = 27/102 (26%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L++ FSQ+GQV E                           A I+MD+  +RSKG+G+VTF
Sbjct: 50  LSEHFSQYGQVVE---------------------------AKIVMDRVSDRSKGFGFVTF 82

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLAR 103
           ++EEEAQKA  +M+GK L+GR IFVD  +P   +    P+AR
Sbjct: 83  ASEEEAQKARTEMDGKELNGRTIFVDYAKPRADFGGGMPIAR 124

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449500867|ref|XP_004161215.1| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Cucumis sativus]

 Score = 75.1 bits (183), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 42/111 (37%), Positives = 62/111 (55%), Gaps = 30/111 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L++AFSQ+GQV E                           AT++MD+  ++SKG+G+VTF
Sbjct: 51  LSEAFSQYGQVIE---------------------------ATVVMDRVSDKSKGFGFVTF 83

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN 112
           ++ +EA  AL++MNGK L+GRVIFV+  +P+       P+AR     PEE 
Sbjct: 84  ASLDEAHTALSEMNGKPLNGRVIFVNYAKPTTSSRGAIPIAR---GPPEEK 131

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449462934|ref|XP_004149190.1| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Cucumis sativus]

 Score = 74.7 bits (182), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 42/111 (37%), Positives = 62/111 (55%), Gaps = 30/111 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L++AFSQ+GQV E                           AT++MD+  ++SKG+G+VTF
Sbjct: 51  LSEAFSQYGQVIE---------------------------ATVVMDRVSDKSKGFGFVTF 83

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN 112
           ++ +EA  AL++MNGK L+GRVIFV+  +P+       P+AR     PEE 
Sbjct: 84  ASLDEAHTALSEMNGKPLNGRVIFVNYAKPTTSSRGAIPIAR---GPPEEK 131

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724633|ref|NP_001238088.1| uncharacterized protein LOC100527061 [Glycine max] gi|255631468|gb|ACU16101.1| unknown [Glycine max]

 Score = 73.9 bits (180), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/92 (44%), Positives = 50/92 (54%), Gaps = 27/92 (29%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           LA AFSQ+G V                             A II++K KNRSKG+GYV F
Sbjct: 49  LAKAFSQYGSV---------------------------LKANIILNKAKNRSKGFGYVIF 81

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
           + EEEA KA  DMNGK+L GRVI+VD   P++
Sbjct: 82  AKEEEACKAQIDMNGKILHGRVIYVDVQLPNK 113

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502672|gb|AFK39402.1| unknown [Medicago truncatula]

 Score = 73.6 bits (179), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 38/102 (37%), Positives = 57/102 (55%), Gaps = 27/102 (26%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L+DAFS +GQV E                           A +I D+   +SKGYG+VTF
Sbjct: 48  LSDAFSNYGQVVE---------------------------AKVITDRISEKSKGYGFVTF 80

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLAR 103
           ++++EA+KA+ +MN K L+GRV+FVD  +P  + +   P+AR
Sbjct: 81  ASQDEAEKAITEMNEKALNGRVVFVDYAKPDTKRSMGMPIAR 122

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565709|ref|XP_002523844.1| Cold-inducible RNA-binding protein, putative [Ricinus communis] gi|223536932|gb|EEF38570.1| Cold-inducible RNA-binding protein, putative [Ricinus communis]

 Score = 73.2 bits (178), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 49/88 (55%), Gaps = 27/88 (30%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L +AFS+FG++ E                             II DK  +R KGY YVTF
Sbjct: 50  LTEAFSKFGEIVE---------------------------VNIIKDKAMDRPKGYAYVTF 82

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNV 89
           +TE EA+KAL +MNGK++DGR +FVDNV
Sbjct: 83  ATENEAKKALTEMNGKVIDGRPVFVDNV 110

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|361067299|gb|AEW07961.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126579|gb|AFG43909.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126581|gb|AFG43910.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126583|gb|AFG43911.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126585|gb|AFG43912.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126587|gb|AFG43913.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126589|gb|AFG43914.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence gi|383126591|gb|AFG43915.1| Pinus taeda anonymous locus 0_15424_01 genomic sequence

 Score = 72.4 bits (176), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/99 (36%), Positives = 56/99 (56%), Gaps = 27/99 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L +AFS+FG+V E                             I+MD+   RSKG+G+V +
Sbjct: 4   LTEAFSRFGEVVE---------------------------VKIVMDRVSQRSKGFGFVQY 36

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           ++E +A++A A+MNGK+L GR+IFVD+V+P  + + D P
Sbjct: 37  ASEADAERAKAEMNGKVLSGRIIFVDDVKPKSQLSGDLP 75

Source: Pinus lambertiana

Species: Pinus lambertiana

Genus: Pinus

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357167535|ref|XP_003581210.1| PREDICTED: 40S ribosomal protein S19, mitochondrial-like [Brachypodium distachyon]

 Score = 72.0 bits (175), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 42/102 (41%), Positives = 58/102 (56%), Gaps = 28/102 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           LA+AF+++GQV E                           ATI+ DK  NRSKG+G+V F
Sbjct: 52  LAEAFARYGQVLE---------------------------ATIVTDKMTNRSKGFGFVKF 84

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA-PLA 102
           ++EEEA KA  +MNGK+L+GRVI+VD  +  +   TD  P+A
Sbjct: 85  ASEEEANKARDEMNGKVLNGRVIYVDIAKAKQDRATDVLPIA 126

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	112
TAIR|locus:2049816	142	AT2G37510 [Arabidopsis thalian	0.616	0.485	0.513	1.2e-14
TAIR|locus:2160752	146	AT5G06210 [Arabidopsis thalian	0.553	0.424	0.468	2.1e-13
TAIR|locus:2206850	181	AT1G73530 [Arabidopsis thalian	0.464	0.287	0.5	7.4e-12
TAIR|locus:2077137	102	AT3G46020 [Arabidopsis thalian	0.410	0.450	0.478	4.9e-11
TAIR|locus:2172144	156	AT5G54580 [Arabidopsis thalian	0.526	0.378	0.389	1.6e-10
ASPGD|ASPL0000040642	128	AN2989 [Emericella nidulans (t	0.473	0.414	0.436	2.6e-10
TAIR|locus:2076096	136	GRP4 "glycine-rich RNA-binding	0.410	0.338	0.478	2.6e-10
TAIR|locus:2039590	116	AT2G27330 [Arabidopsis thalian	0.491	0.474	0.472	4.1e-10
UNIPROTKB|F6RBQ9	160	F6RBQ9 "Uncharacterized protei	0.455	0.318	0.431	4.2e-10
UNIPROTKB|K7ENX8	89	CIRBP "Cold-inducible RNA-bind	0.437	0.550	0.46	4.2e-10

TAIR|locus:2049816 AT2G37510 [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 1.2e-14, Sum P(2) = 1.2e-14
 Identities = 37/72 (51%), Positives = 48/72 (66%)

Query:    39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS--RRYN 96
             L  A +I D+   RSKG+G+VT++T E+A+KA A+MN K LDG VIFVD  RP   RR  
Sbjct:    60 LVDARVITDRDSGRSKGFGFVTYATIEDAEKAKAEMNAKFLDGWVIFVDPARPREPRRPL 119

Query:    97 TDAPLARQSAQS 108
                PL R S++S
Sbjct:   120 QQEPL-RPSSES 130

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2160752 AT5G06210 [Arabidopsis thaliana (taxid:3702)]

 Score = 148 (57.2 bits), Expect = 2.1e-13, Sum P(2) = 2.1e-13
 Identities = 30/64 (46%), Positives = 44/64 (68%)

Query:    42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA-- 99
             A I+MD+  +RSKG+G+VTF++ +EAQKAL + NG+ L+GR IFVD  +  +        
Sbjct:    63 AQIVMDRVSDRSKGFGFVTFASADEAQKALMEFNGQQLNGRTIFVDYAKAKQSLGGGGGY 122

Query:   100 PLAR 103
             P+AR
Sbjct:   123 PIAR 126

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2206850 AT1G73530 [Arabidopsis thaliana (taxid:3702)]

 Score = 140 (54.3 bits), Expect = 7.4e-12, Sum P(2) = 7.4e-12
 Identities = 26/52 (50%), Positives = 36/52 (69%)

Query:    39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR 90
             L    ++MDK  NR KG+ ++ + TEEEA KA+  M+GK LDGRVIFV+  +
Sbjct:   103 LIHMNMVMDKVANRPKGFAFLRYETEEEAMKAIQGMHGKFLDGRVIFVEEAK 154

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2077137 AT3G46020 [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 4.9e-11, Sum P(2) = 4.9e-11
 Identities = 22/46 (47%), Positives = 36/46 (78%)

Query:    42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
             A +I D    R KG+G++TF +E++A+KAL  ++GK++DGR+IFV+
Sbjct:    36 ARLIRDSETQRPKGFGFITFDSEDDARKALKSLDGKIVDGRLIFVE 81

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2172144 AT5G54580 [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 1.6e-10, Sum P(2) = 1.6e-10
 Identities = 23/59 (38%), Positives = 37/59 (62%)

Query:    42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
             A ++ D+    SKG+G+V ++T E++ K +A M+GK LDG VIF +  RP  +  +  P
Sbjct:    85 AKVVTDRVSGYSKGFGFVRYATLEDSAKGIAGMDGKFLDGWVIFAEYARPREQSQSYQP 143

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

ASPGD|ASPL0000040642 AN2989 [Emericella nidulans (taxid:162425)]

 Score = 123 (48.4 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 24/55 (43%), Positives = 36/55 (65%)

Query:    42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV--RPSRR 94
             A ++ D+  NRS+G+G+V F++E EA  A+  MN +  DGR+I VD    RP+ R
Sbjct:    31 AVVVKDRDTNRSRGFGFVRFASEPEADAAMGAMNNQEFDGRIIRVDKASERPAAR 85

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

TAIR|locus:2076096 GRP4 "glycine-rich RNA-binding protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 115 (45.5 bits), Expect = 2.6e-10, Sum P(2) = 2.6e-10
 Identities = 22/46 (47%), Positives = 34/46 (73%)

Query:    42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
             AT+I D+   RS+G+G+V+FS E+ A  A+ +M+GK L+GR I V+
Sbjct:    64 ATVIADRETGRSRGFGFVSFSCEDSANNAIKEMDGKELNGRQIRVN 109

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005739 "mitochondrion" evidence=IDA

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

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

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

GO:0009409 "response to cold" evidence=IEP

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

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0009664 "plant-type cell wall organization" evidence=RCA

GO:0042545 "cell wall modification" evidence=RCA

TAIR|locus:2039590 AT2G27330 [Arabidopsis thaliana (taxid:3702)]

 Score = 144 (55.7 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 26/55 (47%), Positives = 41/55 (74%)

Query:    44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
             +IMDK + R KG+ YVTFS++EEA+KAL ++N +L+DGRV+ +D  + ++    D
Sbjct:    52 VIMDKIRCRPKGFAYVTFSSKEEAEKALLELNAQLVDGRVVILDTTKAAKHNPPD 106

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F6RBQ9 F6RBQ9 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 117 (46.2 bits), Expect = 4.2e-10, Sum P(2) = 4.2e-10
 Identities = 22/51 (43%), Positives = 33/51 (64%)

Query:    44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
             ++ D+   RS+G+G++TF+  E A  A+  MNG+ LDGR I VD+   S R
Sbjct:    37 VVKDRETQRSRGFGFITFTNPEHASNAMRAMNGESLDGRQIRVDHAGKSAR 87

GO:0043023 "ribosomal large subunit binding" evidence=IEA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=IEA

GO:0009409 "response to cold" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|K7ENX8 CIRBP "Cold-inducible RNA-binding protein" [Homo sapiens (taxid:9606)]

 Score = 117 (46.2 bits), Expect = 4.2e-10, Sum P(2) = 4.2e-10
 Identities = 23/50 (46%), Positives = 35/50 (70%)

Query:    44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN-VRPS 92
             ++ D+   RS+G+G+VTF   ++A+ A+  MNGK +DGR I VD  +RPS
Sbjct:    37 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQPLRPS 86

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Your Input:
	estExt_fgenesh4_pg.C_LG_VI1354	hypothetical protein (140 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0049021701	hypothetical protein (272 aa)			•						0.501
	gw1.232.53.1	hypothetical protein (203 aa)			•						0.494
	gw1.XV.2574.1	hypothetical protein (203 aa)			•						0.490
	eugene3.00050125	hypothetical protein (218 aa)			•						0.488
	estExt_fgenesh4_pg.C_LG_VII0461	hypothetical protein (218 aa)			•						0.485
	gw1.VIII.2127.1	hypothetical protein (133 aa)			•						0.476
	gw1.X.2172.1	hypothetical protein (232 aa)			•						0.459
	estExt_fgenesh4_kg.C_LG_X0007	SubName- Full=Putative uncharacterized protein; (252 aa)			•						0.458
	gw1.XVI.1974.1	hypothetical protein (131 aa)			•						0.438
	eugene3.00170125	hypothetical protein (199 aa)			•						0.409

---

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	112
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-15
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-15
smart00360	73	smart00360, RRM, RNA recognition motif	2e-14
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-12
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-11
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-11
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-11
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	5e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-10
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	4e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-09
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	4e-09
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	6e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	4e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-07
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	4e-07
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-07
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	7e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-07
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	9e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-06
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-06
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	2e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	4e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	9e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	2e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-05
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	4e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	4e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	4e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	4e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	6e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	6e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	8e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	8e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	8e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	9e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	9e-05
smart00361	70	smart00361, RRM_1, RNA recognition motif	1e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-04
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	1e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	2e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-04
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	2e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	2e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-04
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-04
cd12287	102	cd12287, RRM_U2AF35_like, RNA recognition motif in	3e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	4e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	5e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	6e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	6e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	6e-04
COG5175	480	COG5175, MOT2, Transcriptional repressor [Transcri	7e-04
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	7e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	7e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	8e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	8e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	8e-04
cd12539	103	cd12539, RRM_U2AF35B, RNA recognition motif in spl	8e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	9e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.001
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.001
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.001
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.001
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	0.001
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.001
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	0.001
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.001
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.002
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.002
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.002
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.002
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.002
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.002
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.002
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.002
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.002
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.003
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.003
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.003
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.003
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	0.003
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.004
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.004
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	0.004
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.004
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.004
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.004
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	0.004

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

 Score = 64.7 bits (158), Expect = 3e-15
 Identities = 24/46 (52%), Positives = 33/46 (71%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          A +I D+   RS+G+GYV F + E+A+KA+  M+GK LDGR I VD
Sbjct: 29 ARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVD 74

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

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

 Score = 64.2 bits (157), Expect = 4e-15
 Identities = 28/90 (31%), Positives = 38/90 (42%), Gaps = 27/90 (30%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L D F QFG+VT                            A +I D+   RS+G+G+V  
Sbjct: 16 LKDLFGQFGEVTS---------------------------ARVITDRETGRSRGFGFVEM 48

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           T EEA  A+  +NG    GR + V+  RP
Sbjct: 49 ETAEEANAAIEKLNGTDFGGRTLTVNEARP 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|214636 smart00360, RRM, RNA recognition motif

 Score = 62.6 bits (153), Expect = 2e-14
 Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 27/86 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L + FS+FG+V                               ++ DK   +SKG+ +V 
Sbjct: 15 ELRELFSKFGKVES---------------------------VRLVRDKETGKSKGFAFVE 47

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFV 86
          F +EE+A+KAL  +NGK LDGR + V
Sbjct: 48 FESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>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 = 57.2 bits (138), Expect = 2e-12
 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 27/91 (29%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   FS++GQ++E                             ++ D+   RS+G+G+VTF
Sbjct: 17 LEQVFSKYGQISE---------------------------VVVVKDRETQRSRGFGFVTF 49

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
             ++A+ A+  MNGK +DGR I VD    S
Sbjct: 50 ENPDDAKDAMMAMNGKSVDGRQIRVDQAGKS 80

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

 Score = 56.1 bits (136), Expect = 7e-12
 Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 28/85 (32%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + FS FG +T                            +  +M   K RSKG+G+V F
Sbjct: 18 LREEFSPFGTIT----------------------------SAKVMTDEKGRSKGFGFVCF 49

Query: 62 STEEEAQKALADMNGKLLDGRVIFV 86
          S+ EEA KA+ +MNG+++ G+ ++V
Sbjct: 50 SSPEEATKAVTEMNGRIIGGKPLYV 74

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

 Score = 55.0 bits (133), Expect = 1e-11
 Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 28/87 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L + FS+FG++                                I+     +SKG+ +V 
Sbjct: 14 DLRELFSKFGEIES----------------------------VRIVRDKDGKSKGFAFVE 45

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          F + E+A+KAL  +NGK LDGR + V 
Sbjct: 46 FESPEDAEKALEALNGKELDGRKLKVS 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|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 = 55.3 bits (134), Expect = 2e-11
 Identities = 20/44 (45%), Positives = 31/44 (70%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          ++ D     S+G+G+VTF + E+A  A+ D+NGK L+GRVI V+
Sbjct: 33 LMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEGRVIKVE 76

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

 Score = 54.9 bits (133), Expect = 2e-11
 Identities = 18/44 (40%), Positives = 29/44 (65%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          ++ DKG  + +G+GYVTF+ EE+A++AL +       GR I V+
Sbjct: 31 VVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVE 74

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

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

 Score = 54.5 bits (132), Expect = 3e-11
 Identities = 18/37 (48%), Positives = 25/37 (67%)

Query: 50 KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
             SKGYG+V F TEE A +A+  +NG LL+ + +FV
Sbjct: 39 NGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDKKVFV 75

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

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

 Score = 53.9 bits (130), Expect = 4e-11
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 27/83 (32%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L  AF+ FG++++                           A ++ D    +SKGYG+V+F
Sbjct: 16 LRAAFAPFGEISD---------------------------ARVVKDMQTGKSKGYGFVSF 48

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
            +E+A+ A+  MNG+ L GR I
Sbjct: 49 VKKEDAENAIQSMNGQWLGGRAI 71

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

 Score = 55.4 bits (133), Expect = 5e-11
 Identities = 31/93 (33%), Positives = 46/93 (49%), Gaps = 29/93 (31%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L DAF+ FG V +                           A +I+D+   RS+G+G+V F
Sbjct: 51  LRDAFAHFGDVVD---------------------------AKVIVDRETGRSRGFGFVNF 83

Query: 62  STEEEAQKALADMNGKLLDGRVIFVD--NVRPS 92
           + E  A  A+++M+GK L+GR I V+  N RPS
Sbjct: 84  NDEGAATAAISEMDGKELNGRHIRVNPANDRPS 116

Length = 144

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

 Score = 52.7 bits (127), Expect = 1e-10
 Identities = 23/43 (53%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          I      RSKG+G+V F+TEE AQKAL   +G+ L GR I VD
Sbjct: 31 IAQDDDGRSKGFGHVEFATEEGAQKALE-KSGEELLGREIRVD 72

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

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

 Score = 51.8 bits (125), Expect = 2e-10
 Identities = 26/84 (30%), Positives = 36/84 (42%), Gaps = 28/84 (33%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L D FS+FG +                               I+ D+   RSKG+ +V 
Sbjct: 14 DLKDLFSKFGPIES---------------------------IRIVRDETG-RSKGFAFVE 45

Query: 61 FSTEEEAQKALADMNGKLLDGRVI 84
          F  EE+A+KAL  +NGK L GR +
Sbjct: 46 FEDEEDAEKALEALNGKELGGREL 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 52.2 bits (126), Expect = 3e-10
 Identities = 17/42 (40%), Positives = 30/42 (71%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +M   + +SKG+G+V F   E AQKA+ ++NGK ++G+ ++V
Sbjct: 33 VMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKKLYV 74

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

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

 Score = 51.9 bits (125), Expect = 3e-10
 Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 24/86 (27%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   FS++G++ +   + + KS PL                       K + +GY +VTF
Sbjct: 16 LLKLFSKYGKI-KKFDFLFHKSGPL-----------------------KGQPRGYCFVTF 51

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
           T+EEA+KAL  +NGK   G+ + V 
Sbjct: 52 ETKEEAEKALKSLNGKTALGKKLVVR 77

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

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

 Score = 51.4 bits (124), Expect = 4e-10
 Identities = 16/41 (39%), Positives = 27/41 (65%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +D+  N  +GY YV F + E+A+KA+  M+G  +DG+ + V
Sbjct: 32 IDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTV 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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 51.5 bits (124), Expect = 4e-10
 Identities = 19/43 (44%), Positives = 26/43 (60%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++MD    RSKGYG+V F  E+E  +AL +MNG     R +
Sbjct: 32 AKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRPM 74

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

 Score = 50.3 bits (121), Expect = 1e-09
 Identities = 20/44 (45%), Positives = 27/44 (61%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           +  D    RSKGYG++ F+  E+A+KAL  +NG  L GR I V
Sbjct: 29 QLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKV 72

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

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

 Score = 50.3 bits (121), Expect = 1e-09
 Identities = 18/46 (39%), Positives = 30/46 (65%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
            ++ D+   RS+G+G+V F + E+A++A   +NG  +DGR I VD
Sbjct: 29 VQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRIRVD 74

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

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

 Score = 48.8 bits (117), Expect = 4e-09
 Identities = 19/45 (42%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          A +  D    RSKG+G V F + E+AQ+A+   NG  L+GR + V
Sbjct: 28 ADVKTDND-GRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEV 71

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

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

 Score = 48.8 bits (117), Expect = 6e-09
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 12/73 (16%)

Query: 12 VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 71
          VT++++   F   P           SF   A ++ DK   +SKGYG+V+FS   +  KA+
Sbjct: 18 VTDEVLARAFSKYP-----------SFQ-KAKVVRDKRTGKSKGYGFVSFSDPNDYLKAM 65

Query: 72 ADMNGKLLDGRVI 84
           +MNGK +  R I
Sbjct: 66 KEMNGKYVGNRPI 78

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

 Score = 48.4 bits (116), Expect = 6e-09
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 28/78 (35%)

Query: 6  FSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEE 65
          FSQFG++ E                           A +I D+   +S+GYG+VTF  +E
Sbjct: 21 FSQFGEIEE---------------------------AVVITDRQTGKSRGYGFVTFKDKE 53

Query: 66 EAQKALADMNGKLLDGRV 83
           A++A  D N  ++DGR 
Sbjct: 54 SAERACKDPN-PIIDGRK 70

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

 Score = 51.1 bits (121), Expect = 8e-09
 Identities = 18/69 (26%), Positives = 42/69 (60%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLAR 103
           ++ D+   +S+G+ +V F +EE A+KA+ ++NGK L+GR + V   +P+ +  ++     
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNL 206

Query: 104 QSAQSPEEN 112
            ++ + + +
Sbjct: 207 DASFAKKLS 215

Length = 306

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

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 19/44 (43%), Positives = 26/44 (59%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          +  D    R KG+GYV FS++E AQ AL  + G  L GR + +D
Sbjct: 30 LPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLLGRPVRLD 73

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

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

 Score = 47.1 bits (112), Expect = 2e-08
 Identities = 18/43 (41%), Positives = 30/43 (69%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++ D    RS+GYG+V+F ++++A+ A+ +MNGK L  R I
Sbjct: 29 ARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPI 71

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

 Score = 47.2 bits (113), Expect = 2e-08
 Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 5/51 (9%)

Query: 39 LFAATII-----MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          + + TI         GK  S GYG+V F ++E AQKAL  + G +LDG  +
Sbjct: 27 VRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRLQGTVLDGHAL 77

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

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

 Score = 47.3 bits (113), Expect = 2e-08
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          II +K   +S GYG+V F+T E A++AL  +NGK +     
Sbjct: 31 IIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQQ 71

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

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

 Score = 47.1 bits (112), Expect = 2e-08
 Identities = 20/46 (43%), Positives = 31/46 (67%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          A ++ D     S+GYG+VTF+  E+AQ+ALA +  K L GR++ +D
Sbjct: 29 AVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRLD 74

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

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

 Score = 46.9 bits (112), Expect = 3e-08
 Identities = 15/40 (37%), Positives = 27/40 (67%)

Query: 48 KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          K   + KG+ +V F+++ +A+KA+  +NGK + GR + VD
Sbjct: 34 KPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRPVAVD 73

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

 Score = 46.5 bits (111), Expect = 3e-08
 Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 1/40 (2%)

Query: 48 KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
            K +SKGY YV F  EE  Q+AL  ++ +L+ GR +FV 
Sbjct: 34 NYKGKSKGYAYVEFENEESVQEALK-LDRELIKGRPMFVS 72

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

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

 Score = 46.0 bits (110), Expect = 4e-08
 Identities = 15/41 (36%), Positives = 29/41 (70%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          + + + K+R +G+ +V F++ E+A+ AL  +NG +LDGR +
Sbjct: 28 VRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

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

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

 Score = 46.1 bits (110), Expect = 4e-08
 Identities = 16/43 (37%), Positives = 28/43 (65%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          + +DK   RSKG+ +V+F   E A KA ++++G +  GR++ V
Sbjct: 31 LPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQGRLLHV 73

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

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

 Score = 49.0 bits (117), Expect = 4e-08
 Identities = 17/42 (40%), Positives = 30/42 (71%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           +M   K  S+G+G+V FS  EEA +A+ +M+G++L G+ ++V
Sbjct: 317 VMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

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|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 45.9 bits (109), Expect = 7e-08
 Identities = 15/36 (41%), Positives = 26/36 (72%)

Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          SKG+G+VTF+   +A +A   ++G +++GR I V+N
Sbjct: 39 SKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNN 74

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|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 = 44.8 bits (107), Expect = 1e-07
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 27/72 (37%)

Query: 6  FSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEE 65
          F ++G + E                            TII DK   +SKG  +V FS+ E
Sbjct: 20 FEEYGNIEE---------------------------VTIIRDKDTGQSKGCAFVKFSSRE 52

Query: 66 EAQKALADMNGK 77
          EAQKA+  ++GK
Sbjct: 53 EAQKAIEALHGK 64

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

 Score = 44.9 bits (107), Expect = 1e-07
 Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          II D+   RSKG  YV F  EE    AL  + G+ L G+ I V
Sbjct: 31 IIRDRNSRRSKGVAYVEFYDEESVPLALG-LTGQRLLGQPIMV 72

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

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

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +I D   N+ KGYG+VT +  EEA  A+A +NG  L GRV+ V
Sbjct: 33 VIRDLTTNKCKGYGFVTMTNYEEAYSAIASLNGYRLGGRVLQV 75

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

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

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 14/34 (41%), Positives = 23/34 (67%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD 80
          DK   +S+G+ +VTF T E+A++A+  +NG   D
Sbjct: 34 DKETGQSRGFAFVTFHTREDAERAIEKLNGFGYD 67

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

 Score = 43.7 bits (104), Expect = 3e-07
 Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + FS++G+V +                             I+ D    RS+G+G+VTF
Sbjct: 15 LREYFSKYGEVVD---------------------------CVIMKDPITGRSRGFGFVTF 47

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
          +      K LA     +LDGR I
Sbjct: 48 ADPSSVDKVLAAKP-HVLDGREI 69

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|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 43.8 bits (104), Expect = 4e-07
 Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 1/36 (2%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
           A +++D+  N S+GYG+V FS E E ++AL +M G
Sbjct: 31 GAKVVLDQNGN-SRGYGFVRFSDESEQKRALTEMQG 65

This subgroup corresponds to the RRM2 of SECp43, 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. . Length = 82

>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 = 43.7 bits (103), Expect = 4e-07
 Identities = 18/46 (39%), Positives = 27/46 (58%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +A I+ D     S+GYG+V FS E + Q+AL +M G    GR + +
Sbjct: 31 SAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRI 76

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

 Score = 45.6 bits (108), Expect = 7e-07
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 52  RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN-VRPSRRYNTDAP 100
           +S+GYG+V F  EE A+ A+  +NG LL+ + ++V   ++   R      
Sbjct: 127 KSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLK 176

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

 Score = 43.3 bits (102), Expect = 7e-07
 Identities = 19/36 (52%), Positives = 23/36 (63%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           SKG  Y+ F TE EA+KAL +  G  +DGR I VD
Sbjct: 39 SSKGIAYIEFKTEAEAEKALEEKQGAEVDGRSIVVD 74

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

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

 Score = 42.7 bits (101), Expect = 8e-07
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          I  D+    S+G+ +V F  + +A+ A+  M+GK LDGR + V 
Sbjct: 30 IPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRELRVQ 73

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

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

 Score = 43.0 bits (102), Expect = 8e-07
 Identities = 16/44 (36%), Positives = 25/44 (56%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          +I DK    S  Y ++ F T+E+ ++A   M+  L+D R I VD
Sbjct: 35 VIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHVD 78

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

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 42.9 bits (101), Expect = 9e-07
 Identities = 20/46 (43%), Positives = 29/46 (63%), Gaps = 3/46 (6%)

Query: 49 GKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          G+  S G+G+V F T+E+AQ AL  M+G +LDG  +    V+ S R
Sbjct: 42 GQTLSMGFGFVGFKTKEQAQAALKAMDGFVLDGHTL---VVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 26/87 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L D FS FG +                          L    I+ D     SKG+ +++
Sbjct: 17 LLYDTFSAFGVI--------------------------LQTPKIMRDPDTGNSKGFAFIS 50

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          + + E +  A+  MNG+ L  R I V 
Sbjct: 51 YDSFEASDAAIEAMNGQYLCNRPITVS 77

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

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +K    + G+ +VTF     A+ AL  +NG  L GR I V
Sbjct: 38 EKQGRLNNGFAFVTFKDASSAENALQ-LNGTELGGRKISV 76

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

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

 Score = 42.1 bits (100), Expect = 1e-06
 Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 3/44 (6%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          I + K K    G+ +V FSTEE A+KA+  +NG L  GR + VD
Sbjct: 14 IKLLKKK---PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

(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|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-06
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
          A + +DK   +SK +G+V++   E AQ A+  MNG  + G+
Sbjct: 28 AKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK 68

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

 Score = 41.9 bits (99), Expect = 2e-06
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          TI+ DK   +SKG  ++ F   E+A K +  +N K L GR +
Sbjct: 32 TIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTL 73

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

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

 Score = 42.2 bits (100), Expect = 2e-06
 Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 1/30 (3%)

Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          YV F  EE A+KAL  +NG   +G  I VD
Sbjct: 63 YVVFKEEESAEKALK-LNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

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

 Score = 41.5 bits (98), Expect = 2e-06
 Identities = 15/35 (42%), Positives = 24/35 (68%)

Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          SKGYG+V ++++  A KA   ++GK + GR + VD
Sbjct: 40 SKGYGFVEYASKASALKAKNQLDGKQIGGRKLQVD 74

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

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

 Score = 44.1 bits (104), Expect = 3e-06
 Identities = 22/57 (38%), Positives = 29/57 (50%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           +  D    RSKG+G++ F   EEA++AL  MNG  L GR I V   + S      A 
Sbjct: 218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAAN 274

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

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

 Score = 41.8 bits (99), Expect = 3e-06
 Identities = 14/45 (31%), Positives = 25/45 (55%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           ++ DK   + +GY ++ F  E + + A    +GK +DGR + VD
Sbjct: 32 RLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGRRVLVD 76

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

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

 Score = 41.1 bits (97), Expect = 3e-06
 Identities = 15/44 (34%), Positives = 23/44 (52%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           I +D    + +G+ +V F   E+A  A+ +MN   L GR I V
Sbjct: 29 QIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGRTIRV 72

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

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

 Score = 41.0 bits (97), Expect = 4e-06
 Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           I+ D    R  G  YV F++ E+A++AL   N K + GR I V
Sbjct: 31 HIVYDD-DGRPTGEAYVEFASPEDARRALRKHNNK-MGGRYIEV 72

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

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

 Score = 41.0 bits (97), Expect = 4e-06
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 5/54 (9%)

Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK-----LLDGRVIFVD 87
          +  A I+ DK    SKG  +V F T+E AQK L   +        LDGR + V 
Sbjct: 27 VKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVT 80

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

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

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 20/45 (44%), Positives = 24/45 (53%), Gaps = 1/45 (2%)

Query: 42  ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
              I D+   RSKG  YV F   E   KALA + G++L GR I V
Sbjct: 119 VQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIV 162

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

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

 Score = 40.8 bits (96), Expect = 6e-06
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 27/86 (31%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   FS++G+V                             A I+ +     ++ +G+VT 
Sbjct: 16 LKQLFSKYGKVV---------------------------GAKIVTNARSPGARCFGFVTM 48

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
          ++ EEA K +  ++   L GRVI V+
Sbjct: 49 ASVEEAAKCIQHLHRTELHGRVISVE 74

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

 Score = 40.4 bits (95), Expect = 7e-06
 Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          TI+ DK   + KG+ Y+ F  +   + AL  +N     GR I V
Sbjct: 30 TILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESEFRGRQIKV 72

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

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

 Score = 40.5 bits (94), Expect = 7e-06
 Identities = 19/52 (36%), Positives = 30/52 (57%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          +A +I DK    S GYG+V +   ++A++A+  +NG  L  + I V   RPS
Sbjct: 30 SAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTIKVSYARPS 81

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 39.9 bits (94), Expect = 9e-06
 Identities = 16/34 (47%), Positives = 23/34 (67%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK 77
           I+DK  N+ KGYG+V F + E A KA+  +NG+
Sbjct: 32 AILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65

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

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

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD----GRVIFVDNVRP-SRRYNTD 98
            +M  G  RS+G+ +V F   E+A KA+ +MNGK +     G+ ++V   +  + R   +
Sbjct: 209 AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAER---E 265

Query: 99  APLARQSAQSPEEN 112
           A L R+  +  +E 
Sbjct: 266 AELRRKFEELQQER 279

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

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          SKGY +V +  E +A +A  D +  ++DG  IFVD
Sbjct: 44 SKGYAFVEYEHERDALRAYRDAHKLVIDGSEIFVD 78

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

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

 Score = 40.1 bits (93), Expect = 1e-05
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++ D    +SKGYG+V+F  + +A+ A+  M G+ L GR I
Sbjct: 31 ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 73

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

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

 Score = 39.7 bits (93), Expect = 1e-05
 Identities = 17/40 (42%), Positives = 22/40 (55%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          D    + KG+ +V +   E AQ AL  MNG +L GR I V
Sbjct: 35 DPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKV 74

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

>gnl|CDD|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 = 39.5 bits (93), Expect = 2e-05
 Identities = 15/44 (34%), Positives = 25/44 (56%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          ++ D+   + KGYG+  F   E A  A+ ++NG   +GR + VD
Sbjct: 30 LVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRALRVD 73

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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 1/43 (2%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          I+ D+     KG+GYV F T++    AL  +NG  L GR I V
Sbjct: 31 IVRDRKTGIGKGFGYVLFKTKDSVALALK-LNGIKLKGRKIRV 72

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

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

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          RS+G   V F   E+A++A+   NG LLDG+ +
Sbjct: 39 RSEGTADVVFEKREDAERAIKQFNGVLLDGQPM 71

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 15/39 (38%), Positives = 23/39 (58%)

Query: 48 KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
            + R  G  Y  FS+ E+A+K + D+NGK+   R +FV
Sbjct: 40 SRRVRPLGIAYAEFSSPEQAEKVVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 39.2 bits (92), Expect = 2e-05
 Identities = 28/93 (30%), Positives = 39/93 (41%), Gaps = 32/93 (34%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L D FS+FG V +                             II D+    SKGYG+VTF
Sbjct: 19 LRDFFSRFGSVKD---------------------------VKIITDR-AGVSKGYGFVTF 50

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           T+E+A+K LA  N      ++    N+ P+ R
Sbjct: 51 ETQEDAEKILAMGNLNFRGKKL----NIGPAIR 79

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

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

 Score = 39.2 bits (91), Expect = 2e-05
 Identities = 20/51 (39%), Positives = 31/51 (60%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          AA I+ D+    SKG+G+V FS+EE+A+ A   M    +DG  + +D  +P
Sbjct: 26 AARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEIDGNKVTLDFAKP 76

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 15/33 (45%), Positives = 21/33 (63%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          K Y +V F   ++A KA+ +MNGK L+G  I V
Sbjct: 35 KDYAFVHFEERDDAVKAMEEMNGKELEGSPIEV 67

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

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 39.1 bits (92), Expect = 3e-05
 Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)

Query: 55 GYG--YVTFSTEEEAQKALADMNGKLLDGRVI 84
          G G  +V F+  E+AQKA   + G+  DGR +
Sbjct: 55 GVGKVFVEFADVEDAQKAQLALAGRKFDGRTV 86

This subfamily corresponds to the RRM3 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 = 89

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

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 19/49 (38%), Positives = 29/49 (59%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          ++ DK   +S GYG+V +   E+A+KA+  +NG  L  + I V   RPS
Sbjct: 35 LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPS 83

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

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-05
 Identities = 17/35 (48%), Positives = 21/35 (60%)

Query: 50 KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          KN  +G  YV F T E AQK +  +NG+  DGR I
Sbjct: 45 KNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQI 79

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 28/85 (32%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + FSQFG+V    V F                           DK    SKGYG+V+F
Sbjct: 16 LKEYFSQFGKVKSCNVPF---------------------------DKETGLSKGYGFVSF 48

Query: 62 STEEEAQKALADMNGKLLDGRVIFV 86
          S+ +  + AL      +L+G  + V
Sbjct: 49 SSRDGLENAL-QKQKHILEGNKLQV 72

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

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

 Score = 38.4 bits (90), Expect = 4e-05
 Identities = 13/41 (31%), Positives = 22/41 (53%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
           I +    + KGY +V F T E A  A+  +NG  ++G+ +
Sbjct: 26 AIEEVRVFKDKGYAFVRFDTHEAAATAIVAVNGTSINGQTV 66

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

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 38.7 bits (91), Expect = 4e-05
 Identities = 16/38 (42%), Positives = 25/38 (65%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
           ++KGY +V F+T EEA++A+  +NG  LD +  F  N
Sbjct: 47 GKTKGYAFVEFATPEEAKEAVKALNGYKLDKKHTFAVN 84

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

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

 Score = 38.5 bits (89), Expect = 4e-05
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++ D    +SKGYG+V+F  + +A+ A+  M G+ L GR I
Sbjct: 31 ARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 73

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

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

 Score = 38.2 bits (89), Expect = 5e-05
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F+++G++TE +V                             D    RS+G+G++TF
Sbjct: 19 LRRHFTRYGKLTECVVMV---------------------------DPNTKRSRGFGFITF 51

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
          S+ +EA +A+       +DG  I
Sbjct: 52 SSADEADEAMEAQ-PHSIDGNQI 73

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

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

 Score = 38.1 bits (89), Expect = 5e-05
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
             I+ DK    S G+G+V + + E+AQ+A+  +NG  L  + I V   RP 
Sbjct: 29 NCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKVAYARPG 80

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           II D   N+ KGYG+V+ +  +EA  A+  +NG  L  RV+ V
Sbjct: 301 IIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

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

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 38.5 bits (89), Expect = 6e-05
 Identities = 18/45 (40%), Positives = 28/45 (62%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          +I+ D+   RS+G+ +V F   ++A++A    NG  LDGR I VD
Sbjct: 40 SIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 84

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

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

 Score = 38.0 bits (89), Expect = 6e-05
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR 90
          I M+K KN     G+VTF   E A +A+A++NG  + G  + V   R
Sbjct: 32 ISMEKEKNC----GFVTFEKMESADRAIAELNGTTVQGVQLKVSLAR 74

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

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

 Score = 37.7 bits (88), Expect = 7e-05
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 28/81 (34%)

Query: 6  FSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEE 65
          FSQFG+V +                           A ++ D    RS+G+G+VTF +E 
Sbjct: 20 FSQFGKVVD---------------------------AQLMQDHDTGRSRGFGFVTFDSES 52

Query: 66 EAQKALADMNGKLLDGRVIFV 86
            ++  +      L G+ + V
Sbjct: 53 AVERVFS-AGMLELGGKQVEV 72

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

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

 Score = 38.2 bits (88), Expect = 8e-05
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +I D   N+ KG+G+VT +  +EA  A+A +NG  L  RV+ V
Sbjct: 35 VIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 37.8 bits (88), Expect = 8e-05
 Identities = 17/44 (38%), Positives = 26/44 (59%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          +I DK   +S GYG+V +   E+A+KA+  +NG  L  + I V 
Sbjct: 33 LIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKTIKVS 76

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

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

 Score = 38.1 bits (88), Expect = 8e-05
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +I D   N+ KG+G+VT +  +EA  A+A +NG  L  RV+ V
Sbjct: 35 VIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQV 77

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

 Score = 37.7 bits (88), Expect = 9e-05
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
          ++ DK    SKG  YV F+    A +A+ +MNGK L G 
Sbjct: 34 VVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGD 72

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

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

 Score = 37.7 bits (87), Expect = 9e-05
 Identities = 17/43 (39%), Positives = 27/43 (62%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +I D   N+ KG+G+VT +  EEA  A+A +NG  L  +++ V
Sbjct: 33 VIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQV 75

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 2/43 (4%)

Query: 44 IIMDK--GKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          I +D    +N  +G  Y+TF   E+A +A+ D+NG+  DGR++
Sbjct: 25 IYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLV 67

Length = 70

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

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          K YG+V    EE+A+ A+  +NG    G+ I V
Sbjct: 33 KNYGFVHMEEEEDAEDAIKALNGYEFMGKRINV 65

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

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

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 14/77 (18%)

Query: 11 QVTEDLVYFYF-KSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQK 69
          +VTE+L++  F ++ P+  +H             I  D+     +GYG+V F +EE+A  
Sbjct: 9  KVTEELLWELFIQAGPVVNVH-------------IPKDRVTQAHQGYGFVEFLSEEDADY 55

Query: 70 ALADMNGKLLDGRVIFV 86
          A+  MN   L G+ I V
Sbjct: 56 AIKIMNMIKLYGKPIRV 72

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

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

 Score = 37.5 bits (88), Expect = 1e-04
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 13/79 (16%)

Query: 12 VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 71
           TE+ +     +    P+              +I DK    S+G+ +V F + E+A + +
Sbjct: 14 TTEEDILQALSAIASVPIK----------DVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 72 ADMNGKL---LDGRVIFVD 87
            +N      +DGRV+ V 
Sbjct: 64 DALNNLDPFVIDGRVVRVS 82

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

 Score = 37.6 bits (88), Expect = 1e-04
 Identities = 16/34 (47%), Positives = 23/34 (67%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          KGY  + + T++EAQ A+  +NGK L G+ I VD
Sbjct: 48 KGYALIEYETKKEAQAAIEGLNGKELLGQTISVD 81

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

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 38 FLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          F  A +I + +   R KGY +V F + E+A++AL   N   ++GR I
Sbjct: 22 FEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTEIEGRSI 68

This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 72

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 21/52 (40%), Positives = 27/52 (51%), Gaps = 2/52 (3%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV--DNVRPSRRYN 96
          D    RS GYGYV F    +A++AL  MN K L G+ I +      PS R +
Sbjct: 35 DSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRS 86

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 6/40 (15%)

Query: 42 ATIIMDK------GKNRSKGYGYVTFSTEEEAQKALADMN 75
            I+ D       GK +SKGYG+V F+  E A KAL  +N
Sbjct: 39 VKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALN 78

This subfamily corresponds to the RRM4 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 = 98

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

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          +  ++ DK   +S GYG+V +    +A KA+  +NG  L  + I V   RPS
Sbjct: 32 SCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYARPS 83

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

 Score = 37.0 bits (86), Expect = 2e-04
 Identities = 17/43 (39%), Positives = 28/43 (65%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          + +DK   +SKG+ YV F   E+A KA  +++GK+  GR+I +
Sbjct: 34 VAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQGRLIHI 76

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

>gnl|CDD|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 = 37.1 bits (86), Expect = 2e-04
 Identities = 16/45 (35%), Positives = 28/45 (62%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          ++ D+   + KGYG+  +  +E A  A+ ++NG  L+GR + VDN
Sbjct: 30 LVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLRVDN 74

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

 Score = 37.0 bits (85), Expect = 2e-04
 Identities = 18/43 (41%), Positives = 27/43 (62%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +I D   N+ KG+G+VT +  +EA  A+A +NG  L  RV+ V
Sbjct: 33 VIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQV 75

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 37.1 bits (87), Expect = 2e-04
 Identities = 11/27 (40%), Positives = 20/27 (74%)

Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVI 84
          YVT+S +E+A + +  ++G  LDGR++
Sbjct: 57 YVTYSRKEDALRCIQAVDGFYLDGRLL 83

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

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

 Score = 36.9 bits (85), Expect = 2e-04
 Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 10/72 (13%)

Query: 27 FPLHYFLISDSF-----LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
          F   + ++ D F     +  A I M+ GK  SKG G V F + E A++A   MNG  L+G
Sbjct: 9  FDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVRFESPEVAERACRMMNGYKLNG 66

Query: 82 RVIFVDNVRPSR 93
          R I   +VR  R
Sbjct: 67 REI---DVRIDR 75

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 2/46 (4%)

Query: 44 IIM--DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          IIM  D+      G+ +V + T E+A+ A+  +NG  LD R+I VD
Sbjct: 28 IIMGLDRFTKTPCGFCFVEYYTREDAENAVKYLNGTKLDDRIIRVD 73

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

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 36.6 bits (85), Expect = 2e-04
 Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 31/79 (39%)

Query: 6  FSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEE 65
          FSQFG+V +                           A ++ DK  NR +G+G+VTF +E+
Sbjct: 20 FSQFGKVED---------------------------AMLMFDKQTNRHRGFGFVTFESED 52

Query: 66 EAQKALA----DMNGKLLD 80
             K       ++N K+++
Sbjct: 53 VVDKVCEIHFHEINNKMVE 71

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 36.5 bits (84), Expect = 2e-04
 Identities = 24/52 (46%), Positives = 30/52 (57%), Gaps = 5/52 (9%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          A I M+ GK  SKG G V F + E A+KA   MNG  ++GR I   +VR  R
Sbjct: 29 AEIKMENGK--SKGCGTVRFDSPESAEKACRLMNGIKINGREI---DVRLDR 75

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 36.5 bits (84), Expect = 3e-04
 Identities = 17/49 (34%), Positives = 29/49 (59%)

Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          L    ++ D+   RS+G+ +V F   +++++A+   NG  LDGR I VD
Sbjct: 26 LAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRVD 74

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

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

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 30/52 (57%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          +  ++ DK   +S GYG+V +   ++A+KA+  +NG  L  + I V   RPS
Sbjct: 31 SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS 82

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240733 cd12287, RRM_U2AF35_like, RNA recognition motif in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 13/30 (43%), Positives = 20/30 (66%)

Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          YV F TEE+A+ AL  +NG+   GR ++ +
Sbjct: 70 YVKFETEEDAEAALQALNGRYYAGRPLYPE 99

This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 102

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

 Score = 36.2 bits (84), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 13/73 (17%)

Query: 14 EDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALAD 73
          EDL   + K  PL  +H  +             DK   + KG+ +VT+   E A KA A+
Sbjct: 17 EDLEKLFSKYGPLSEVHLPI-------------DKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 74 MNGKLLDGRVIFV 86
          ++G +  GR++ +
Sbjct: 64 LDGTVFQGRLLHL 76

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

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

 Score = 36.4 bits (85), Expect = 3e-04
 Identities = 13/34 (38%), Positives = 20/34 (58%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
           RS GY YV F    +A++AL  +N  ++ G+ I
Sbjct: 38 RRSLGYAYVNFQNPADAERALDTLNFDVIKGKPI 71

This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 36.2 bits (84), Expect = 4e-04
 Identities = 12/28 (42%), Positives = 16/28 (57%)

Query: 48 KGKNRSKGYGYVTFSTEEEAQKALADMN 75
          K     KG+ ++ F T EEAQKA   +N
Sbjct: 35 KHTGDIKGFAFIEFETPEEAQKACKHLN 62

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

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 83
          + + + +VTF +EEE QKAL  ++G    GRV
Sbjct: 40 KRQDFAFVTFRSEEERQKALEILDGFKWKGRV 71

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

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

 Score = 35.8 bits (83), Expect = 4e-04
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          ++ D    RS+G+G+VTF++  E   A+     K +DGR +
Sbjct: 31 VMKDPNTKRSRGFGFVTFASASEVDAAMNARPHK-VDGREV 70

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

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

 Score = 35.8 bits (83), Expect = 4e-04
 Identities = 14/33 (42%), Positives = 22/33 (66%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
          I+ D+   +S GYG+V +  E +AQKA+  +NG
Sbjct: 32 IVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

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

 Score = 35.7 bits (83), Expect = 5e-04
 Identities = 14/31 (45%), Positives = 22/31 (70%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          KGYG+V F  EE+A+ A+A  NG+ + G+ +
Sbjct: 35 KGYGFVQFDNEEDARAAVAGENGREIAGQKL 65

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

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 31/76 (40%)

Query: 6  FSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEE 65
          FSQFG VTE                             ++ D  K R +G+G++TF +E+
Sbjct: 23 FSQFGTVTE---------------------------VVVMYDHEKKRPRGFGFITFESED 55

Query: 66 EAQKALA----DMNGK 77
             + +     D+NGK
Sbjct: 56 SVDQVVNEHFHDINGK 71

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 10/54 (18%)

Query: 44  IIMD-KGKNRSKGYGYVTFSTEEEAQKALADMN------GKLLDGRVIFVDNVR 90
           ++MD  G+NR  GY +VTF  +EEA++A+  +N      G+LL G  I VDN R
Sbjct: 90  LMMDFSGQNR--GYAFVTFCGKEEAKEAVKLLNNYEIRPGRLL-GVCISVDNCR 140

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 35.4 bits (82), Expect = 6e-04
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
          I+ D     S+G G++ F    EA++A+  +NG +  G
Sbjct: 32 ILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPG 69

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

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

 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 18/44 (40%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          TI+ DK     KG+ Y+ FS +E  + ALA ++  L  GR I V
Sbjct: 30 TILCDKFSGHPKGFAYIEFSDKESVRTALA-LDESLFRGRQIKV 72

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

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

 Score = 35.5 bits (81), Expect = 6e-04
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          +  ++ DK   +S GYG+V +   ++A+KA+  +NG  L  + I V   RP
Sbjct: 33 SCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP 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|227502 COG5175, MOT2, Transcriptional repressor [Transcription]

 Score = 37.4 bits (86), Expect = 7e-04
 Identities = 14/27 (51%), Positives = 24/27 (88%)

Query: 58  YVTFSTEEEAQKALADMNGKLLDGRVI 84
           Y+T+ST+E+A + +A+++G LLDGRV+
Sbjct: 169 YITYSTKEDAARCIAEVDGSLLDGRVL 195

Length = 480

>gnl|CDD|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 35.2 bits (82), Expect = 7e-04
 Identities = 16/35 (45%), Positives = 23/35 (65%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          R KG  +VTF +EE A KAL  +NG +L G+ + +
Sbjct: 45 RMKGQAFVTFPSEEIATKALNLVNGYVLKGKPMVI 79

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

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

 Score = 35.6 bits (82), Expect = 7e-04
 Identities = 15/23 (65%), Positives = 19/23 (82%)

Query: 53 SKGYGYVTFSTEEEAQKALADMN 75
          SKGYG+VTF T+E+AQK L + N
Sbjct: 42 SKGYGFVTFETQEDAQKILQEAN 64

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

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

 Score = 35.0 bits (80), Expect = 8e-04
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          KGY ++ FST E A  A+  +NG  ++G V+
Sbjct: 36 KGYSFIRFSTHESAAHAIVSVNGTTIEGHVV 66

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 35.2 bits (80), Expect = 8e-04
 Identities = 15/30 (50%), Positives = 21/30 (70%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADM 74
          I+DK  N+ KGYG+V F +   AQKA+A +
Sbjct: 37 ILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 35.2 bits (82), Expect = 8e-04
 Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 13/50 (26%)

Query: 46 MD-KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          MD  G NR  GY +VT++ +E AQ+A+     K L    I     RP +R
Sbjct: 35 MDFSGLNR--GYAFVTYTNKEAAQRAV-----KQLHNYEI-----RPGKR 72

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240983 cd12539, RRM_U2AF35B, RNA recognition motif in splicing factor U2AF 35 kDa subunit B (U2AF35B)

 Score = 35.4 bits (82), Expect = 8e-04
 Identities = 14/30 (46%), Positives = 17/30 (56%)

Query: 58  YVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           YV F  EE A  AL  + G+  DGR I V+
Sbjct: 71  YVKFRDEEHAAAALKALQGRFYDGRPIIVE 100

This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. . Length = 103

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

 Score = 35.0 bits (80), Expect = 9e-04
 Identities = 23/83 (27%), Positives = 34/83 (40%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L D F++FG+VT+                            TI MD    RS+G+G++ F
Sbjct: 16 LKDYFTKFGEVTD---------------------------CTIKMDPNTGRSRGFGFILF 48

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
                +K L     + LDGR+I
Sbjct: 49 KDASSVEKVLEQKEHR-LDGRLI 70

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

>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 54  KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP-----SRRYNTDAPLARQSAQS 108
           + Y +V F   E+A KA+ ++NGK L+G  I V   +P       RY        +  Q+
Sbjct: 269 RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQA 328

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 11/35 (31%), Positives = 18/35 (51%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          + KG  YV +  E  A +A+  M+G  +  + I V
Sbjct: 41 KPKGLAYVEYENESSASQAVLKMDGTEIKEKTISV 75

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

 Score = 34.6 bits (80), Expect = 0.001
 Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          DK   +SKG  +V F T E   KAL  ++  LL GR I V+
Sbjct: 35 DKKTGKSKGCAFVEFDTAEAMTKAL-KLHHTLLKGRKINVE 74

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

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

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          ++GK  S+G G V F  +E  QKAL  MN   L GR + V
Sbjct: 36 EEGK--SRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 14/37 (37%), Positives = 23/37 (62%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR 90
          K + +V F   E+A KAL  ++G  +DG V+ V+ V+
Sbjct: 34 KTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70

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

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 16/40 (40%), Positives = 24/40 (60%)

Query: 55 GYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          GYG+V F    +A  A+ ++NGK L G  + V++ R  RR
Sbjct: 34 GYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARGPRR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 34.7 bits (80), Expect = 0.001
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
           R + Y +V F+ +++A+ ALA   G +LDGR I  +  + +R
Sbjct: 42 WRQRPYAFVQFTNDDDAKNALAKGQGTILDGRHIRCERAKVNR 84

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

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 34.4 bits (79), Expect = 0.001
 Identities = 14/36 (38%), Positives = 23/36 (63%)

Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG 76
          +A + +D+  N+SK +G+V+F     AQ A+  MNG
Sbjct: 33 SAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNG 68

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 15/43 (34%), Positives = 23/43 (53%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          I  K   +  G+ +VT    + A+ AL + NG  +DGR + VD
Sbjct: 33 IPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 33.9 bits (78), Expect = 0.002
 Identities = 12/35 (34%), Positives = 19/35 (54%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
            + + ++TF   E AQ A+  +NG  +DG  I V
Sbjct: 35 TVQPHAFITFENLEAAQLAIETLNGASVDGNCIKV 69

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

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

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 13/33 (39%), Positives = 19/33 (57%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          +SKGY +V F + E A+     MN  LL  R++
Sbjct: 39 KSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 14/30 (46%), Positives = 20/30 (66%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADM 74
          I+DK  N+ KGYG+V F +   AQKA+  +
Sbjct: 34 ILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 63

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

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

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 12/38 (31%), Positives = 23/38 (60%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
          I+ D+    S+G G++ F    EA++A+  +NG+  +G
Sbjct: 32 ILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEG 69

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

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

 Score = 34.1 bits (78), Expect = 0.002
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
          ++ DK     +G  +V +   EEAQ A++ +NG +  G 
Sbjct: 32 LLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGS 70

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

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

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 6/62 (9%)

Query: 26 LFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIF 85
           F  H   I+D        ++     +S+   ++ + TEEEAQKA    N   ++   I 
Sbjct: 20 HFSKHGGEITDVK------LLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNNTYINTSKIS 73

Query: 86 VD 87
          V+
Sbjct: 74 VE 75

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

>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVI 84
          +V FS  +EA KA+  +NG+   GR +
Sbjct: 53 FVEFSDADEAIKAVRALNGRFFGGRKV 79

This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain. . Length = 85

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 10/31 (32%), Positives = 15/31 (48%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALA 72
          A  ++DK   R+KG G+V F  +      L 
Sbjct: 31 ALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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

>gnl|CDD|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 = 33.7 bits (78), Expect = 0.003
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          L A  ++ D     SKGY +  +       +A+A +NG  L  + + V
Sbjct: 27 LKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLTV 74

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

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

 Score = 33.7 bits (77), Expect = 0.003
 Identities = 15/34 (44%), Positives = 20/34 (58%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          K Y +V    EEEA  A+  +NGK + GR I V+
Sbjct: 34 KDYAFVHMEREEEALAAIEALNGKEVKGRRINVE 67

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

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

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          DK  ++ KG+ YV F   E  ++AL + +G L D R + VD
Sbjct: 35 DKETDKFKGFCYVEFEDVESLKEAL-EYDGALFDDRSLRVD 74

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

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 33.8 bits (78), Expect = 0.003
 Identities = 14/42 (33%), Positives = 22/42 (52%)

Query: 40 FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
           +  II +K      GY +V F+ E  A++ L  +NGK + G
Sbjct: 28 LSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIPG 69

This subgroup corresponds to the RRM1 of SECp43, 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. . Length = 84

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 34.0 bits (77), Expect = 0.003
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADM 74
          I+DK  N+ KGYG+V F +   AQKA++ +
Sbjct: 40 ILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 47  DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
           D    + KG+ +V +   E AQ AL  MNG++L GR I V   RPS
Sbjct: 142 DPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG--RPS 185

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

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 33.4 bits (76), Expect = 0.004
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           SKGYG+V +  ++ A +A +D+ GK L  R ++V
Sbjct: 39 HSKGYGFVEYMKKDSAARAKSDLLGKQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|241088 cd12644, RRM_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins

 Score = 33.8 bits (77), Expect = 0.004
 Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
          ++   +SKGY  V  ++E    K L  + GK+L+G  +   +VRP+ R N
Sbjct: 38 NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV---DVRPATRQN 84

This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. . Length = 90

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 33.5 bits (76), Expect = 0.004
 Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          ++ D    RS+G+G+VTFS   E   A+A      +DGRV+
Sbjct: 34 VMRDPASKRSRGFGFVTFSCMNEVDAAMA-ARPHTIDGRVV 73

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

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

 Score = 33.0 bits (76), Expect = 0.004
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
           K   +SKG+ YV F++E  A      + G+  +G+
Sbjct: 35 HKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNGK 70

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

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 33.2 bits (75), Expect = 0.004
 Identities = 18/39 (46%), Positives = 24/39 (61%), Gaps = 3/39 (7%)

Query: 52 RSKG---YGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          RS G   YG+VT ST EEA K +  ++   L GR+I V+
Sbjct: 38 RSPGARCYGFVTMSTSEEATKCINHLHRTELHGRMISVE 76

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. 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. Length = 76

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 33.2 bits (76), Expect = 0.004
 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG 81
          +I  +    + GY +V F +   AQ AL+ +NG  +  
Sbjct: 32 VIRSRNSGLNAGYCFVEFPSPHAAQNALS-LNGTPIPN 68

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	112
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.61
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.54
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.45
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.43
smart00361	70	RRM_1 RNA recognition motif.	99.42
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.42
KOG0122	270	consensus Translation initiation factor 3, subunit	99.41
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.41
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.4
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.35
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.33
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.32
smart00360	71	RRM RNA recognition motif.	99.25
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.25
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.24
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.23
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.21
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.21
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.17
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.17
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.15
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.15
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.15
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.14
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.11
smart00362	72	RRM_2 RNA recognition motif.	99.11
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.1
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.07
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.06
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.05
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.05
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.03
PLN03120	260	nucleic acid binding protein; Provisional	99.03
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.01
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.98
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.98
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.97
PLN03213	759	repressor of silencing 3; Provisional	98.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.94
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.94
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.94
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.93
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.93
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.87
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.87
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.85
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.83
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.8
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.76
PLN03121	243	nucleic acid binding protein; Provisional	98.76
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.76
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.74
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.74
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.73
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.73
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.73
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.7
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.7
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.69
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.66
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.56
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.48
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.47
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.45
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.37
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.33
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.33
KOG0226	290	consensus RNA-binding proteins [General function p	98.32
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.19
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.11
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.11
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.89
KOG2314	698	consensus Translation initiation factor 3, subunit	97.84
KOG0533	243	consensus RRM motif-containing protein [RNA proces	97.79
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.69
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	97.54
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	97.52
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	97.48
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.44
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	97.43
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.31
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.29
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.26
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.25
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.2
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.2
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.03
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	96.98
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.88
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.82
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.71
KOG0151	877	consensus Predicted splicing regulator, contains R	96.64
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.5
KOG4210	285	consensus Nuclear localization sequence binding pr	96.46
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	96.38
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.32
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.29
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	95.32
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	95.26
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	95.22
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.2
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.19
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	95.05
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	94.4
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.04
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.0
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	93.88
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	93.57
KOG1855	484	consensus Predicted RNA-binding protein [General f	93.17
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.63
KOG2135	526	consensus Proteins containing the RNA recognition	92.38
KOG2068	327	consensus MOT2 transcription factor [Transcription	91.0
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	90.49
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	90.36
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	89.14
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	88.33
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	87.95
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	87.8
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	87.31
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	85.3
KOG1457	284	consensus RNA binding protein (contains RRM repeat	84.93
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	84.88
KOG3152	278	consensus TBP-binding protein, activator of basal	82.07
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	80.37

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

Probab=99.61  E-value=1e-14  Score=102.51  Aligned_cols=67  Identities=40%  Similarity=0.740  Sum_probs=62.8

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|++||.|.+                           +.|+.|+.+++++|||||+|.+.++|++|+..||+..++
T Consensus        50 ~L~~~F~~~G~I~~---------------------------v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~  102 (144)
T PLN03134         50 SLRDAFAHFGDVVD---------------------------AKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN  102 (144)
T ss_pred             HHHHHHhcCCCeEE---------------------------EEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      |+.|+|+++++++.
T Consensus       103 Gr~l~V~~a~~~~~  116 (144)
T PLN03134        103 GRHIRVNPANDRPS  116 (144)
T ss_pred             CEEEEEEeCCcCCC
Confidence            99999999976543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.54  E-value=3.6e-14  Score=109.82  Aligned_cols=66  Identities=35%  Similarity=0.524  Sum_probs=62.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++|++|+.++.++|||||+|.+.++|.+|+..|||..++|
T Consensus       286 L~~~F~~fG~v~~---------------------------v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~g  338 (352)
T TIGR01661       286 LWQLFGPFGAVQN---------------------------VKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGN  338 (352)
T ss_pred             HHHHHHhCCCeEE---------------------------EEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|+|++...+..
T Consensus       339 r~i~V~~~~~~~~  351 (352)
T TIGR01661       339 RVLQVSFKTNKAY  351 (352)
T ss_pred             eEEEEEEccCCCC
Confidence            9999999876543

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

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

Probab=99.45  E-value=3.4e-13  Score=104.15  Aligned_cols=66  Identities=30%  Similarity=0.589  Sum_probs=62.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||+|..                           ++||+|+.||+++|||||+|.++.++..|.++.+|.+|+|
T Consensus       118 LrreF~~YG~Ikr---------------------------irlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idg  170 (335)
T KOG0113|consen  118 LRREFEKYGPIKR---------------------------IRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDG  170 (335)
T ss_pred             HHHHHHhcCccee---------------------------EEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++.+..+-
T Consensus       171 rri~VDvERgRTv  183 (335)
T KOG0113|consen  171 RRILVDVERGRTV  183 (335)
T ss_pred             cEEEEEecccccc
Confidence            9999999875543

>PF13893 RRM_5: RNA recognition motif

Probab=99.43  E-value=1.3e-12  Score=77.26  Aligned_cols=56  Identities=38%  Similarity=0.716  Sum_probs=49.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|++||+|.+                           +.+..+.     +++|||+|.+.++|+.|+..|||..++|
T Consensus         1 L~~~f~~fG~V~~---------------------------i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g   48 (56)
T PF13893_consen    1 LYKLFSKFGEVKK---------------------------IKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNG   48 (56)
T ss_dssp             HHHHHTTTS-EEE---------------------------EEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             ChHHhCCcccEEE---------------------------EEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            6789999999988                           7765443     6899999999999999999999999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      ++|+|++|
T Consensus        49 ~~l~V~~a   56 (56)
T PF13893_consen   49 RPLKVSYA   56 (56)
T ss_dssp             EEEEEEEE
T ss_pred             cEEEEEEC
Confidence            99999886

(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 ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.42  E-value=1.1e-12  Score=81.26  Aligned_cols=59  Identities=36%  Similarity=0.689  Sum_probs=53.1

Q ss_pred             HHHHhh----ccCcceecceeeeccCCCCCcccccccccccceEEE-EEeeCCC--CCcccEEEEEeCCHHHHHHHHHhh
Q 033734            2 LADAFS----QFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAAT-IIMDKGK--NRSKGYGYVTFSTEEEAQKALADM   74 (112)
Q Consensus         2 l~~~f~----~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~d~~t--~~~rG~afV~f~~~~~a~~Ai~~l   74 (112)
                      |+++|+    +||+|.+                           +. ++.++.+  ++++|++||+|.++++|++|+..|
T Consensus         5 l~~~~~~~~~~fG~v~~---------------------------v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l   57 (70)
T smart00361        5 FEREFSEEEEYFGEVGK---------------------------INKIYIDNVGYENHKRGNVYITFERSEDAARAIVDL   57 (70)
T ss_pred             HHHHHHHHHHhcCCeeE---------------------------EEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHh
Confidence            677888    9999999                           75 7777767  899999999999999999999999


Q ss_pred             CCceeCCeeEEEE
Q 033734           75 NGKLLDGRVIFVD   87 (112)
Q Consensus        75 ~g~~l~g~~i~V~   87 (112)
                      ||..++|+.|.++
T Consensus        58 ~g~~~~gr~l~~~   70 (70)
T smart00361       58 NGRYFDGRTVKAE   70 (70)
T ss_pred             CCCEECCEEEEeC
Confidence            9999999998763

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.42  E-value=7.6e-13  Score=102.42  Aligned_cols=67  Identities=31%  Similarity=0.587  Sum_probs=62.9

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|+.||+|.+                           |+|++|+.+|+++|||||+|.++++|++||..|||..+.
T Consensus        19 ~l~~~F~~~G~i~~---------------------------v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~   71 (352)
T TIGR01661        19 EIRSLFTSIGEIES---------------------------CKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQ   71 (352)
T ss_pred             HHHHHHHccCCEEE---------------------------EEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEEC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      |+.|.|+++++...
T Consensus        72 g~~i~v~~a~~~~~   85 (352)
T TIGR01661        72 NKTIKVSYARPSSD   85 (352)
T ss_pred             CeeEEEEeeccccc
Confidence            99999999876543

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

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

Probab=99.41  E-value=6.4e-13  Score=100.31  Aligned_cols=64  Identities=36%  Similarity=0.636  Sum_probs=62.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|.+||.|.+                           +.|.+|++||.++|||||+|.+.++|++||..|||+-.++
T Consensus       206 L~eLf~~fg~i~r---------------------------vylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~  258 (270)
T KOG0122|consen  206 LEELFRPFGPITR---------------------------VYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDN  258 (270)
T ss_pred             HHHHhhccCccce---------------------------eEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccce
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      --|+|+|++|+
T Consensus       259 LILrvEwskP~  269 (270)
T KOG0122|consen  259 LILRVEWSKPS  269 (270)
T ss_pred             EEEEEEecCCC
Confidence            99999999986

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

Probab=99.41  E-value=2e-13  Score=101.38  Aligned_cols=62  Identities=34%  Similarity=0.642  Sum_probs=60.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|++||.|-+                           |.|++|+.|..++|||||-|....+|++|+++|||..|+|
T Consensus        30 LrrvFekYG~vgD---------------------------VyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldg   82 (256)
T KOG4207|consen   30 LRRVFEKYGRVGD---------------------------VYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDG   82 (256)
T ss_pred             HHHHHHHhCcccc---------------------------eecccccccccccceeEEEeeecchHHHHHHhhcceeecc
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      ++|+|.+|+
T Consensus        83 RelrVq~ar   91 (256)
T KOG4207|consen   83 RELRVQMAR   91 (256)
T ss_pred             ceeeehhhh
Confidence            999999986

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

Probab=99.40  E-value=6.9e-13  Score=101.57  Aligned_cols=69  Identities=36%  Similarity=0.643  Sum_probs=64.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |++.|.+||+|.+                           ++|++|..|++++||+||.|.+.++|++||.+|+|.=|++
T Consensus        79 lr~aF~pFGevS~---------------------------akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~  131 (321)
T KOG0148|consen   79 LREAFAPFGEVSD---------------------------AKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGR  131 (321)
T ss_pred             HHHHhcccccccc---------------------------ceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeecc
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      |.|+-.||+.++....
T Consensus       132 R~IRTNWATRKp~e~n  147 (321)
T KOG0148|consen  132 RTIRTNWATRKPSEMN  147 (321)
T ss_pred             ceeeccccccCccccC
Confidence            9999999987664433

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.35  E-value=2.1e-12  Score=102.02  Aligned_cols=65  Identities=28%  Similarity=0.511  Sum_probs=61.6

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|+.||+|++                           |+|++|+.+++++|||||+|.++++|++|+..|||..+.
T Consensus       123 ~L~~lF~~~G~V~~---------------------------v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~  175 (346)
T TIGR01659       123 ELYALFRTIGPINT---------------------------CRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVR  175 (346)
T ss_pred             HHHHHHHhcCCEEE---------------------------EEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      +++|+|.++++.
T Consensus       176 gr~i~V~~a~p~  187 (346)
T TIGR01659       176 NKRLKVSYARPG  187 (346)
T ss_pred             Cceeeeeccccc
Confidence            999999998764

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.33  E-value=1.1e-11  Score=74.59  Aligned_cols=56  Identities=45%  Similarity=0.824  Sum_probs=52.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+..+ .++..+|+|||+|.+.++|+.|+..|||..++|
T Consensus        15 l~~~f~~~g~i~~---------------------------~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~   66 (70)
T PF00076_consen   15 LRDFFSQFGKIES---------------------------IKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKING   66 (70)
T ss_dssp             HHHHHHTTSTEEE---------------------------EEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHHhhhccc---------------------------cccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence            7899999999999                           999998 589999999999999999999999999999999


Q ss_pred             eeEE
Q 033734           82 RVIF   85 (112)
Q Consensus        82 ~~i~   85 (112)
                      +.|+
T Consensus        67 ~~ir   70 (70)
T PF00076_consen   67 RKIR   70 (70)
T ss_dssp             EEEE
T ss_pred             cCcC
Confidence            9885

(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 ....

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

Probab=99.32  E-value=9.9e-12  Score=104.26  Aligned_cols=67  Identities=21%  Similarity=0.396  Sum_probs=62.7

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|+.||.|..                           ++|++|+.+++++|||||+|.+.++|.+||..|||..++
T Consensus       220 dLk~lFs~FG~I~s---------------------------vrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elg  272 (612)
T TIGR01645       220 DIKSVFEAFGEIVK---------------------------CQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLG  272 (612)
T ss_pred             HHHHHHhhcCCeeE---------------------------EEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      |+.|+|.++.+.+.
T Consensus       273 Gr~LrV~kAi~pP~  286 (612)
T TIGR01645       273 GQYLRVGKCVTPPD  286 (612)
T ss_pred             CeEEEEEecCCCcc
Confidence            99999999986543

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.

>smart00360 RRM RNA recognition motif

Probab=99.25  E-value=4.3e-11  Score=70.44  Aligned_cols=59  Identities=44%  Similarity=0.804  Sum_probs=54.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+..++.++.++|+|||+|.+.++|..|+..+++..++|
T Consensus        13 l~~~f~~~g~v~~---------------------------~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~   65 (71)
T smart00360       13 LRELFSKFGKIES---------------------------VRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDG   65 (71)
T ss_pred             HHHHHHhhCCEeE---------------------------EEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCC
Confidence            6889999999999                           9998888788999999999999999999999999999999


Q ss_pred             eeEEEE
Q 033734           82 RVIFVD   87 (112)
Q Consensus        82 ~~i~V~   87 (112)
                      +.+.|+
T Consensus        66 ~~~~v~   71 (71)
T smart00360       66 RPLKVK   71 (71)
T ss_pred             cEEEeC
Confidence            988773

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

Probab=99.25  E-value=1.3e-11  Score=99.48  Aligned_cols=66  Identities=32%  Similarity=0.533  Sum_probs=60.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |..+|++.|+|.+                           ++|++|+.+|.+||||||+|.+.++|+.||+.||+++|. 
T Consensus       100 LvplfEkiG~I~e---------------------------lRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~  152 (506)
T KOG0117|consen  100 LVPLFEKIGKIYE---------------------------LRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRP  152 (506)
T ss_pred             hHHHHHhccceee---------------------------EEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccC
Confidence            6789999999999                           999999999999999999999999999999999999985 


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      |+.|.|+.+....+
T Consensus       153 GK~igvc~Svan~R  166 (506)
T KOG0117|consen  153 GKLLGVCVSVANCR  166 (506)
T ss_pred             CCEeEEEEeeecce
Confidence            99999988865443

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

Probab=99.24  E-value=9.4e-12  Score=93.45  Aligned_cols=61  Identities=43%  Similarity=0.688  Sum_probs=56.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|++                           +.|+.|+.+|+++||+||+|.+.++|.+|++.- .-.|+|
T Consensus        29 l~~yFeqfGeI~e---------------------------avvitd~~t~rskGyGfVTf~d~~aa~rAc~dp-~piIdG   80 (247)
T KOG0149|consen   29 LRRYFEQFGEIVE---------------------------AVVITDKNTGRSKGYGFVTFRDAEAATRACKDP-NPIIDG   80 (247)
T ss_pred             HHHHHHHhCceEE---------------------------EEEEeccCCccccceeeEEeecHHHHHHHhcCC-CCcccc
Confidence            7899999999999                           999999999999999999999999999999855 367999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      |+..|.+|-
T Consensus        81 R~aNcnlA~   89 (247)
T KOG0149|consen   81 RKANCNLAS   89 (247)
T ss_pred             cccccchhh
Confidence            999999874

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.23  E-value=4.9e-11  Score=94.30  Aligned_cols=64  Identities=28%  Similarity=0.525  Sum_probs=59.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++|++|+.+++++|||||+|.+.++|++||..||+..+.+
T Consensus       210 L~~~F~~fG~V~~---------------------------v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g  262 (346)
T TIGR01659       210 LDTIFGKYGQIVQ---------------------------KNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEG  262 (346)
T ss_pred             HHHHHHhcCCEEE---------------------------EEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            7899999999999                           9999999999999999999999999999999999999876


Q ss_pred             --eeEEEEeccCC
Q 033734           82 --RVIFVDNVRPS   92 (112)
Q Consensus        82 --~~i~V~~a~~~   92 (112)
                        ++|.|+++...
T Consensus       263 ~~~~l~V~~a~~~  275 (346)
T TIGR01659       263 GSQPLTVRLAEEH  275 (346)
T ss_pred             CceeEEEEECCcc
Confidence              68999988643

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).

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

Probab=99.21  E-value=4.1e-11  Score=100.61  Aligned_cols=62  Identities=34%  Similarity=0.606  Sum_probs=59.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+++++|||||+|.++++|+.|+..|||..++|
T Consensus       124 Lr~lF~~fG~I~s---------------------------V~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~G  176 (612)
T TIGR01645       124 IRRAFDPFGPIKS---------------------------INMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG  176 (612)
T ss_pred             HHHHHHccCCEEE---------------------------EEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEec
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|+|....
T Consensus       177 R~IkV~rp~  185 (612)
T TIGR01645       177 RNIKVGRPS  185 (612)
T ss_pred             ceeeecccc
Confidence            999998653

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.

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

Probab=99.21  E-value=3.2e-11  Score=94.35  Aligned_cols=62  Identities=35%  Similarity=0.699  Sum_probs=57.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|++||.|.+                           +.|+.+.  .-+||||||+|.+++||++|-.+|||+.+.|
T Consensus       113 L~aMF~kfG~Vld---------------------------VEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEG  163 (376)
T KOG0125|consen  113 LRAMFEKFGKVLD---------------------------VEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEG  163 (376)
T ss_pred             HHHHHHhhCceee---------------------------EEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeec
Confidence            7899999999999                           9988884  5589999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      |.|.|..++.+
T Consensus       164 RkIEVn~ATar  174 (376)
T KOG0125|consen  164 RKIEVNNATAR  174 (376)
T ss_pred             eEEEEeccchh
Confidence            99999998754

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

Probab=99.17  E-value=1.4e-10  Score=95.54  Aligned_cols=63  Identities=38%  Similarity=0.546  Sum_probs=60.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|++||+|..                           |+|++|..|++++|||||+|.++++|++|+..+++..+.|
T Consensus        17 L~~~F~~~G~v~~---------------------------v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~g   69 (562)
T TIGR01628        17 LYDLFKPFGPVLS---------------------------VRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGG   69 (562)
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|+|.++..
T Consensus        70 k~i~i~~s~~   79 (562)
T TIGR01628        70 KPIRIMWSQR   79 (562)
T ss_pred             eeEEeecccc
Confidence            9999999853

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

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

Probab=99.17  E-value=1.1e-10  Score=96.15  Aligned_cols=63  Identities=37%  Similarity=0.764  Sum_probs=59.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++++.| .++.++|||||+|.+.++|.+|+..|||..++|
T Consensus       302 L~~~F~~~G~i~~---------------------------~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~g  353 (562)
T TIGR01628       302 LRELFSECGEITS---------------------------AKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGG  353 (562)
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCC
Confidence            7899999999999                           999999 589999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      ++|.|.++..+
T Consensus       354 k~l~V~~a~~k  364 (562)
T TIGR01628       354 KPLYVALAQRK  364 (562)
T ss_pred             ceeEEEeccCc
Confidence            99999998753

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

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

Probab=99.15  E-value=2e-10  Score=92.06  Aligned_cols=62  Identities=39%  Similarity=0.640  Sum_probs=59.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+|+++|||||+|.+.++|..|+..|||..+.|
T Consensus       203 l~~~f~~~G~i~~---------------------------v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g  255 (457)
T TIGR01622       203 LRQIFEPFGDIED---------------------------VQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAG  255 (457)
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|.|.++.
T Consensus       256 ~~i~v~~a~  264 (457)
T TIGR01622       256 RPIKVGYAQ  264 (457)
T ss_pred             EEEEEEEcc
Confidence            999999975

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.

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

Probab=99.15  E-value=3.3e-11  Score=90.53  Aligned_cols=68  Identities=32%  Similarity=0.586  Sum_probs=63.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |...|-+||.|.+                           +.++.|.++++.||||||+|...++|.+||..||+.+|.|
T Consensus        27 LhaAFIPFGDI~d---------------------------IqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~G   79 (298)
T KOG0111|consen   27 LHAAFIPFGDIKD---------------------------IQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFG   79 (298)
T ss_pred             HHhccccccchhh---------------------------cccccchhcccccceeEEEeeccchhHHHhhcCchhhhcc
Confidence            5677889999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      |.|+|.+|+|.+-+.
T Consensus        80 rtirVN~AkP~kike   94 (298)
T KOG0111|consen   80 RTIRVNLAKPEKIKE   94 (298)
T ss_pred             eeEEEeecCCccccC
Confidence            999999998866543

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

Probab=99.15  E-value=2.1e-10  Score=92.96  Aligned_cols=65  Identities=22%  Similarity=0.390  Sum_probs=60.9

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|+.||.|..                           +.++.++.+|.++|||||+|.+.++|..|+..|||..++
T Consensus       311 ~l~~~f~~~G~i~~---------------------------~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~  363 (509)
T TIGR01642       311 QIKELLESFGDLKA---------------------------FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTG  363 (509)
T ss_pred             HHHHHHHhcCCeeE---------------------------EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|.|.++...
T Consensus       364 ~~~l~v~~a~~~  375 (509)
T TIGR01642       364 DNKLHVQRACVG  375 (509)
T ss_pred             CeEEEEEECccC
Confidence            999999998643

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

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

Probab=99.14  E-value=1e-10  Score=89.68  Aligned_cols=67  Identities=31%  Similarity=0.572  Sum_probs=64.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      ++.+|+..|+|..                           |++++|+.+|++-||+||.|-++.+|++||.-|||..+..
T Consensus        58 ~rSLF~SiGeiES---------------------------cKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~  110 (360)
T KOG0145|consen   58 LRSLFGSIGEIES---------------------------CKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQN  110 (360)
T ss_pred             HHHHhhcccceee---------------------------eeeeeccccccccccceeeecChHHHHHHHhhhcceeecc
Confidence            6789999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|++++|+...
T Consensus       111 KTIKVSyARPSs~~  124 (360)
T KOG0145|consen  111 KTIKVSYARPSSDS  124 (360)
T ss_pred             ceEEEEeccCChhh
Confidence            99999999987664

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.11  E-value=5.1e-10  Score=68.16  Aligned_cols=56  Identities=43%  Similarity=0.774  Sum_probs=52.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|+.||.|..                           +.+..++. +..+|+|||+|.++++|+.|+..+++..++|
T Consensus        15 l~~~f~~~g~v~~---------------------------v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g   66 (70)
T PF14259_consen   15 LRNFFSRFGPVEK---------------------------VRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDG   66 (70)
T ss_dssp             HHHHCTTSSBEEE---------------------------EEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhcCCcce---------------------------EEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECC
Confidence            6789999999988                           99999986 8999999999999999999999999999999


Q ss_pred             eeEE
Q 033734           82 RVIF   85 (112)
Q Consensus        82 ~~i~   85 (112)
                      +.|+
T Consensus        67 ~~l~   70 (70)
T PF14259_consen   67 RKLR   70 (70)
T ss_dssp             EEEE
T ss_pred             EEcC
Confidence            9874

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 ....

>smart00362 RRM_2 RNA recognition motif

Probab=99.11  E-value=5.7e-10  Score=65.88  Aligned_cols=57  Identities=40%  Similarity=0.747  Sum_probs=51.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|.+||++..                           +.+..++  +.++|+|||+|.+.++|+.|+..++|..+.|
T Consensus        16 l~~~~~~~g~v~~---------------------------~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~   66 (72)
T smart00362       16 LKELFSKFGPIES---------------------------VKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGG   66 (72)
T ss_pred             HHHHHHhcCCEEE---------------------------EEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECC
Confidence            6789999999999                           8888776  7889999999999999999999999999999


Q ss_pred             eeEEEE
Q 033734           82 RVIFVD   87 (112)
Q Consensus        82 ~~i~V~   87 (112)
                      +.+.|+
T Consensus        67 ~~i~v~   72 (72)
T smart00362       67 RPLRVE   72 (72)
T ss_pred             EEEeeC
Confidence            998773

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

Probab=99.10  E-value=1.8e-10  Score=80.96  Aligned_cols=65  Identities=29%  Similarity=0.482  Sum_probs=60.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      +.+.|.-||+|+-                           +.+-.|+.||-.+|||+|+|.+..+|++|+.++||..|.|
T Consensus        89 i~d~F~dyGeiKN---------------------------ihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~  141 (170)
T KOG0130|consen   89 IHDKFADYGEIKN---------------------------IHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG  141 (170)
T ss_pred             HHHHHhhcccccc---------------------------eeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC
Confidence            6789999999999                           8899999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      ..|.|+||-.+.
T Consensus       142 q~v~VDw~Fv~g  153 (170)
T KOG0130|consen  142 QNVSVDWCFVKG  153 (170)
T ss_pred             CceeEEEEEecC
Confidence            999999985433

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

Probab=99.07  E-value=1.8e-10  Score=92.88  Aligned_cols=82  Identities=26%  Similarity=0.366  Sum_probs=68.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+.+|++||.|.+                           |.|++|+.|+.++|||||+|.+.++|.+|+.+||..+.  
T Consensus        51 lr~lFe~yg~V~e---------------------------inl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlp  103 (510)
T KOG0144|consen   51 LRELFEKYGNVYE---------------------------INLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLP  103 (510)
T ss_pred             HHHHHHHhCceeE---------------------------EEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccC
Confidence            7899999999999                           99999999999999999999999999999999998774  


Q ss_pred             -CCeeEEEEeccCCCCC---CCCCCCcCCCCCCCC
Q 033734           80 -DGRVIFVDNVRPSRRY---NTDAPLARQSAQSPE  110 (112)
Q Consensus        80 -~g~~i~V~~a~~~~~~---~~~~~~~~~~~~~~~  110 (112)
                       +.++|.|++|...+.+   .+....+..+...+|
T Consensus       104 G~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te  138 (510)
T KOG0144|consen  104 GMHHPVQVKYADGERERIVEERKLFVGMLSKQCTE  138 (510)
T ss_pred             CCCcceeecccchhhhccccchhhhhhhccccccH
Confidence             4689999999776655   444455555554444

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

Probab=99.06  E-value=5.2e-10  Score=81.17  Aligned_cols=61  Identities=26%  Similarity=0.463  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|..||+|..                           +.|...     +.|||||+|.++.+|..|+..|||+.|.|
T Consensus        27 LE~~F~~yG~lrs---------------------------vWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG   74 (195)
T KOG0107|consen   27 LERAFSKYGPLRS---------------------------VWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICG   74 (195)
T ss_pred             HHHHHHhcCccee---------------------------EEEeec-----CCCceEEeccCcccHHHHHhhcCCccccC
Confidence            7889999999988                           766443     57999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      .+|+|++++....
T Consensus        75 ~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   75 SRIRVELSTGRPR   87 (195)
T ss_pred             ceEEEEeecCCcc
Confidence            9999999976554

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

Probab=99.05  E-value=8.3e-10  Score=79.14  Aligned_cols=63  Identities=37%  Similarity=0.768  Sum_probs=59.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|..||.|..                           +.+..|+.+++++|+|||+|.++++|..|+..++|..+.|
T Consensus       132 l~~~F~~~g~~~~---------------------------~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~  184 (306)
T COG0724         132 LRELFKKFGPVKR---------------------------VRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG  184 (306)
T ss_pred             HHHHHHhcCceeE---------------------------EEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECC
Confidence            7899999999999                           9999998899999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|..+..
T Consensus       185 ~~~~v~~~~~  194 (306)
T COG0724         185 RPLRVQKAQP  194 (306)
T ss_pred             ceeEeecccc
Confidence            9999999653

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

Probab=99.05  E-value=7.5e-10  Score=88.74  Aligned_cols=62  Identities=40%  Similarity=0.624  Sum_probs=58.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.|+.+++++|||||+|.+.++|++||. |+|..+.|
T Consensus       106 l~~~F~~~G~v~~---------------------------v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g  157 (457)
T TIGR01622       106 LYEFFSKVGKVRD---------------------------VQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLG  157 (457)
T ss_pred             HHHHHHhcCCeeE---------------------------EEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECC
Confidence            7899999999999                           9999999999999999999999999999997 99999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|..+..
T Consensus       158 ~~i~v~~~~~  167 (457)
T TIGR01622       158 RPIIVQSSQA  167 (457)
T ss_pred             eeeEEeecch
Confidence            9999988653

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.

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

Probab=99.03  E-value=5.3e-10  Score=77.84  Aligned_cols=63  Identities=25%  Similarity=0.435  Sum_probs=59.4

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|.++|+..|+|.+                           +.|-.|+.+-.+.|||||+|.+.++|..|+..++|..++
T Consensus        52 qiyELFs~cG~irr---------------------------iiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLd  104 (153)
T KOG0121|consen   52 QIYELFSKCGDIRR---------------------------IIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLD  104 (153)
T ss_pred             HHHHHHHhccchhe---------------------------eEeccccCCcCccceEEEEEecchhHHHHHHHhccCccc
Confidence            47899999999999                           888899988999999999999999999999999999999


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      .+.|++++.-
T Consensus       105 dr~ir~D~D~  114 (153)
T KOG0121|consen  105 DRPIRIDWDA  114 (153)
T ss_pred             ccceeeeccc
Confidence            9999999874

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.03  E-value=2.3e-09  Score=81.91  Aligned_cols=60  Identities=18%  Similarity=0.311  Sum_probs=54.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|.+                           +.|++|+.   .+|||||+|.++++|+.|+. |+|..+.|
T Consensus        21 LrefFS~~G~I~~---------------------------V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~g   69 (260)
T PLN03120         21 IKEFFSFSGDIEY---------------------------VEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVD   69 (260)
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCC
Confidence            7899999999999                           99998864   57999999999999999996 99999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|..+..-
T Consensus        70 r~V~Vt~a~~~   80 (260)
T PLN03120         70 QSVTITPAEDY   80 (260)
T ss_pred             ceEEEEeccCC
Confidence            99999998643

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

Probab=99.01  E-value=1.4e-09  Score=83.48  Aligned_cols=63  Identities=38%  Similarity=0.573  Sum_probs=60.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|.+||.|..                           +++++|..|++.+||+||++.+-++|.-||..|||+.+++
T Consensus       295 LWQlFgpFGAv~n---------------------------VKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~  347 (360)
T KOG0145|consen  295 LWQLFGPFGAVTN---------------------------VKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGD  347 (360)
T ss_pred             HHHHhCcccceee---------------------------EEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccc
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.+.|.+-..
T Consensus       348 rvLQVsFKtn  357 (360)
T KOG0145|consen  348 RVLQVSFKTN  357 (360)
T ss_pred             eEEEEEEecC
Confidence            9999988654

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

Probab=98.98  E-value=1.9e-09  Score=82.78  Aligned_cols=59  Identities=29%  Similarity=0.581  Sum_probs=54.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |++.|++||+|.+                           +|+.+|+      ||+||.|.+.|.|.+||.+||+.++.|
T Consensus       181 mr~~Fs~fG~I~E---------------------------VRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G  227 (321)
T KOG0148|consen  181 MRQTFSPFGPIQE---------------------------VRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGG  227 (321)
T ss_pred             HHHhcccCCcceE---------------------------EEEeccc------ceEEEEecchhhHHHHHHHhcCceeCc
Confidence            6899999999999                           9998886      899999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.++|.|-+...
T Consensus       228 ~~VkCsWGKe~~  239 (321)
T KOG0148|consen  228 QLVRCSWGKEGD  239 (321)
T ss_pred             eEEEEeccccCC
Confidence            999999976543

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

Probab=98.98  E-value=4.2e-10  Score=86.64  Aligned_cols=67  Identities=31%  Similarity=0.543  Sum_probs=62.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|-+||-|+.                           .++..|+.|+.++.|+||.|+++.+++.||.+|||.+|+-
T Consensus       302 liQmF~PFGhivS---------------------------aKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGM  354 (371)
T KOG0146|consen  302 LIQMFLPFGHIVS---------------------------AKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGM  354 (371)
T ss_pred             HHHHhccccceee---------------------------eeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhh
Confidence            5678999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      ++++|.+-+++...
T Consensus       355 KRLKVQLKRPkdan  368 (371)
T KOG0146|consen  355 KRLKVQLKRPKDAN  368 (371)
T ss_pred             hhhhhhhcCccccC
Confidence            99999998876543

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

Probab=98.97  E-value=1.4e-09  Score=90.93  Aligned_cols=61  Identities=31%  Similarity=0.482  Sum_probs=55.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |+++|++||+|.+                           ++|++| .+++++|||||+|.++++|++||+.||+..+. 
T Consensus        75 L~~~F~~~G~I~~---------------------------vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~  126 (578)
T TIGR01648        75 LVPLFEKAGPIYE---------------------------LRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRP  126 (578)
T ss_pred             HHHHHHhhCCEEE---------------------------EEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecC
Confidence            7899999999999                           999999 69999999999999999999999999999985 


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      ++.|.|..+.
T Consensus       127 Gr~l~V~~S~  136 (578)
T TIGR01648       127 GRLLGVCISV  136 (578)
T ss_pred             Cccccccccc
Confidence            7777776553

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=98.96  E-value=1.6e-09  Score=89.06  Aligned_cols=59  Identities=22%  Similarity=0.488  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCH--HHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTE--EEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~--~~a~~Ai~~l~g~~l   79 (112)
                      |+.+|+.||.|.+                           +.|+  +++|  ||||||+|.+.  .++.+||..|||...
T Consensus        27 LravFSeFGsVkd---------------------------VEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEW   75 (759)
T PLN03213         27 LLKIFSPMGTVDA---------------------------VEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVW   75 (759)
T ss_pred             HHHHHHhcCCeeE---------------------------EEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCee
Confidence            7889999999999                           9998  4467  99999999987  789999999999999


Q ss_pred             CCeeEEEEeccC
Q 033734           80 DGRVIFVDNVRP   91 (112)
Q Consensus        80 ~g~~i~V~~a~~   91 (112)
                      +|+.|+|..|++
T Consensus        76 KGR~LKVNKAKP   87 (759)
T PLN03213         76 KGGRLRLEKAKE   87 (759)
T ss_pred             cCceeEEeeccH
Confidence            999999999974

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

Probab=98.94  E-value=3.4e-09  Score=85.94  Aligned_cols=63  Identities=21%  Similarity=0.393  Sum_probs=55.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeC---CCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK---GKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~---~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|++||.|..                           |.|+++.   .++...|++||+|.++++|++|+..|||..
T Consensus       436 l~~~f~~~G~v~~---------------------------v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~  488 (509)
T TIGR01642       436 VKTEFSKYGPLIN---------------------------IVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRK  488 (509)
T ss_pred             HHHHHHhcCCeeE---------------------------EEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCE
Confidence            6788999999999                           8888752   345678999999999999999999999999


Q ss_pred             eCCeeEEEEeccC
Q 033734           79 LDGRVIFVDNVRP   91 (112)
Q Consensus        79 l~g~~i~V~~a~~   91 (112)
                      ++|+.|.|.+...
T Consensus       489 ~~gr~v~~~~~~~  501 (509)
T TIGR01642       489 FNDRVVVAAFYGE  501 (509)
T ss_pred             ECCeEEEEEEeCH
Confidence            9999999998753

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

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

Probab=98.94  E-value=1.4e-09  Score=87.82  Aligned_cols=66  Identities=27%  Similarity=0.466  Sum_probs=59.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      ++++|++||.|.+                           |.|.+|. -+.+||||||.|.+.+-|..||+.|||...+ 
T Consensus       141 vr~iFs~fG~Ied---------------------------~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tme  192 (510)
T KOG0144|consen  141 VREIFSRFGHIED---------------------------CYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTME  192 (510)
T ss_pred             HHHHHHhhCccch---------------------------hhheecc-cccccceeEEEEehHHHHHHHHHhhccceeec
Confidence            6789999999999                           9999997 6899999999999999999999999998864 


Q ss_pred             --CeeEEEEeccCCCCC
Q 033734           81 --GRVIFVDNVRPSRRY   95 (112)
Q Consensus        81 --g~~i~V~~a~~~~~~   95 (112)
                        ..+|.|++|.+.+++
T Consensus       193 Gcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  193 GCSQPLVVKFADTQKDK  209 (510)
T ss_pred             cCCCceEEEecccCCCc
Confidence              469999999876654

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

Probab=98.94  E-value=3e-09  Score=86.82  Aligned_cols=59  Identities=25%  Similarity=0.356  Sum_probs=54.5

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|+.||.|.+                           +++++++     +|+|||+|.++++|+.|+..|||..++
T Consensus       292 ~L~~lF~~yG~V~~---------------------------vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~  339 (481)
T TIGR01649       292 RLFNLFCVYGNVER---------------------------VKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLF  339 (481)
T ss_pred             HHHHHHHhcCCeEE---------------------------EEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            37899999999999                           9998873     699999999999999999999999999


Q ss_pred             CeeEEEEeccC
Q 033734           81 GRVIFVDNVRP   91 (112)
Q Consensus        81 g~~i~V~~a~~   91 (112)
                      |+.|.|.+++.
T Consensus       340 g~~l~v~~s~~  350 (481)
T TIGR01649       340 GKPLRVCPSKQ  350 (481)
T ss_pred             CceEEEEEccc
Confidence            99999999854

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).

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

Probab=98.94  E-value=1.5e-10  Score=84.57  Aligned_cols=60  Identities=32%  Similarity=0.603  Sum_probs=56.9

Q ss_pred             HHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCe
Q 033734            3 ADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR   82 (112)
Q Consensus         3 ~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~   82 (112)
                      ..+|++||.|+.                           +.+++|+.||+++||||..|.+-.+.--|+..|||-.|.||
T Consensus        53 l~VFSqyGe~vd---------------------------inLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gR  105 (219)
T KOG0126|consen   53 LCVFSQYGEIVD---------------------------INLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGR  105 (219)
T ss_pred             EEEeeccCceEE---------------------------EEEEecCCCCcccceEEEEecCccceEEEEeccCCceecce
Confidence            467999999999                           99999999999999999999999999999999999999999


Q ss_pred             eEEEEec
Q 033734           83 VIFVDNV   89 (112)
Q Consensus        83 ~i~V~~a   89 (112)
                      .|+|+-.
T Consensus       106 tirVDHv  112 (219)
T KOG0126|consen  106 TIRVDHV  112 (219)
T ss_pred             eEEeeec
Confidence            9999865

>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=98.93  E-value=1e-08  Score=60.65  Aligned_cols=59  Identities=46%  Similarity=0.772  Sum_probs=52.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|..+|.|..                           +.+..++.+ ..+|+|||+|.+.++|+.|+..+++..+.|
T Consensus        16 i~~~~~~~g~i~~---------------------------~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~   67 (74)
T cd00590          16 LRELFSKFGKVES---------------------------VRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGG   67 (74)
T ss_pred             HHHHHHhcCCEEE---------------------------EEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            6788999999988                           888888744 789999999999999999999999999999


Q ss_pred             eeEEEEe
Q 033734           82 RVIFVDN   88 (112)
Q Consensus        82 ~~i~V~~   88 (112)
                      +.+.|.+
T Consensus        68 ~~~~v~~   74 (74)
T cd00590          68 RPLRVEF   74 (74)
T ss_pred             eEEEEeC
Confidence            9998863

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).

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

Probab=98.93  E-value=1.5e-09  Score=88.26  Aligned_cols=66  Identities=29%  Similarity=0.596  Sum_probs=61.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|+..|.|..                           .+++.|++||+++||||++|.++++|..|++.|||.++.|
T Consensus        35 l~~~~~~~g~v~s---------------------------~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~g   87 (435)
T KOG0108|consen   35 LLSIFSGVGPVLS---------------------------FRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNG   87 (435)
T ss_pred             HHHHHhccCccce---------------------------eeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCC
Confidence            6788999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|+|.++.....
T Consensus        88 r~l~v~~~~~~~~  100 (435)
T KOG0108|consen   88 RKLRVNYASNRKN  100 (435)
T ss_pred             ceEEeecccccch
Confidence            9999999864433

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

Probab=98.91  E-value=1.2e-09  Score=87.14  Aligned_cols=61  Identities=34%  Similarity=0.623  Sum_probs=58.1

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+..|.+||+|+.                           +.+-+|+.|++.+|||||+|.-++.|+-|+++|||..++
T Consensus       129 tiR~AF~PFGPIKS---------------------------InMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlG  181 (544)
T KOG0124|consen  129 TIRRAFDPFGPIKS---------------------------INMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG  181 (544)
T ss_pred             HHHhhccCCCCcce---------------------------eecccccccccccceEEEEEeCcHHHHHHHHHhcccccc
Confidence            47899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEe
Q 033734           81 GRVIFVDN   88 (112)
Q Consensus        81 g~~i~V~~   88 (112)
                      ||.|+|..
T Consensus       182 GRNiKVgr  189 (544)
T KOG0124|consen  182 GRNIKVGR  189 (544)
T ss_pred             CccccccC
Confidence            99999863

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

Probab=98.87  E-value=3e-09  Score=77.68  Aligned_cols=62  Identities=35%  Similarity=0.493  Sum_probs=59.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|-+.|+|+.                           +++++|+.++..+||||++|.++++|+=||+.|+.-.+.|
T Consensus        26 l~EL~iqagpVv~---------------------------i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYg   78 (203)
T KOG0131|consen   26 LYELFIQAGPVVN---------------------------LHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYG   78 (203)
T ss_pred             HHHHHHhcCceee---------------------------eecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcC
Confidence            6789999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      ++|+|..+.
T Consensus        79 rpIrv~kas   87 (203)
T KOG0131|consen   79 RPIRVNKAS   87 (203)
T ss_pred             ceeEEEecc
Confidence            999999886

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

Probab=98.87  E-value=5.3e-09  Score=86.52  Aligned_cols=68  Identities=35%  Similarity=0.586  Sum_probs=61.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|+.||.|.+                           +.|++.++ |+.+|||||.|....+|..|+..+||..|+|
T Consensus       134 Lk~vFs~~G~V~E---------------------------i~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~g  185 (678)
T KOG0127|consen  134 LKNVFSNFGKVVE---------------------------IVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDG  185 (678)
T ss_pred             HHHHHhhcceEEE---------------------------EEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecC
Confidence            7889999999999                           99998774 5555999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      |+|.|+||.+...+..
T Consensus       186 R~VAVDWAV~Kd~ye~  201 (678)
T KOG0127|consen  186 RPVAVDWAVDKDTYED  201 (678)
T ss_pred             ceeEEeeecccccccc
Confidence            9999999987766544

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

Probab=98.85  E-value=6e-09  Score=77.13  Aligned_cols=51  Identities=31%  Similarity=0.434  Sum_probs=48.0

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS   92 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~   92 (112)
                      .++-+++.||.++|||||+|.+++.|.-|-+.||++.++++.|.|.+..+.
T Consensus        80 ~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   80 FRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             EEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            788899999999999999999999999999999999999999999887665

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

Probab=98.83  E-value=5.7e-09  Score=85.88  Aligned_cols=65  Identities=40%  Similarity=0.691  Sum_probs=60.7

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      ||+.+|++||.|..                           +.+.+|.+||+++||+||+|.+.++|++|+.+|||.+|-
T Consensus       294 ~lr~ifepfg~Ie~---------------------------v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelA  346 (549)
T KOG0147|consen  294 MLRGIFEPFGKIEN---------------------------VQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELA  346 (549)
T ss_pred             HHhhhccCccccee---------------------------eeeccccccccccCcceEEEecHHHHHHHHHHhccceec
Confidence            57889999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|+|...+.+
T Consensus       347 Gr~ikV~~v~~r  358 (549)
T KOG0147|consen  347 GRLIKVSVVTER  358 (549)
T ss_pred             CceEEEEEeeee
Confidence            999999877543

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

Probab=98.80  E-value=1.3e-08  Score=81.30  Aligned_cols=64  Identities=34%  Similarity=0.480  Sum_probs=59.5

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      ||.+.|+++|+++.                           +++++|- |  +-|||||.|.++++|.+|+..||...+.
T Consensus        14 ~l~~~f~~~~~v~s---------------------------~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~   63 (369)
T KOG0123|consen   14 MLFDKFSPAGPVLS---------------------------IRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLK   63 (369)
T ss_pred             HHHHHhcccCCcee---------------------------EEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccC
Confidence            58899999999999                           9999998 6  9999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      |++|++.|+.....
T Consensus        64 ~~~~rim~s~rd~~   77 (369)
T KOG0123|consen   64 GKPIRIMWSQRDPS   77 (369)
T ss_pred             CcEEEeehhccCCc
Confidence            99999999975543

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

Probab=98.76  E-value=1.3e-08  Score=84.19  Aligned_cols=69  Identities=33%  Similarity=0.664  Sum_probs=63.5

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|.++|+..|+|..                           |.++.++.++.+|||+||+|...++++.|+....++.+.
T Consensus        21 qL~e~FS~vGPik~---------------------------~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~   73 (678)
T KOG0127|consen   21 QLEEFFSYVGPIKH---------------------------AVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFE   73 (678)
T ss_pred             HHHHhhhcccCcce---------------------------eEEecCCCcccccCccceeeehHhHHHHHHHHhhcCccc
Confidence            47889999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYN   96 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~   96 (112)
                      |+.|+|+.+..+.+..
T Consensus        74 Gr~l~v~~A~~R~r~e   89 (678)
T KOG0127|consen   74 GRILNVDPAKKRARSE   89 (678)
T ss_pred             ceecccccccccccch
Confidence            9999999997665543

>PLN03121 nucleic acid binding protein; Provisional

Probab=98.76  E-value=3.4e-08  Score=74.79  Aligned_cols=59  Identities=20%  Similarity=0.288  Sum_probs=52.8

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|+.||+|..                           ++|++|.   +.+|+|||+|.++++++.|+. |+|..|.
T Consensus        21 dLrefFS~~G~I~~---------------------------V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~   69 (243)
T PLN03121         21 DVYDFFSHCGAIEH---------------------------VEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIV   69 (243)
T ss_pred             HHHHHHHhcCCeEE---------------------------EEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeC
Confidence            37899999999999                           9999984   445899999999999999996 9999999


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      +++|.|....
T Consensus        70 d~~I~It~~~   79 (243)
T PLN03121         70 DQRVCITRWG   79 (243)
T ss_pred             CceEEEEeCc
Confidence            9999997754

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

Probab=98.76  E-value=1.3e-08  Score=82.42  Aligned_cols=60  Identities=37%  Similarity=0.588  Sum_probs=54.1

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|+.||.|.+                           ++.++|        ||||+|.+-++|.+|++.+||++|+
T Consensus       275 ~lk~~F~~~G~veR---------------------------Vkk~rD--------YaFVHf~eR~davkAm~~~ngkeld  319 (506)
T KOG0117|consen  275 TLKKLFNEFGKVER---------------------------VKKPRD--------YAFVHFAEREDAVKAMKETNGKELD  319 (506)
T ss_pred             HHHHHHHhccceEE---------------------------eecccc--------eeEEeecchHHHHHHHHHhcCceec
Confidence            48999999999999                           776655        9999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCC
Q 033734           81 GRVIFVDNVRPSRRY   95 (112)
Q Consensus        81 g~~i~V~~a~~~~~~   95 (112)
                      |..|.|.+|+|....
T Consensus       320 G~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  320 GSPIEVTLAKPVDKK  334 (506)
T ss_pred             CceEEEEecCChhhh
Confidence            999999999876543

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

Probab=98.74  E-value=3.7e-08  Score=72.53  Aligned_cols=61  Identities=21%  Similarity=0.384  Sum_probs=52.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|.+||.|.+                           +.|...   -..-.||||+|.++.+|+.||..-||..++|
T Consensus        23 ieDlFyKyg~i~~---------------------------ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg   72 (241)
T KOG0105|consen   23 IEDLFYKYGRIRE---------------------------IELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDG   72 (241)
T ss_pred             HHHHHhhhcceEE---------------------------EEeccC---CCCCCeeEEEecCccchhhhhhcccccccCc
Confidence            6899999999999                           665322   2345799999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      .+|+|+++...
T Consensus        73 ~rLRVEfprgg   83 (241)
T KOG0105|consen   73 CRLRVEFPRGG   83 (241)
T ss_pred             ceEEEEeccCC
Confidence            99999999754

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

Probab=98.74  E-value=4e-08  Score=82.36  Aligned_cols=59  Identities=36%  Similarity=0.682  Sum_probs=52.4

Q ss_pred             CHHHHhhcc--CcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            1 MLADAFSQF--GQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         1 ~l~~~f~~~--G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      .|+++|++|  |.|.+                           ++++        ++||||+|.+.++|++|+..|||..
T Consensus       249 ~L~~~F~~f~~G~I~r---------------------------V~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~  293 (578)
T TIGR01648       249 IIEKSFSEFKPGKVER---------------------------VKKI--------RDYAFVHFEDREDAVKAMDELNGKE  293 (578)
T ss_pred             HHHHHHHhcCCCceEE---------------------------EEee--------cCeEEEEeCCHHHHHHHHHHhCCCE
Confidence            378999999  99988                           7654        4699999999999999999999999


Q ss_pred             eCCeeEEEEeccCCCC
Q 033734           79 LDGRVIFVDNVRPSRR   94 (112)
Q Consensus        79 l~g~~i~V~~a~~~~~   94 (112)
                      |+|+.|.|+++++...
T Consensus       294 i~Gr~I~V~~Akp~~~  309 (578)
T TIGR01648       294 LEGSEIEVTLAKPVDK  309 (578)
T ss_pred             ECCEEEEEEEccCCCc
Confidence            9999999999976543

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.

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

Probab=98.73  E-value=4.6e-08  Score=79.90  Aligned_cols=59  Identities=22%  Similarity=0.332  Sum_probs=51.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +.|+++..    .|+|||+|.++++|.+|+..|||..+.+
T Consensus       113 L~~~F~~~G~V~~---------------------------v~i~~~~~----~~~afVef~~~~~A~~A~~~Lng~~i~~  161 (481)
T TIGR01649       113 LYQIFNPYGKVLR---------------------------IVTFTKNN----VFQALVEFESVNSAQHAKAALNGADIYN  161 (481)
T ss_pred             HHHHHhccCCEEE---------------------------EEEEecCC----ceEEEEEECCHHHHHHHHHHhcCCcccC
Confidence            7899999999999                           88877642    4799999999999999999999999975


Q ss_pred             --eeEEEEeccC
Q 033734           82 --RVIFVDNVRP   91 (112)
Q Consensus        82 --~~i~V~~a~~   91 (112)
                        +.|+|++++.
T Consensus       162 ~~~~l~v~~sk~  173 (481)
T TIGR01649       162 GCCTLKIEYAKP  173 (481)
T ss_pred             CceEEEEEEecC
Confidence              5888888865

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

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

Probab=98.73  E-value=2.8e-08  Score=77.15  Aligned_cols=68  Identities=26%  Similarity=0.499  Sum_probs=58.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|++||.|.+                           |.|+++        ||||+..+...++.||..|||..|+|
T Consensus        19 lr~lFe~ygkVlE---------------------------CDIvKN--------YgFVHiEdktaaedairNLhgYtLhg   63 (346)
T KOG0109|consen   19 LRSLFEQYGKVLE---------------------------CDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHG   63 (346)
T ss_pred             HHHHHHhhCceEe---------------------------eeeecc--------cceEEeecccccHHHHhhcccceecc
Confidence            7889999999999                           999887        89999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCCCCCcCC
Q 033734           82 RVIFVDNVRPSRRYNTDAPLARQ  104 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~~~~~~~  104 (112)
                      ..|.|+-++.+..-......+.-
T Consensus        64 ~nInVeaSksKsk~stkl~vgNi   86 (346)
T KOG0109|consen   64 VNINVEASKSKSKASTKLHVGNI   86 (346)
T ss_pred             eEEEEEeccccCCCccccccCCC
Confidence            99999998877554444444433

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

Probab=98.73  E-value=1.7e-08  Score=80.17  Aligned_cols=63  Identities=30%  Similarity=0.544  Sum_probs=59.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.-+|+.||.|..                           |.|++|..||.+--||||+|.+.+++++|.-.|+...|+.
T Consensus       256 LeiIFSrFG~i~s---------------------------ceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD  308 (479)
T KOG0415|consen  256 LEIIFSRFGKIVS---------------------------CEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD  308 (479)
T ss_pred             hhhHHhhccccee---------------------------eeEEecccccchhheeeeeecchhhHHHHHhhhcceeecc
Confidence            5668999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      ++|.|+++++
T Consensus       309 rRIHVDFSQS  318 (479)
T KOG0415|consen  309 RRIHVDFSQS  318 (479)
T ss_pred             ceEEeehhhh
Confidence            9999999864

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

Probab=98.70  E-value=4.6e-08  Score=78.12  Aligned_cols=65  Identities=38%  Similarity=0.716  Sum_probs=58.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.+.|+.||+|+.                           |++..|. .| ++|| ||+|.++++|++||..+||..+.+
T Consensus        93 ~~d~f~~~g~ilS---------------------------~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~  142 (369)
T KOG0123|consen   93 LYDTFSEFGNILS---------------------------CKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNG  142 (369)
T ss_pred             HHHHHHhhcCeeE---------------------------EEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCC
Confidence            6899999999999                           9999997 44 9999 999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|....++..+.
T Consensus       143 kki~vg~~~~~~er~  157 (369)
T KOG0123|consen  143 KKIYVGLFERKEERE  157 (369)
T ss_pred             CeeEEeeccchhhhc
Confidence            999998886554443

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

Probab=98.70  E-value=2.9e-08  Score=76.62  Aligned_cols=64  Identities=27%  Similarity=0.474  Sum_probs=57.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      ++++|..||.|.+                           |.+.+.+ .|.++|++||.|.+..+|+.||..|||+..+ 
T Consensus        36 vrrlf~pfG~~~e---------------------------~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmp   87 (371)
T KOG0146|consen   36 VRRLFQPFGNIEE---------------------------CTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMP   87 (371)
T ss_pred             HHHHhcccCCcce---------------------------eEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCC
Confidence            5789999999999                           9998887 6899999999999999999999999999976 


Q ss_pred             --CeeEEEEeccCCC
Q 033734           81 --GRVIFVDNVRPSR   93 (112)
Q Consensus        81 --g~~i~V~~a~~~~   93 (112)
                        ...+.|+++...+
T Consensus        88 GASSSLVVK~ADTdk  102 (371)
T KOG0146|consen   88 GASSSLVVKFADTDK  102 (371)
T ss_pred             CCccceEEEeccchH
Confidence              4689999986443

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

Probab=98.69  E-value=2.2e-08  Score=77.67  Aligned_cols=63  Identities=25%  Similarity=0.490  Sum_probs=56.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+..|++||++.+                           |.|++|        |+||+|.-.++|..||..||++++.|
T Consensus        95 lRa~fe~ygpvie---------------------------cdivkd--------y~fvh~d~~eda~~air~l~~~~~~g  139 (346)
T KOG0109|consen   95 LRAKFEKYGPVIE---------------------------CDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQG  139 (346)
T ss_pred             HhhhhcccCCcee---------------------------eeeecc--------eeEEEEeeccchHHHHhccccccccc
Confidence            6788999999999                           999877        99999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTDA   99 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~~   99 (112)
                      +++.|.+++++-+-.++.
T Consensus       140 k~m~vq~stsrlrtapgm  157 (346)
T KOG0109|consen  140 KRMHVQLSTSRLRTAPGM  157 (346)
T ss_pred             ceeeeeeeccccccCCCC
Confidence            999999998876655543

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

Probab=98.66  E-value=3.5e-08  Score=72.10  Aligned_cols=70  Identities=29%  Similarity=0.513  Sum_probs=61.6

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|.+.|++||.+..                          .-.+++|..||.++|+|||.|.+.+.+.+|+..|+|..+.
T Consensus       112 ~L~dtFsafG~l~~--------------------------~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~  165 (203)
T KOG0131|consen  112 LLYDTFSAFGVLIS--------------------------PPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLC  165 (203)
T ss_pred             HHHHHHHhcccccc--------------------------CCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhc
Confidence            47889999999876                          1478999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYN   96 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~   96 (112)
                      ++++.|+.+.....++
T Consensus       166 nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  166 NRPITVSYAFKKDTKG  181 (203)
T ss_pred             CCceEEEEEEecCCCc
Confidence            9999999996554443

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

Probab=98.56  E-value=1.4e-07  Score=70.48  Aligned_cols=62  Identities=24%  Similarity=0.430  Sum_probs=54.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|++||.|.+                           +...   .+.+.||-|||.|.+++.|-.|+.+|+|..+.|
T Consensus        30 L~~LFsqfG~ild---------------------------I~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg   79 (221)
T KOG4206|consen   30 LYLLFSQFGKILD---------------------------ISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYG   79 (221)
T ss_pred             HHHHHHhhCCeEE---------------------------EEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccC
Confidence            5569999999988                           4332   367899999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +++++.+|....
T Consensus        80 K~mriqyA~s~s   91 (221)
T KOG4206|consen   80 KPMRIQYAKSDS   91 (221)
T ss_pred             chhheecccCcc
Confidence            999999997544

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

Probab=98.48  E-value=5.1e-07  Score=75.63  Aligned_cols=63  Identities=32%  Similarity=0.595  Sum_probs=58.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|++||.|+-                           ++|+++-.+---+.|+||++++.++|.+||..||-++|.|
T Consensus       422 LKnlFSKyGKVvG---------------------------AKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHG  474 (940)
T KOG4661|consen  422 LKNLFSKYGKVVG---------------------------AKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHG  474 (940)
T ss_pred             HHHHHHHhcceec---------------------------eeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcc
Confidence            7899999999998                           8999987666678899999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|+.++.
T Consensus       475 rmISVEkaKN  484 (940)
T KOG4661|consen  475 RMISVEKAKN  484 (940)
T ss_pred             eeeeeeeccc
Confidence            9999998864

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

Probab=98.47  E-value=2.4e-07  Score=74.12  Aligned_cols=63  Identities=22%  Similarity=0.441  Sum_probs=59.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|+.||+|+.                           |.+.+++.++..+||+|++|++..+...||..||-..++|
T Consensus       227 iKSVFEAFG~I~~---------------------------C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGG  279 (544)
T KOG0124|consen  227 IKSVFEAFGEIVK---------------------------CQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGG  279 (544)
T ss_pred             HHHHHHhhcceee---------------------------EEeeccCCCCCccceeeEEeccccchHHHhhhcchhhccc
Confidence            6889999999999                           9999999888999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      .-++|-.+..
T Consensus       280 QyLRVGk~vT  289 (544)
T KOG0124|consen  280 QYLRVGKCVT  289 (544)
T ss_pred             ceEecccccC
Confidence            9999987753

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

Probab=98.45  E-value=1.3e-07  Score=80.00  Aligned_cols=65  Identities=26%  Similarity=0.527  Sum_probs=59.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      ++.+|.+||++..                           ++|+.....+.++|||||+|.++.+|.+|+.+|.++.+.|
T Consensus       630 Vr~LF~aFGqlks---------------------------vRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyG  682 (725)
T KOG0110|consen  630 VRKLFTAFGQLKS---------------------------VRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYG  682 (725)
T ss_pred             HHHHHhcccceee---------------------------eccchhhcchhhccceeeeccCcHHHHHHHHhhcccceec
Confidence            6789999999999                           8888876677889999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      |++.++|+....
T Consensus       683 RrLVLEwA~~d~  694 (725)
T KOG0110|consen  683 RRLVLEWAKSDN  694 (725)
T ss_pred             hhhheehhccch
Confidence            999999997553

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

Probab=98.37  E-value=1.1e-06  Score=59.42  Aligned_cols=59  Identities=25%  Similarity=0.444  Sum_probs=50.3

Q ss_pred             HHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCe
Q 033734            3 ADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR   82 (112)
Q Consensus         3 ~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~   82 (112)
                      -++|.+||+|..                           ++|-..+   .-+|-|||.|++..+|++|+.+|.|..++++
T Consensus        36 ydlFGkyg~IrQ---------------------------IRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~r   85 (124)
T KOG0114|consen   36 YDLFGKYGTIRQ---------------------------IRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNR   85 (124)
T ss_pred             HHHhhcccceEE---------------------------EEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCc
Confidence            578999999988                           6664443   4589999999999999999999999999999


Q ss_pred             eEEEEeccC
Q 033734           83 VIFVDNVRP   91 (112)
Q Consensus        83 ~i~V~~a~~   91 (112)
                      -+.|-+-.+
T Consensus        86 yl~vlyyq~   94 (124)
T KOG0114|consen   86 YLVVLYYQP   94 (124)
T ss_pred             eEEEEecCH
Confidence            999876543

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

Probab=98.33  E-value=3.3e-07  Score=71.86  Aligned_cols=66  Identities=35%  Similarity=0.587  Sum_probs=59.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |++.|++||+|.+                           |.+++|+.+++++||+||+|.+++...+++. ..-+.|+|
T Consensus        23 Lr~yf~~~Gev~d---------------------------~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dg   74 (311)
T KOG4205|consen   23 LREYFSQFGEVTD---------------------------CVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDG   74 (311)
T ss_pred             HHHHhcccCceee---------------------------EEEeccCCCCCcccccceecCCCcchheeec-ccccccCC
Confidence            7899999999999                           9999999999999999999999999988887 44578999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.+..|.++...
T Consensus        75 r~ve~k~av~r~~~   88 (311)
T KOG4205|consen   75 RSVEPKRAVSREDQ   88 (311)
T ss_pred             ccccceeccCcccc
Confidence            99999998776544

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

Probab=98.33  E-value=1.8e-06  Score=73.18  Aligned_cols=62  Identities=35%  Similarity=0.530  Sum_probs=51.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKN---RSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~---~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      +..+|.+.|.|..                           +.|.+-+...   -+.|||||+|.++++|++|+..|+|+.
T Consensus       532 l~~~F~k~G~VlS---------------------------~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtv  584 (725)
T KOG0110|consen  532 LEDLFSKQGTVLS---------------------------IEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTV  584 (725)
T ss_pred             HHHHHHhcCeEEE---------------------------EEEeccccccccccccceeEEEecCHHHHHHHHHHhcCce
Confidence            5678888999888                           6555544221   356999999999999999999999999


Q ss_pred             eCCeeEEEEecc
Q 033734           79 LDGRVIFVDNVR   90 (112)
Q Consensus        79 l~g~~i~V~~a~   90 (112)
                      |+|+.|.|+++-
T Consensus       585 ldGH~l~lk~S~  596 (725)
T KOG0110|consen  585 LDGHKLELKISE  596 (725)
T ss_pred             ecCceEEEEecc
Confidence            999999999987

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

Probab=98.32  E-value=2.9e-07  Score=70.35  Aligned_cols=52  Identities=35%  Similarity=0.582  Sum_probs=48.5

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR   93 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~   93 (112)
                      .++++|+.||+++||+||.|.+++++..|...|||.-++.+.|.++.+..+.
T Consensus       220 akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  220 AKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             ccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhHHh
Confidence            8999999999999999999999999999999999999999999988775544

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

Probab=98.19  E-value=3.8e-06  Score=68.59  Aligned_cols=49  Identities=27%  Similarity=0.488  Sum_probs=45.4

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP   91 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~   91 (112)
                      |.+..|. +|++||+|.|+|.+++.+++|++.||-+.+.|++|.|+-...
T Consensus        75 veLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   75 VELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             eeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            8888996 899999999999999999999999999999999999986643

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

Probab=98.11  E-value=6.9e-06  Score=62.01  Aligned_cols=48  Identities=33%  Similarity=0.481  Sum_probs=45.0

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      +.|..|+.++.++||+||+|.+.+.+++|+. |||..+.++.+.|...+
T Consensus       131 ~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  131 VTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             eeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            7899999898999999999999999999999 99999999999988765

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

Probab=98.11  E-value=3.2e-06  Score=66.35  Aligned_cols=66  Identities=30%  Similarity=0.578  Sum_probs=59.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      +++.|++||.|.+                           +.++.|..+.+++||+||+|.+++++.+++. .+.+.|.+
T Consensus       114 ~r~yfe~~g~v~~---------------------------~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~g  165 (311)
T KOG4205|consen  114 FKDYFEQFGKVAD---------------------------VVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNG  165 (311)
T ss_pred             HhhhhhccceeEe---------------------------eEEeecccccccccceeeEeccccccceecc-cceeeecC
Confidence            6789999999999                           9999999999999999999999999999987 77899999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.+.|+.|.++...
T Consensus       166 k~vevkrA~pk~~~  179 (311)
T KOG4205|consen  166 KKVEVKRAIPKEVM  179 (311)
T ss_pred             ceeeEeeccchhhc
Confidence            99999999765443

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

Probab=97.89  E-value=1.7e-05  Score=65.80  Aligned_cols=61  Identities=36%  Similarity=0.554  Sum_probs=57.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|+..|.|.+                           ++++.|+.+++++|.+||+|.++.....||. |.|..+.|
T Consensus       196 L~efFs~~gkVrd---------------------------VriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg  247 (549)
T KOG0147|consen  196 LEEFFSIVGKVRD---------------------------VRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLG  247 (549)
T ss_pred             HHHHHHhhcCcce---------------------------eEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccC
Confidence            6789999999999                           9999999999999999999999999999996 99999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      -+|.|....
T Consensus       248 ~pv~vq~sE  256 (549)
T KOG0147|consen  248 VPVIVQLSE  256 (549)
T ss_pred             ceeEecccH
Confidence            999998764

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

Probab=97.84  E-value=4.1e-05  Score=64.12  Aligned_cols=65  Identities=29%  Similarity=0.536  Sum_probs=55.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |..+|+++|+|+-                           .-++-+.++| .+||.|++|.+..+|+.|++.|||+.++ 
T Consensus        81 l~kvfsk~gk~vn---------------------------~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   81 LTKVFSKAGKIVN---------------------------MYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             HHHHHHhhccccc---------------------------eeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecc
Confidence            6789999999988                           6777776554 9999999999999999999999999997 


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      ++...|...+.-.+
T Consensus       133 nHtf~v~~f~d~ek  146 (698)
T KOG2314|consen  133 NHTFFVRLFKDFEK  146 (698)
T ss_pred             cceEEeehhhhHHH
Confidence            78888887654433

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

Probab=97.79  E-value=6.9e-05  Score=57.04  Aligned_cols=61  Identities=30%  Similarity=0.594  Sum_probs=55.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|..||.+..                           +.|-.|+ .|++.|.|-|.|..-++|..|+..++|..++|
T Consensus       100 l~eLF~~~~~~~r---------------------------~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG  151 (243)
T KOG0533|consen  100 LKELFAEFGELKR---------------------------VAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDG  151 (243)
T ss_pred             HHHHHHHhccceE---------------------------EeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCC
Confidence            7899999998888                           7788886 89999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      ++|.+....
T Consensus       152 ~~mk~~~i~  160 (243)
T KOG0533|consen  152 RPMKIEIIS  160 (243)
T ss_pred             ceeeeEEec
Confidence            999988764

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

Probab=97.69  E-value=4.4e-05  Score=57.18  Aligned_cols=57  Identities=30%  Similarity=0.670  Sum_probs=49.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|..||++.+                           +.|        ..||+||+|.+..+|..|+..+||..+.+
T Consensus        18 ~E~~f~~yg~~~d---------------------------~~m--------k~gf~fv~fed~rda~Dav~~l~~~~l~~   62 (216)
T KOG0106|consen   18 VERFFKGYGKIPD---------------------------ADM--------KNGFGFVEFEDPRDADDAVHDLDGKELCG   62 (216)
T ss_pred             HHHHHhhcccccc---------------------------cee--------ecccceeccCchhhhhcccchhcCceecc
Confidence            6788999999988                           654        45799999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      -.+.|++++...
T Consensus        63 e~~vve~~r~~~   74 (216)
T KOG0106|consen   63 ERLVVEHARGKR   74 (216)
T ss_pred             eeeeeecccccc
Confidence            889999988543

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

Probab=97.54  E-value=0.00034  Score=55.60  Aligned_cols=57  Identities=32%  Similarity=0.520  Sum_probs=47.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCC-ceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g-~~l~   80 (112)
                      |+++|.+||+|..                           +++...+      ++|||+|.+-.+|+.|....-. ..|+
T Consensus       245 IrdhFyqyGeirs---------------------------i~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~  291 (377)
T KOG0153|consen  245 IRDHFYQYGEIRS---------------------------IRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVIN  291 (377)
T ss_pred             HHHHHhhcCCeee---------------------------EEeeccc------ccceeeehhhHHHHHHHHhhcceeeec
Confidence            6889999999988                           7765553      5999999999999988876544 3479


Q ss_pred             CeeEEEEeccC
Q 033734           81 GRVIFVDNVRP   91 (112)
Q Consensus        81 g~~i~V~~a~~   91 (112)
                      |.+|.|.|..+
T Consensus       292 G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  292 GFRLKIKWGRP  302 (377)
T ss_pred             ceEEEEEeCCC
Confidence            99999999987

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

Probab=97.52  E-value=0.00032  Score=57.12  Aligned_cols=63  Identities=27%  Similarity=0.501  Sum_probs=49.2

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+.+|..||+|.+                           ..|......++...||||+|.+.++++.||.+- -..++
T Consensus       304 ~l~~~Fk~FG~Ik~---------------------------~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig  355 (419)
T KOG0116|consen  304 ELEEVFKQFGPIKE---------------------------GGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIG  355 (419)
T ss_pred             HHHHHHhhcccccc---------------------------cceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccC
Confidence            47899999999998                           444443323444489999999999999999954 56688


Q ss_pred             CeeEEEEeccC
Q 033734           81 GRVIFVDNVRP   91 (112)
Q Consensus        81 g~~i~V~~a~~   91 (112)
                      ++++.|+--++
T Consensus       356 ~~kl~Veek~~  366 (419)
T KOG0116|consen  356 GRKLNVEEKRP  366 (419)
T ss_pred             CeeEEEEeccc
Confidence            99999987654

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

Probab=97.48  E-value=0.00014  Score=59.57  Aligned_cols=57  Identities=47%  Similarity=0.628  Sum_probs=49.1

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      ||++-|..||.|..                           +.| +  +.|+++|  .|.|.++++|+.|+..|+|..++
T Consensus       552 mlrDKfre~G~v~y---------------------------adi-m--e~GkskG--VVrF~s~edAEra~a~Mngs~l~  599 (608)
T KOG4212|consen  552 MLRDKFREIGHVLY---------------------------ADI-M--ENGKSKG--VVRFFSPEDAERACALMNGSRLD  599 (608)
T ss_pred             HHHHHHHhccceeh---------------------------hhh-h--ccCCccc--eEEecCHHHHHHHHHHhccCccc
Confidence            57888888998877                           666 2  3578887  89999999999999999999999


Q ss_pred             CeeEEEEec
Q 033734           81 GRVIFVDNV   89 (112)
Q Consensus        81 g~~i~V~~a   89 (112)
                      |+.|.|.+.
T Consensus       600 Gr~I~V~y~  608 (608)
T KOG4212|consen  600 GRNIKVTYF  608 (608)
T ss_pred             CceeeeeeC
Confidence            999999763

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

Probab=97.44  E-value=0.00051  Score=55.83  Aligned_cols=58  Identities=24%  Similarity=0.400  Sum_probs=52.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|+.||.|.+                           ++|...+.     .-|.|.|.+...|+-|+++|+|..+.|
T Consensus       315 LftlFgvYGdVqR---------------------------Vkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~g  362 (492)
T KOG1190|consen  315 LFTLFGVYGDVQR---------------------------VKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYG  362 (492)
T ss_pred             HHHHHhhhcceEE---------------------------EEeeecCC-----cceeeeecchhHHHHHHHHhhcceecC
Confidence            5678999999999                           99887752     579999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|+|.+++.
T Consensus       363 k~lrvt~SKH  372 (492)
T KOG1190|consen  363 KKLRVTLSKH  372 (492)
T ss_pred             ceEEEeeccC
Confidence            9999999874

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

Probab=97.43  E-value=0.00035  Score=60.32  Aligned_cols=61  Identities=20%  Similarity=0.404  Sum_probs=53.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|+.||+|..                           +.++      ..+|+|||.+.+-.+|.+|+.+|....+.+
T Consensus       438 L~~~feefGeiqS---------------------------i~li------~~R~cAfI~M~~RqdA~kalqkl~n~kv~~  484 (894)
T KOG0132|consen  438 LANLFEEFGEIQS---------------------------IILI------PPRGCAFIKMVRRQDAEKALQKLSNVKVAD  484 (894)
T ss_pred             HHHHHHhccccee---------------------------Eeec------cCCceeEEEEeehhHHHHHHHHHhcccccc
Confidence            7889999999988                           6653      356899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|.|+.....+
T Consensus       485 k~Iki~Wa~g~G~k  498 (894)
T KOG0132|consen  485 KTIKIAWAVGKGPK  498 (894)
T ss_pred             eeeEEeeeccCCcc
Confidence            99999999755433

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

Probab=97.31  E-value=0.0001  Score=61.25  Aligned_cols=52  Identities=25%  Similarity=0.470  Sum_probs=46.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |..+|+.||+|..                           ++.     +-..+|..||+|.+..+|+.|+++|++..+.|
T Consensus        92 L~~~f~~yGeir~---------------------------ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~  139 (549)
T KOG4660|consen   92 LLRIFGAYGEIRE---------------------------IRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAG  139 (549)
T ss_pred             HHHHHHhhcchhh---------------------------hhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhh
Confidence            7889999999988                           654     55678999999999999999999999999999


Q ss_pred             eeEE
Q 033734           82 RVIF   85 (112)
Q Consensus        82 ~~i~   85 (112)
                      ++|.
T Consensus       140 ~~~k  143 (549)
T KOG4660|consen  140 KRIK  143 (549)
T ss_pred             hhhc
Confidence            9887

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

Probab=97.29  E-value=0.00021  Score=56.76  Aligned_cols=52  Identities=25%  Similarity=0.267  Sum_probs=48.5

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR   93 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~   93 (112)
                      +.|.+|++|++.+|-|.|+|.++..|++||..+++..+.+..|.|.+|..++
T Consensus       104 i~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  104 IKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERRT  155 (351)
T ss_pred             hhccccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhcc
Confidence            7889999999999999999999999999999999999999999999886544

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

Probab=97.26  E-value=0.0002  Score=59.34  Aligned_cols=52  Identities=19%  Similarity=0.405  Sum_probs=47.5

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR   93 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~   93 (112)
                      -.++.|..+|-++||||.+|.++.....|+..|||.+++++.+.|..|....
T Consensus       319 f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~  370 (500)
T KOG0120|consen  319 FRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGA  370 (500)
T ss_pred             heeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccc
Confidence            6788898899999999999999999999999999999999999999886443

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

Probab=97.25  E-value=0.00098  Score=55.36  Aligned_cols=62  Identities=19%  Similarity=0.376  Sum_probs=50.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCC---CCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGK---NRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t---~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      ++...++||.|..                           |.+.++...   .-..|--||+|.+.+++++|.++|+|.+
T Consensus       426 vr~ec~k~g~v~~---------------------------v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrK  478 (500)
T KOG0120|consen  426 VRTECAKFGAVRS---------------------------VEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRK  478 (500)
T ss_pred             HHHHhcccCceeE---------------------------EecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCce
Confidence            4567788888888                           777777222   2345889999999999999999999999


Q ss_pred             eCCeeEEEEecc
Q 033734           79 LDGRVIFVDNVR   90 (112)
Q Consensus        79 l~g~~i~V~~a~   90 (112)
                      +.|+.|...+-.
T Consensus       479 F~nRtVvtsYyd  490 (500)
T KOG0120|consen  479 FANRTVVASYYD  490 (500)
T ss_pred             eCCcEEEEEecC
Confidence            999999888754

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.20  E-value=0.00082  Score=53.72  Aligned_cols=33  Identities=42%  Similarity=0.774  Sum_probs=30.6

Q ss_pred             EEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           58 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        58 fV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      +|+|.+.++|..||.+.||+.++|+.|+..+-+
T Consensus       169 YITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             EEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            899999999999999999999999999987643

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

Probab=97.20  E-value=0.0014  Score=52.28  Aligned_cols=71  Identities=18%  Similarity=0.258  Sum_probs=58.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      +.++|+++|-|.+.-       ++            .-+.|++.++. .|..+|=|.+.|...+++.-|+..||+..+.|
T Consensus       151 ~~~~~sKcGiI~~d~-------~t------------~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  151 FAEVMSKCGIIMRDP-------QT------------GEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             HHHHHHhcceEeccC-------CC------------CCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            356788888887610       11            11238999997 59999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|+.|+-.
T Consensus       211 ~~~rVerAkfq  221 (382)
T KOG1548|consen  211 KKLRVERAKFQ  221 (382)
T ss_pred             cEEEEehhhhh
Confidence            99999999643

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

Probab=97.03  E-value=0.0032  Score=47.88  Aligned_cols=43  Identities=21%  Similarity=0.425  Sum_probs=37.6

Q ss_pred             cccEEEEEeCCHHHHHHHHHhhCCceeC---CeeEEEEeccCCCCC
Q 033734           53 SKGYGYVTFSTEEEAQKALADMNGKLLD---GRVIFVDNVRPSRRY   95 (112)
Q Consensus        53 ~rG~afV~f~~~~~a~~Ai~~l~g~~l~---g~~i~V~~a~~~~~~   95 (112)
                      .+-+||++|.+..+|++|.++|||..++   +..++++++++..+.
T Consensus        76 ~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSNtK~  121 (284)
T KOG1457|consen   76 CKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSNTKR  121 (284)
T ss_pred             ccceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcCccc
Confidence            4579999999999999999999999997   789999999765544

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

Probab=96.98  E-value=0.00068  Score=51.30  Aligned_cols=59  Identities=27%  Similarity=0.255  Sum_probs=50.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|-+-|+|.+                           +.|..++ -++.+ ||||.|.++.+.+-|+.-+||-.+.+
T Consensus        26 L~ElfiqaGPV~k---------------------------v~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~   76 (267)
T KOG4454|consen   26 LSELFIQAGPVYK---------------------------VGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEE   76 (267)
T ss_pred             HHHHhhccCceEE---------------------------EeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhcc
Confidence            5678888999988                           8777776 45666 99999999999999999999999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      .++.+.+-
T Consensus        77 ~e~q~~~r   84 (267)
T KOG4454|consen   77 DEEQRTLR   84 (267)
T ss_pred             chhhcccc
Confidence            88888664

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

Probab=96.88  E-value=0.0034  Score=41.57  Aligned_cols=49  Identities=22%  Similarity=0.348  Sum_probs=42.5

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC----CeeEEEEecc
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD----GRVIFVDNVR   90 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~----g~~i~V~~a~   90 (112)
                      .-++.|..++...|||||.|.+++.+..-...++|....    .+.+.|.+|+
T Consensus        33 ~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   33 FYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             EEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            678889888899999999999999999999999999875    5666777775

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

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

Probab=96.82  E-value=0.0061  Score=43.22  Aligned_cols=54  Identities=30%  Similarity=0.506  Sum_probs=42.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.+.|..||.+.-                           +|.+-+        --.|+|.+-.+|-+|+. ++|.++.|
T Consensus        53 ll~~~~~~GevvL---------------------------vRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g   96 (146)
T PF08952_consen   53 LLQKFAQYGEVVL---------------------------VRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNG   96 (146)
T ss_dssp             HHHHHHCCS-ECE---------------------------EEEETT--------CEEEEESSCHHHHHHHH-GCCSEETT
T ss_pred             HHHHHHhCCceEE---------------------------EEEeCC--------eEEEEECccHHHHHHHc-cCCcEECC
Confidence            4567888888777                           666544        36899999999999998 99999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|++-.+
T Consensus        97 ~~l~i~LKtp  106 (146)
T PF08952_consen   97 RTLKIRLKTP  106 (146)
T ss_dssp             EEEEEEE---
T ss_pred             EEEEEEeCCc
Confidence            9999988654

; PDB: 1UFW_A 2DNR_A.

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

Probab=96.71  E-value=0.0082  Score=47.93  Aligned_cols=44  Identities=25%  Similarity=0.444  Sum_probs=38.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCC
Q 033734           51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR   94 (112)
Q Consensus        51 ~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~   94 (112)
                      ..+.|.+-|.|.+.++|..||..|+|+-++||.|.......+..
T Consensus       311 ~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t~  354 (382)
T KOG1548|consen  311 RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKTK  354 (382)
T ss_pred             cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcce
Confidence            35789999999999999999999999999999999988765444

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

Probab=96.64  E-value=0.0047  Score=53.26  Aligned_cols=62  Identities=23%  Similarity=0.476  Sum_probs=52.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeC---CCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK---GKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~---~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |...|..||+|..                           ++++..+   +..+.+-++||-|++-.+|++|++.|+|..
T Consensus       191 ll~tfGrfgPlas---------------------------vKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~i  243 (877)
T KOG0151|consen  191 LLRTFGRFGPLAS---------------------------VKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGII  243 (877)
T ss_pred             HHHHhcccCcccc---------------------------eeeecccchhhhccccccceeeehhhhhHHHHHHHhccee
Confidence            5567888899988                           7777654   344567899999999999999999999999


Q ss_pred             eCCeeEEEEecc
Q 033734           79 LDGRVIFVDNVR   90 (112)
Q Consensus        79 l~g~~i~V~~a~   90 (112)
                      +++.++++-|.+
T Consensus       244 v~~~e~K~gWgk  255 (877)
T KOG0151|consen  244 VMEYEMKLGWGK  255 (877)
T ss_pred             eeeeeeeecccc
Confidence            999999998884

>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=96.50  E-value=0.011  Score=39.39  Aligned_cols=36  Identities=25%  Similarity=0.393  Sum_probs=29.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHhhCCceeCCe-eEEEEecc
Q 033734           54 KGYGYVTFSTEEEAQKALADMNGKLLDGR-VIFVDNVR   90 (112)
Q Consensus        54 rG~afV~f~~~~~a~~Ai~~l~g~~l~g~-~i~V~~a~   90 (112)
                      ..+-.|+|.++.+|++||. -||..+.|. .+.|.++.
T Consensus        54 ~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mvGV~~~~   90 (100)
T PF05172_consen   54 GNWIHITYDNPLSAQRALQ-KNGTIFSGSLMVGVKPCD   90 (100)
T ss_dssp             TTEEEEEESSHHHHHHHHT-TTTEEETTCEEEEEEE-H
T ss_pred             CCEEEEECCCHHHHHHHHH-hCCeEEcCcEEEEEEEcH
Confidence            3588999999999999998 899999885 45677764

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.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=96.46  E-value=0.0023  Score=49.66  Aligned_cols=56  Identities=25%  Similarity=0.460  Sum_probs=49.1

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCCCCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~~~~~   98 (112)
                      +++..++.++..+|++++.|.+...+..++.. +...+.++.+.+....+.......
T Consensus       215 ~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  270 (285)
T KOG4210|consen  215 VRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRPKSDGG  270 (285)
T ss_pred             eccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCcccccc
Confidence            88999999999999999999999999999987 788899999999988776555433

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

Probab=96.38  E-value=0.0029  Score=47.47  Aligned_cols=37  Identities=38%  Similarity=0.735  Sum_probs=33.7

Q ss_pred             cccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEec
Q 033734           53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV   89 (112)
Q Consensus        53 ~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a   89 (112)
                      ..+++||.|...++|..|+..++|.++.++.|.+...
T Consensus       132 ~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  132 RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            4579999999999999999999999999999999654

>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=96.32  E-value=0.012  Score=38.29  Aligned_cols=37  Identities=27%  Similarity=0.297  Sum_probs=29.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        54 rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      .+-|.+.|.+++.|..|.+.|+|..+-|+.|.|++..
T Consensus        39 ~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   39 GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            4789999999999999999999999999999999874

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

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

Probab=96.29  E-value=0.0021  Score=49.22  Aligned_cols=41  Identities=34%  Similarity=0.542  Sum_probs=36.9

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           50 KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        50 t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      .-...|=.+|.|..+++|++|+..||+.-+.|++|...++.
T Consensus       106 ~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen  106 GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34567889999999999999999999999999999998873

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

Probab=95.32  E-value=0.057  Score=43.88  Aligned_cols=37  Identities=30%  Similarity=0.451  Sum_probs=32.7

Q ss_pred             EEEEEeCCHHHHHHHHHhhCCceeC-C-eeEEEEeccCC
Q 033734           56 YGYVTFSTEEEAQKALADMNGKLLD-G-RVIFVDNVRPS   92 (112)
Q Consensus        56 ~afV~f~~~~~a~~Ai~~l~g~~l~-g-~~i~V~~a~~~   92 (112)
                      .|.|+|++.+.|++|-+.|||..|. | ..|+|++|++.
T Consensus       161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcc
Confidence            6899999999999999999999986 3 58888888765

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

Probab=95.26  E-value=0.045  Score=41.24  Aligned_cols=58  Identities=24%  Similarity=0.429  Sum_probs=46.7

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      ++..+|.+|....+                           ++++...     .+.|||+|.+...+..|...+.|-.+.
T Consensus       162 ~l~~lf~qf~g~ke---------------------------ir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it  209 (221)
T KOG4206|consen  162 MLSDLFEQFPGFKE---------------------------IRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKIT  209 (221)
T ss_pred             HHHHHHhhCcccce---------------------------eEeccCC-----CceeEEecchhhhhHHHhhhhccceec
Confidence            35677888877777                           7776653     479999999999999999999998876


Q ss_pred             -CeeEEEEecc
Q 033734           81 -GRVIFVDNVR   90 (112)
Q Consensus        81 -g~~i~V~~a~   90 (112)
                       .+.|.|..+.
T Consensus       210 ~~~~m~i~~a~  220 (221)
T KOG4206|consen  210 KKNTMQITFAK  220 (221)
T ss_pred             cCceEEecccC
Confidence             7888887663

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

Probab=95.22  E-value=0.072  Score=43.32  Aligned_cols=58  Identities=21%  Similarity=0.290  Sum_probs=50.3

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|..+|=.||.|.+                           ++.++.+     -|-|.|++.+..+.++|+..||+..+-
T Consensus       304 rlFNl~ClYGNV~r---------------------------vkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lf  351 (494)
T KOG1456|consen  304 RLFNLFCLYGNVER---------------------------VKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLF  351 (494)
T ss_pred             hhhhhhhhcCceee---------------------------EEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccc
Confidence            35667888999998                           8887775     368999999999999999999999999


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      |.+|.|.+++
T Consensus       352 G~kl~v~~Sk  361 (494)
T KOG1456|consen  352 GGKLNVCVSK  361 (494)
T ss_pred             cceEEEeecc
Confidence            9999998875

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

Probab=95.20  E-value=0.071  Score=42.10  Aligned_cols=61  Identities=25%  Similarity=0.351  Sum_probs=45.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCc-ccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRS-KGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~-rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      ++...++||+|..                           |.|.-++.--.. .---||+|...++|-+|+-.|||+-++
T Consensus       303 ~keEceKyg~V~~---------------------------viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFG  355 (378)
T KOG1996|consen  303 TKEECEKYGKVGN---------------------------VIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFG  355 (378)
T ss_pred             HHHHHHhhcceee---------------------------EEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceec
Confidence            3566789999988                           555544311111 134799999999999999999999999


Q ss_pred             CeeEEEEec
Q 033734           81 GRVIFVDNV   89 (112)
Q Consensus        81 g~~i~V~~a   89 (112)
                      |+.+...+-
T Consensus       356 Gr~v~A~Fy  364 (378)
T KOG1996|consen  356 GRVVSACFY  364 (378)
T ss_pred             ceeeeheec
Confidence            998877653

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

Probab=95.19  E-value=0.042  Score=32.20  Aligned_cols=37  Identities=24%  Similarity=0.611  Sum_probs=29.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHH
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL   71 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai   71 (112)
                      +.+.|..||+|.+                           ..+.      ...-..++.|.+..+|+.|+
T Consensus        17 vl~~F~~fGeI~~---------------------------~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   17 VLEHFASFGEIVD---------------------------IYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHHHHHhcCCEEE---------------------------EEcC------CCCcEEEEEECCHHHHHhhC
Confidence            4678999999988                           5553      22348999999999999985

>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=95.05  E-value=0.035  Score=36.96  Aligned_cols=54  Identities=35%  Similarity=0.557  Sum_probs=31.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCc----
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK----   77 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~----   77 (112)
                      |+++|+.||.|..                           +.+...      .--|+|-|.+++.|+.|+..+...    
T Consensus        18 iK~~f~~~g~V~y---------------------------VD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~   64 (105)
T PF08777_consen   18 IKEAFSQFGEVAY---------------------------VDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGK   64 (105)
T ss_dssp             HHHHT-SS--EEE---------------------------EE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-
T ss_pred             HHHHHHhcCCcce---------------------------EEecCC------CCEEEEEECCcchHHHHHHHHHhccCCc
Confidence            7889999998877                           655332      237999999999999999977544    


Q ss_pred             -eeCCeeEEEEe
Q 033734           78 -LLDGRVIFVDN   88 (112)
Q Consensus        78 -~l~g~~i~V~~   88 (112)
                       .+.+..+.+++
T Consensus        65 ~~i~~~~~~~~v   76 (105)
T PF08777_consen   65 LKIKGKEVTLEV   76 (105)
T ss_dssp             B-TTSSSEEEE-
T ss_pred             eEEcCceEEEEE
Confidence             34455555544

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

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

Probab=94.40  E-value=0.088  Score=43.77  Aligned_cols=46  Identities=28%  Similarity=0.429  Sum_probs=37.0

Q ss_pred             EEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        44 l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      ++..+.+|+..|-|||+|.+++++++|++ .|-..+.++-|.|=.+.
T Consensus        39 ~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~   84 (510)
T KOG4211|consen   39 LEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAG   84 (510)
T ss_pred             EEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccC
Confidence            44455589999999999999999999998 66666777777775553

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

Probab=94.04  E-value=0.15  Score=40.40  Aligned_cols=56  Identities=29%  Similarity=0.479  Sum_probs=42.8

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|..+|++||.|++                           ...  .    ..--+-+|.|.+..+|++||. .||..|+
T Consensus       212 ~vL~~F~~cG~Vvk---------------------------hv~--~----~ngNwMhirYssr~~A~KALs-kng~ii~  257 (350)
T KOG4285|consen  212 IVLNLFSRCGEVVK---------------------------HVT--P----SNGNWMHIRYSSRTHAQKALS-KNGTIID  257 (350)
T ss_pred             HHHHHHHhhCeeee---------------------------eec--C----CCCceEEEEecchhHHHHhhh-hcCeeec
Confidence            36789999999977                           322  1    122378999999999999999 8999998


Q ss_pred             Ce-eEEEEecc
Q 033734           81 GR-VIFVDNVR   90 (112)
Q Consensus        81 g~-~i~V~~a~   90 (112)
                      |. -|.|+.|.
T Consensus       258 g~vmiGVkpCt  268 (350)
T KOG4285|consen  258 GDVMIGVKPCT  268 (350)
T ss_pred             cceEEeeeecC
Confidence            75 45677654

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

Probab=94.00  E-value=0.033  Score=48.82  Aligned_cols=62  Identities=23%  Similarity=0.258  Sum_probs=50.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      ++.+++++|.+..                           .+++..+ .|+++|.|+|.|.++.++..+...++...+.-
T Consensus       753 ~k~l~~~~gn~~~---------------------------~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE  804 (881)
T KOG0128|consen  753 LKSLASKTGNVTS---------------------------LRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRE  804 (881)
T ss_pred             HHhhccccCCccc---------------------------cchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhh
Confidence            4667777888777                           6666665 78999999999999999999999888877777


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.+.|..+.+
T Consensus       805 ~~~~v~vsnp  814 (881)
T KOG0128|consen  805 NNGEVQVSNP  814 (881)
T ss_pred             cCccccccCC
Confidence            7677776554

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=93.88  E-value=0.17  Score=44.05  Aligned_cols=44  Identities=27%  Similarity=0.437  Sum_probs=39.0

Q ss_pred             EeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEe
Q 033734           45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN   88 (112)
Q Consensus        45 ~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~   88 (112)
                      ++-.+.|+..|-|-|-|.+.++|++|...|++++|.++.|.+.+
T Consensus       900 ~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  900 IRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            34445799999999999999999999999999999999988764

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

Probab=93.57  E-value=0.12  Score=42.31  Aligned_cols=57  Identities=25%  Similarity=0.374  Sum_probs=42.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCccc-EEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKG-YGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG-~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |..+|++||.|.+                           +  ++-   .+..| -|.|.|.+.+.|+.|-..|||..|.
T Consensus       167 LHqvFS~fG~VlK---------------------------I--iTF---~Knn~FQALvQy~d~~sAq~AK~aLdGqnIy  214 (492)
T KOG1190|consen  167 LHQVFSKFGFVLK---------------------------I--ITF---TKNNGFQALVQYTDAVSAQAAKLALDGQNIY  214 (492)
T ss_pred             HHHHHhhcceeEE---------------------------E--EEE---ecccchhhhhhccchhhHHHHHHhccCCccc
Confidence            6789999999977                           3  222   11223 4899999999999999999999987


Q ss_pred             C--eeEEEEecc
Q 033734           81 G--RVIFVDNVR   90 (112)
Q Consensus        81 g--~~i~V~~a~   90 (112)
                      +  ..+++++++
T Consensus       215 ngcCtLrId~Sk  226 (492)
T KOG1190|consen  215 NGCCTLRIDFSK  226 (492)
T ss_pred             CceeEEEeehhh
Confidence            5  466666653

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

Probab=93.17  E-value=0.036  Score=45.47  Aligned_cols=60  Identities=23%  Similarity=0.293  Sum_probs=41.6

Q ss_pred             HHHHhhccCcceecceeeec---cCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYF---KSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |.++|+.+|.|..|++|.-.   .+.-.++..||.++                 -+-+|+|+|...+.|.+|.+.|+.-.
T Consensus       248 l~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~-----------------tk~~AlvEye~~~~A~KA~e~~~~e~  310 (484)
T KOG1855|consen  248 LSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQ-----------------TKECALVEYEEVEAARKARELLNPEQ  310 (484)
T ss_pred             HHHHhhcccceeeeeecCCCCCCcccccCCccchhhh-----------------hhhhhhhhhhhhHHHHHHHHhhchhh
Confidence            67899999999997776552   22223334444421                 13489999999999999999775433

>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=92.63  E-value=0.47  Score=34.75  Aligned_cols=38  Identities=26%  Similarity=0.305  Sum_probs=29.1

Q ss_pred             cEEEEEeCCHHHHHHHHHhhC--CceeCCeeEEEEeccCC
Q 033734           55 GYGYVTFSTEEEAQKALADMN--GKLLDGRVIFVDNVRPS   92 (112)
Q Consensus        55 G~afV~f~~~~~a~~Ai~~l~--g~~l~g~~i~V~~a~~~   92 (112)
                      +-..|.|.+.++|..|...|+  +..+.|..++|-++...
T Consensus        32 rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen   32 RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            467899999999999999999  99999999999888543

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.

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

Probab=92.38  E-value=0.18  Score=41.99  Aligned_cols=60  Identities=32%  Similarity=0.377  Sum_probs=46.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |...|.+||.|..                           |.+-..      .--|.|+|.+..+|-.|.. .++-.|++
T Consensus       390 ln~hfA~fG~i~n---------------------------~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnn  435 (526)
T KOG2135|consen  390 LNPHFAQFGEIEN---------------------------IQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNN  435 (526)
T ss_pred             hhhhhhhcCcccc---------------------------ccccCc------hhhheeeeeccccccchhc-cccceecC
Confidence            5678999999988                           544222      2368999999999977776 78999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|.|-.++...
T Consensus       436 r~iKl~whnps~~t  449 (526)
T KOG2135|consen  436 RFIKLFWHNPSPVT  449 (526)
T ss_pred             ceeEEEEecCCccc
Confidence            99999998875543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=91.00  E-value=0.1  Score=41.45  Aligned_cols=35  Identities=29%  Similarity=0.492  Sum_probs=29.9

Q ss_pred             EEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        56 ~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      -++|+|...++|..||...+|..++|+.++..+..
T Consensus       127 s~yITy~~~eda~rci~~v~g~~~dg~~lka~~gt  161 (327)
T KOG2068|consen  127 SVYITYEEEEDADRCIDDVDGFVDDGRALKASLGT  161 (327)
T ss_pred             cccccccchHhhhhHHHHhhhHHhhhhhhHHhhCC
Confidence            38999999999999999999999999876655543

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

Probab=90.49  E-value=0.37  Score=42.80  Aligned_cols=58  Identities=31%  Similarity=0.546  Sum_probs=46.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|..||+|..                           +.+      .+..-|++|.|.+...++.|.+.|-|..+++
T Consensus       472 l~r~fd~fGpir~---------------------------Idy------~hgq~yayi~yes~~~aq~a~~~~rgap~G~  518 (975)
T KOG0112|consen  472 LNREFDRFGPIRI---------------------------IDY------RHGQPYAYIQYESPPAAQAATHDMRGAPLGG  518 (975)
T ss_pred             HHHHhhccCccee---------------------------eec------ccCCcceeeecccCccchhhHHHHhcCcCCC
Confidence            6778889998877                           543      2234599999999999999999999999985


Q ss_pred             --eeEEEEeccCC
Q 033734           82 --RVIFVDNVRPS   92 (112)
Q Consensus        82 --~~i~V~~a~~~   92 (112)
                        ++++|.++.+.
T Consensus       519 P~~r~rvdla~~~  531 (975)
T KOG0112|consen  519 PPRRLRVDLASPP  531 (975)
T ss_pred             CCcccccccccCC
Confidence              67888888543

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

Probab=90.36  E-value=0.58  Score=39.07  Aligned_cols=46  Identities=28%  Similarity=0.385  Sum_probs=37.5

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEec
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV   89 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a   89 (112)
                      +.++.|+ .+++.|-|||.|.+.+.|++|+. -|-..++.+-|.|-.+
T Consensus       134 i~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  134 ILLPMDQ-RGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             eeeeccC-CCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            5567776 67899999999999999999998 5566788887777555

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

Probab=89.14  E-value=1.1  Score=29.08  Aligned_cols=39  Identities=23%  Similarity=0.466  Sum_probs=31.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN   75 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~   75 (112)
                      |.++|++||.|.-                            ..+.|-       -|||...+.+.+..++..+.
T Consensus        25 I~qlFspfG~I~V----------------------------sWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   25 IYQLFSPFGQIYV----------------------------SWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             HHHHCCCCCCEEE----------------------------EEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             HHHHhccCCcEEE----------------------------EEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            5688999998743                            444442       79999999999999998775

; 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.

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

Probab=88.33  E-value=0.47  Score=42.11  Aligned_cols=64  Identities=30%  Similarity=0.351  Sum_probs=51.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |..++++||.+..                           ++..+|-      -.|.|.|.+.+.|-.|+.+++|+++. 
T Consensus       315 L~~l~s~yg~v~s---------------------------~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~  361 (1007)
T KOG4574|consen  315 LATLCSDYGSVAS---------------------------AWTLRDL------NMALVSFSSVESAILALDALQGKEVSV  361 (1007)
T ss_pred             HHHHHHhhcchhh---------------------------heecccc------cchhhhhHHHHHHHHhhhhhcCCcccc
Confidence            5678899999988                           7766664      37899999999999999999999964 


Q ss_pred             -CeeEEEEeccCCCCCCCC
Q 033734           81 -GRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        81 -g~~i~V~~a~~~~~~~~~   98 (112)
                       |-+.+|.+|+..+-..++
T Consensus       362 ~g~Ps~V~~ak~~~~~ep~  380 (1007)
T KOG4574|consen  362 TGAPSRVSFAKTLPMYEPP  380 (1007)
T ss_pred             cCCceeEEeccccccccCC
Confidence             778899999866555443

>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=87.95  E-value=1.5  Score=27.03  Aligned_cols=33  Identities=30%  Similarity=0.594  Sum_probs=20.2

Q ss_pred             EEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEec
Q 033734           56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV   89 (112)
Q Consensus        56 ~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a   89 (112)
                      |+||+-.. +.|..++..|++..+.|+++.|+.|
T Consensus        42 ~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   42 FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             -EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            88998875 4788899999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=87.80  E-value=1.9  Score=30.91  Aligned_cols=35  Identities=17%  Similarity=0.152  Sum_probs=28.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEec
Q 033734           54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV   89 (112)
Q Consensus        54 rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a   89 (112)
                      +--|.|.|.+..+|=+|+.+.+. ...|..+.+.+-
T Consensus       125 rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen  125 RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            34799999999999999998864 667778888764

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

Probab=87.31  E-value=0.096  Score=46.04  Aligned_cols=47  Identities=23%  Similarity=0.359  Sum_probs=35.1

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEe
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN   88 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~   88 (112)
                      +++.--..+++.+|+|++.|.+++++.+|+...++..++...+.++.
T Consensus       697 vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~g  743 (881)
T KOG0128|consen  697 VQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAISG  743 (881)
T ss_pred             HHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhheeC
Confidence            33333345788999999999999999999998877666655555544

>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=85.30  E-value=1.7  Score=26.72  Aligned_cols=39  Identities=23%  Similarity=0.467  Sum_probs=31.2

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEE
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV   86 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V   86 (112)
                      .+|..|+ |    || ||.|++..+|+++....||..+.+.+|.+
T Consensus        27 ~~I~~d~-t----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   27 DRIRDDR-T----GF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             ceEEecC-C----EE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4555564 2    44 79999999999999999999988877654

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

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

Probab=84.93  E-value=1.5  Score=33.61  Aligned_cols=26  Identities=27%  Similarity=0.517  Sum_probs=23.5

Q ss_pred             cEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734           55 GYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus        55 G~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      -.||++|.+.+.|..|+..|.|..|.
T Consensus       249 ~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  249 PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             ceEeecHHHHHHHHHHHHHhhcceec
Confidence            48999999999999999999998764

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

Probab=84.88  E-value=5.7  Score=29.76  Aligned_cols=45  Identities=24%  Similarity=0.409  Sum_probs=38.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++.-.-|.|+.                           +.+.+|       |++.|+|...++++-|+..|+.+.+.
T Consensus       132 LKDHmReaGdvCf---------------------------adv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  132 LKDHMREAGDVCF---------------------------ADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             HHHHHHhhCCeee---------------------------eeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            6777888888888                           777777       48999999999999999999987754

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=82.07  E-value=0.48  Score=36.66  Aligned_cols=28  Identities=21%  Similarity=0.401  Sum_probs=25.2

Q ss_pred             EEEEEeCCHHHHHHHHHhhCCceeCCee
Q 033734           56 YGYVTFSTEEEAQKALADMNGKLLDGRV   83 (112)
Q Consensus        56 ~afV~f~~~~~a~~Ai~~l~g~~l~g~~   83 (112)
                      -|.|+|.+...|......||+.+|+|+.
T Consensus       130 EGWvEF~~KrvAK~iAe~Lnn~~Iggkk  157 (278)
T KOG3152|consen  130 EGWVEFISKRVAKRIAELLNNTPIGGKK  157 (278)
T ss_pred             hHHHHHHHHHHHHHHHHHhCCCccCCCC
Confidence            4779999999999999999999999863

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

Probab=80.37  E-value=0.92  Score=38.95  Aligned_cols=38  Identities=26%  Similarity=0.349  Sum_probs=31.5

Q ss_pred             cccEEEEEeCCHHHHHHHHHhhCCcee---CCeeEEEEecc
Q 033734           53 SKGYGYVTFSTEEEAQKALADMNGKLL---DGRVIFVDNVR   90 (112)
Q Consensus        53 ~rG~afV~f~~~~~a~~Ai~~l~g~~l---~g~~i~V~~a~   90 (112)
                      .+..|||.|++.++|-+.+.+|||.+-   +.+.|.+.+..
T Consensus       480 IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~~  520 (718)
T KOG2416|consen  480 IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFVR  520 (718)
T ss_pred             hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeecc
Confidence            567899999999999999999999773   35677777764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	112
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		4e-06
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		8e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		2e-04
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		3e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		5e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-04

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 39  LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           + +  ++ D+  N SKGYG+V F T+E A++A+  MNG LL+ R +FV
Sbjct: 125 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 39  LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           + +  ++ D+  N SKGYG+V F T+E A++A+  MNG LL+ R +FV
Sbjct: 130 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 39  LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
           + +  ++ D+  N SKGYG+V F T+E A++A+  MNG LL+ R +FV   R   R   +
Sbjct: 32  ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG--RFKSRKERE 87
Query: 99  APLARQSAQ 107
           A L  ++ +
Sbjct: 88  AELGARAKE 96

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          + +  ++ D+  N SKGYG+V F T+E A++A+  MNG LL+ R +FV
Sbjct: 38 ILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 32/49 (65%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          ++ D+   RS+G+G+VTF   ++A+ A+  MNGK +DGR I VD    S
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 36/48 (75%), Gaps = 2/48 (4%)
Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          + +A ++M+ G  RSKG+G+V FS+ EEA KA+ +MNG+++  + ++V
Sbjct: 42 ITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 31/46 (67%)
Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV 89
           ++MD    RSKGYG++TFS  E A+KAL  +NG  L GR + V +V
Sbjct: 58  LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 41  AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           +A +I DK    S GYG+V + T ++A++A+  +NG  L  + I V   RPS     DA 
Sbjct: 31  SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDAN 90
Query: 101 L 101
           L
Sbjct: 91  L 91

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 34/61 (55%)
Query: 41  AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           +A +I DK    S GYG+V + T ++A++A+  +NG  L  + I V   RPS     DA 
Sbjct: 31  SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDAN 90
Query: 101 L 101
           L
Sbjct: 91  L 91

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV 89
           ++ D    RSKGYG++TFS  E A++AL  +NG  L GR + V +V
Sbjct: 36 VLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV 82

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 31/52 (59%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          +A +I DK    S GYG+V + T ++A++A+  +NG  L  + I V   RPS
Sbjct: 48 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 99

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 31/52 (59%)
Query: 41 AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          +A +I DK    S GYG+V + T ++A++A+  +NG  L  + I V   RPS
Sbjct: 33 SAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS 84

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 32/48 (66%)
Query: 40 FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           +  ++ D     S+GYG+V+F+++++AQ A+  M G+ L+GR + ++
Sbjct: 29 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 76

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++ D    +SKGYG+V+F  + +A+ A+  M G+ L GR I
Sbjct: 36 ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 29/43 (67%)
Query: 40  FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
            +  ++ D     S+GYG+V+F+++++AQ A+  M G+ L+GR
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++ D    +SKGYG+V+F  + +A+ A+  M G+ L GR I
Sbjct: 45 ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          A ++ D    +SKGYG+V+F  + +A+ A+  M G+ L GR I
Sbjct: 45 ARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          A I+ D+    SKG+G+V F++EE+A+ A   M    +DG  + +D  +P
Sbjct: 42 ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP 91

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 41  AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           +  ++ DK   +S GYG+V +S   +A KA+  +NG  L  + I V   RPS     DA 
Sbjct: 33  SCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIRDAN 92
Query: 101 L 101
           L
Sbjct: 93  L 93

>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 = 38.9 bits (89), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 27/45 (60%)
Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          ++ D+   + KGYG+  +  +E A  A+ ++NG+   GR + VDN
Sbjct: 40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	112
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-21
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-20
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-20
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-20
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-18
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-20
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-20
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-20
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-19
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-19
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-19
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-19
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-19
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-19
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-19
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-18
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-18
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-18
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-18
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-17
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-17
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-17
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-17
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-17
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-17
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	5e-17
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-17
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-16
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-16
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-15
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-16
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-16
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-14
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	9e-16
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-15
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-15
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	7e-15
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-13
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	9e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-13
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-13
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-13
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	4e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	8e-13
2div_A	99	TRNA selenocysteine associated protein; structural	8e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-12
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-12
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-12
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-12
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-12
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-11
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-10
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-10
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-09
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	7e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	8e-09
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	9e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	3e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-05
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	5e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	6e-05
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	7e-05

>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 = 81.2 bits (201), Expect = 1e-21
 Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 29/110 (26%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            +  AF+ FG++++                           A ++ D    +SKGYG+V+
Sbjct: 31  DIKAAFAPFGRISD---------------------------ARVVKDMATGKSKGYGFVS 63

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD--NVRPSRRYNTDAPLARQSAQS 108
           F  + +A+ A+  M G+ L GR I  +    +P    +T     +QS  S
Sbjct: 64  FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPS 113

>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 = 79.1 bits (196), Expect = 5e-21
 Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 27/91 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L +AF  F                                  ++ D     S+GYG+V+
Sbjct: 17 TLRNAFKDFPSYLS---------------------------GHVMWDMQTGSSRGYGFVS 49

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          F+++++AQ A+  M G+ L+GR + ++    
Sbjct: 50 FTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 80

>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 = 78.1 bits (193), Expect = 2e-20
 Identities = 28/100 (28%), Positives = 43/100 (43%), Gaps = 28/100 (28%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   FS++GQ++E                             ++ D+   RS+G+G+VT
Sbjct: 28  SLEQVFSKYGQISE---------------------------VVVVKDRETQRSRGFGFVT 60

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           F   ++A+ A+  MNGK +DGR I VD        N   P
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQIRVDQAGK-SSDNRSGP 99

>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 = 76.5 bits (189), Expect = 6e-20
 Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 26/91 (28%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L D FS FG + +                             I+ D     SKGY ++ 
Sbjct: 21 LLYDTFSAFGVILQT--------------------------PKIMRDPDTGNSKGYAFIN 54

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          F++ + +  A+  MNG+ L  R I V     
Sbjct: 55 FASFDASDAAIEAMNGQYLCNRPITVSYAFK 85

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 79.7 bits (197), Expect = 6e-20
 Identities = 24/112 (21%), Positives = 38/112 (33%), Gaps = 29/112 (25%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            +  AF+ FG +                               +  D    + KG+ +V 
Sbjct: 44  TIRQAFAPFGPIKS---------------------------IDMSWDSVTMKHKGFAFVE 76

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN 112
           +   E AQ AL  MN  +L GR I V   RPS        + + + ++   N
Sbjct: 77  YEVPEAAQLALEQMNSVMLGGRNIKVG--RPSNIGQAQPIIDQLAEEARAFN 126

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 74.3 bits (183), Expect = 7e-18
 Identities = 19/102 (18%), Positives = 33/102 (32%), Gaps = 29/102 (28%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            +   F  FG++                             AT+  D    + KGYG++ 
Sbjct: 141 DIKSVFEAFGKIKS---------------------------ATLARDPTTGKHKGYGFIE 173

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD--NVRPSRRYNTDAP 100
           +   + +Q A++ MN   L G+ + V      P        P
Sbjct: 174 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATP 215

>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 = 76.1 bits (188), Expect = 7e-20
 Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 27/91 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           +A AF+ FG++++                           A ++ D    +SKGYG+V+
Sbjct: 22 AIAAAFAPFGRISD---------------------------ARVVKDMATGKSKGYGFVS 54

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          F  + +A+ A+  M G+ L GR I  +    
Sbjct: 55 FFNKWDAENAIQQMGGQWLGGRQIRTNWATR 85

>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 = 76.1 bits (188), Expect = 9e-20
 Identities = 22/97 (22%), Positives = 33/97 (34%), Gaps = 30/97 (30%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK---GKNRSKGYG 57
           L   FS+ G +                              TI   K   G   S G+G
Sbjct: 21 TLKGVFSKVGAIKS---------------------------CTISKKKNKAGVLLSMGFG 53

Query: 58 YVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          +V +   E+AQKAL  + G  +DG  + V     + +
Sbjct: 54 FVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 90

>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 = 76.1 bits (188), Expect = 9e-20
 Identities = 26/91 (28%), Positives = 37/91 (40%), Gaps = 27/91 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          ML   F  FG++                               ++ D    RSKGYG++T
Sbjct: 21 MLRGIFEPFGKIDN---------------------------IVLMKDSDTGRSKGYGFIT 53

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          FS  E A++AL  +NG  L GR + V +V  
Sbjct: 54 FSDSECARRALEQLNGFELAGRPMRVGHVTE 84

>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 = 76.7 bits (189), Expect = 1e-19
 Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 27/92 (29%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L + FS++G + +                            +I+ D+   RS+G+ +V F
Sbjct: 63  LREVFSKYGPIAD---------------------------VSIVYDQQSRRSRGFAFVYF 95

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
              ++A++A    NG  LDGR I VD     R
Sbjct: 96  ENVDDAKEAKERANGMELDGRRIRVDFSITKR 127

>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 = 75.8 bits (187), Expect = 2e-19
 Identities = 28/91 (30%), Positives = 38/91 (41%), Gaps = 27/91 (29%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           ML   F  FG++                               ++MD    RSKGYG++T
Sbjct: 42  MLRGIFEPFGRIES---------------------------IQLMMDSETGRSKGYGFIT 74

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           FS  E A+KAL  +NG  L GR + V +V  
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHVTE 105

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 74.5 bits (184), Expect = 3e-19
 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 28/95 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGK-NRSKGYGYV 59
           + + FS +G++                               + +++   + SKGY YV
Sbjct: 20 HIMEIFSTYGKIKM---------------------------IDMPVERMHPHLSKGYAYV 52

Query: 60 TFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           F   +EA+KAL  M+G  +DG+ I    V     
Sbjct: 53 EFENPDEAEKALKHMDGGQIDGQEITATAVLAPWP 87

>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 = 74.9 bits (185), Expect = 3e-19
 Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 27/94 (28%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L  AF  FG +T+                             I +D    + +G+ +V 
Sbjct: 28 VLHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVE 60

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          F   E+A  A+ +MN   L GR I V+  +P R 
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94

>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 = 75.0 bits (185), Expect = 3e-19
 Identities = 24/100 (24%), Positives = 39/100 (39%), Gaps = 30/100 (30%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   F QFG++ +                             II ++    SKG+G+VT
Sbjct: 31  DLRQMFGQFGKILD---------------------------VEIIFNER--GSKGFGFVT 61

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           F    +A +A   ++G +++GR I V+N    R      P
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEVNNATA-RVMTNSGP 100

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 74.1 bits (183), Expect = 5e-19
 Identities = 28/96 (29%), Positives = 35/96 (36%), Gaps = 31/96 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          ML D F++ G V                             A I M+ G  +SKG G V 
Sbjct: 24 MLKDKFNECGHVLY---------------------------ADIKMENG--KSKGCGVVK 54

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFV--DNVRPSRR 94
          F + E A++A   MNG  L GR I V  D       
Sbjct: 55 FESPEVAERACRMMNGMKLSGREIDVRIDRNASGPS 90

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 74.2 bits (183), Expect = 5e-19
 Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 27/87 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L + FS++G + +                            +I+ D+   RS+G+ +V 
Sbjct: 31 DLREVFSKYGPIAD---------------------------VSIVYDQQSRRSRGFAFVY 63

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          F   ++A++A    NG  LDGR I V 
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVS 90

>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 = 74.6 bits (184), Expect = 5e-19
 Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 29/91 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L  AFS FG +T                            A ++M+ G  RSKG+G+V 
Sbjct: 31 RLRKAFSPFGTITS---------------------------AKVMMEGG--RSKGFGFVC 61

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          FS+ EEA KA+ +MNG+++  + ++V   + 
Sbjct: 62 FSSPEEATKAVTEMNGRIVATKPLYVALAQR 92

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 74.7 bits (184), Expect = 5e-19
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 29/91 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   F QFG++ +                             II ++    SKG+G+VT
Sbjct: 45  DLRQMFGQFGKILD---------------------------VEIIFNER--GSKGFGFVT 75

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           F    +A +A   ++G +++GR I V+N   
Sbjct: 76  FENSADADRAREKLHGTVVEGRKIEVNNATA 106

>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 = 74.7 bits (184), Expect = 5e-19
 Identities = 28/109 (25%), Positives = 39/109 (35%), Gaps = 30/109 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L + FS  G V                             A I+ DK   +S+G G VTF
Sbjct: 32  LKEVFSMAGVVVR---------------------------ADILEDK-DGKSRGIGTVTF 63

Query: 62  STEEEAQKALADMNGKLLDGRVIFV--DNVRPSRRYNTDAPLARQSAQS 108
               EA +A++  NG+LL  R + V  D     +         +QS  S
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPS 112

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 73.4 bits (181), Expect = 1e-18
 Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 27/100 (27%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   FS +G ++E                               +D    + KG+ +VT
Sbjct: 24  DLEKLFSAYGPLSE---------------------------LHYPIDSLTKKPKGFAFVT 56

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           F   E A KA A+++G++  GR++ V      +  +   P
Sbjct: 57  FMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGP 96

>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 = 73.9 bits (182), Expect = 1e-18
 Identities = 21/93 (22%), Positives = 37/93 (39%), Gaps = 28/93 (30%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F + G ++E                             +I D+  ++S+G+ ++TF
Sbjct: 24 LKAVFGKHGPISE---------------------------VLLIKDR-TSKSRGFAFITF 55

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
              +A+ A  DMNGK L G+ I V+  +    
Sbjct: 56 ENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF 88

>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 = 73.4 bits (181), Expect = 1e-18
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 27/93 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L + F  FG ++                              +  DK   +SKG+ +++
Sbjct: 31 DLQELFRPFGSISR---------------------------IYLAKDKTTGQSKGFAFIS 63

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          F   E+A +A+A ++G   D  ++ V+  +PS 
Sbjct: 64 FHRREDAARAIAGVSGFGYDHLILNVEWAKPST 96

>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 = 72.7 bits (179), Expect = 3e-18
 Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 29/90 (32%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L D FS FG +                               ++ D+    SKGYG+V F
Sbjct: 22 LYDTFSAFGNILS---------------------------CKVVCDEN--GSKGYGFVHF 52

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           T+E A++A+  MNG LL+ R +FV   + 
Sbjct: 53 ETQEAAERAIEKMNGMLLNDRKVFVGRFKS 82

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 73.8 bits (181), Expect = 3e-18
 Identities = 19/112 (16%), Positives = 31/112 (27%), Gaps = 30/112 (26%)

Query: 1   MLADAFSQFG--QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGY 58
            L       G   V E                                ++   +SKGY  
Sbjct: 71  QLIQVIRSIGVYDVVE---------------------------LKFAENRANGQSKGYAE 103

Query: 59  VTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP-SRRYNTDAPLARQSAQSP 109
           V  ++E    K L  + GK+L+G  + V      +          R+  + P
Sbjct: 104 VVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRVP 155

>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 = 73.2 bits (180), Expect = 3e-18
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 27/94 (28%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   F ++G +                               I+ D+   +S+GYG+V 
Sbjct: 58  QLRQLFERYGPIES---------------------------VKIVCDRETRQSRGYGFVK 90

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           F +   AQ+A+A +NG  +  + + V       +
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 71.9 bits (177), Expect = 4e-18
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 27/93 (29%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F ++G+V +                             I  +      +G+ +V F
Sbjct: 30 LRRVFEKYGRVGD---------------------------VYIPREPHTKAPRGFAFVRF 62

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
              +AQ A A M+G  LDGR + V   R  RR
Sbjct: 63 HDRRDAQDAEAAMDGAELDGRELRVQVARYGRR 95

>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 = 71.9 bits (177), Expect = 4e-18
 Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 27/87 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   FS++G+V +                            TI+ DK   +SKG  ++ 
Sbjct: 32 DLYRIFSKYGKVVK---------------------------VTIMKDKDTRKSKGVAFIL 64

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          F  ++ AQ     +N K L GRVI   
Sbjct: 65 FLDKDSAQNCTRAINNKQLFGRVIKAS 91

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 71.9 bits (177), Expect = 5e-18
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          A I+ D+    SKG+G+V F++EE+A+ A   M    +DG  + +D  +P
Sbjct: 42 ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKP 91

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

 Score = 72.9 bits (179), Expect = 5e-18
 Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 27/87 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           +L  AF  FG +T+                             I +D    + +G+ +V 
Sbjct: 79  VLHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVE 111

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           F   E+A  A+ +MN   L GR I V+
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRVN 138

>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 = 71.0 bits (175), Expect = 7e-18
 Identities = 18/92 (19%), Positives = 30/92 (32%), Gaps = 29/92 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L      +G++                                I+DK  N+ KGYG+V 
Sbjct: 21 DLVKLCQPYGKIVS---------------------------TKAILDKTTNKCKGYGFVD 53

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          F +   AQKA+  +    +  ++       PS
Sbjct: 54 FDSPSAAQKAVTALKASGVQAQMAKQS--GPS 83

>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 = 72.6 bits (179), Expect = 1e-17
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 27/87 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L +AF  F                                  ++ D     S+GYG+V+
Sbjct: 103 TLRNAFKDFPSYLS---------------------------GHVMWDMQTGSSRGYGFVS 135

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           F+++++AQ A+  M G+ L+GR + ++
Sbjct: 136 FTSQDDAQNAMDSMQGQDLNGRPLRIN 162

>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 = 6e-14
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 28/98 (28%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L   F   G +                               I++DK  N++  Y +V 
Sbjct: 16 ILKQYFQVGGPIA---------------------------NIKIMIDK-NNKNVNYAFVE 47

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
          +    +A  AL  +NGK ++  ++ ++    S++ ++D
Sbjct: 48 YHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSD 85

>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 = 70.4 bits (173), Expect = 1e-17
 Identities = 14/48 (29%), Positives = 24/48 (50%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          I +     +SKG  Y+ F +E +A+K L +  G  +DGR + +     
Sbjct: 43 IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 71.2 bits (175), Expect = 1e-17
 Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 27/108 (25%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           + D F+++G++                               + +D+     KGY  V +
Sbjct: 39  IHDKFAEYGEIKN---------------------------IHLNLDRRTGYLKGYTLVEY 71

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSP 109
            T +EAQ A+  +NG+ L G+ I VD               R+ ++SP
Sbjct: 72  ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSP 119

>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 = 69.9 bits (172), Expect = 2e-17
 Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 27/87 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L  AF  FG +T+                             I +D    + +G+ +V 
Sbjct: 23 VLHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVE 55

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          F   E+A  A+ +MN   L GR I V+
Sbjct: 56 FELAEDAAAAIDNMNESELFGRTIRVN 82

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 70.9 bits (174), Expect = 3e-17
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 27/92 (29%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L   F ++G+V +                             I  D+    S+G+ +V F
Sbjct: 64  LRRVFEKYGRVGD---------------------------VYIPRDRYTKESRGFAFVRF 96

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
             + +A+ A+  M+G +LDGR + V   R  R
Sbjct: 97  HDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128

>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 = 69.6 bits (171), Expect = 3e-17
 Identities = 18/98 (18%), Positives = 28/98 (28%), Gaps = 27/98 (27%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           + D  S  G V                               ++ D    RSKGY ++ 
Sbjct: 18 QILDLCSNVGPVIN---------------------------LKMMFDPQTGRSKGYAFIE 50

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
          F   E +  A+ ++NG  L  R +       S      
Sbjct: 51 FRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGVS 88

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 70.0 bits (172), Expect = 3e-17
 Identities = 21/90 (23%), Positives = 31/90 (34%), Gaps = 27/90 (30%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L   F  FG V                             A + +DK  N SK +G+V++
Sbjct: 42  LLQMFMPFGNVVS---------------------------AKVFIDKQTNLSKCFGFVSY 74

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
                AQ A+  MNG  +  + + V   R 
Sbjct: 75  DNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>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 = 71.0 bits (174), Expect = 4e-17
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 27/93 (29%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L   F ++G+V +                             I  D+    S+G+ +V F
Sbjct: 87  LRRVFEKYGRVGD---------------------------VYIPRDRYTKESRGFAFVRF 119

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
             + +A+ A+  M+G +LDGR + V   R  R 
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP 152

>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 = 69.6 bits (171), Expect = 4e-17
 Identities = 20/94 (21%), Positives = 34/94 (36%), Gaps = 27/94 (28%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L + F Q G V                               +  D+   + +GYG+V 
Sbjct: 31 LLWELFLQAGPVVN---------------------------THMPKDRVTGQHQGYGFVE 63

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          F +EE+A  A+  M+   L G+ I V+      +
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 97

>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 = 69.7 bits (171), Expect = 4e-17
 Identities = 22/92 (23%), Positives = 31/92 (33%), Gaps = 28/92 (30%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L D FS  G+V +                             II D+   RSKG  YV F
Sbjct: 42  LEDFFSAVGKVRD---------------------------VRIISDRNSRRSKGIAYVEF 74

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
              +    A+  + G+ L G  I V   +  +
Sbjct: 75  CEIQSVPLAIG-LTGQRLLGVPIIVQASQAEK 105

>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 = 69.6 bits (171), Expect = 5e-17
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 28/89 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + + F++FG + +                           A +  D+   RS G   V 
Sbjct: 45  DIQELFAEFGTLKK---------------------------AAVHYDR-SGRSLGTADVH 76

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNV 89
           F  + +A KA+   NG  LDGR + +  V
Sbjct: 77  FERKADALKAMKQYNGVPLDGRPMNIQLV 105

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 6e-17
 Identities = 14/110 (12%), Positives = 35/110 (31%), Gaps = 27/110 (24%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L D   ++G+V E                             I++     +  G   V 
Sbjct: 22  FLKDMCRKYGEVEE---------------------------VEILLHPRTRKHLGLARVL 54

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPE 110
           F++   A++ + +++   + G +I        ++      L    + +P+
Sbjct: 55  FTSTRGAKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQ 104

>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 = 68.8 bits (169), Expect = 6e-17
 Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 28/87 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          +L + F Q G +T+                            TI  D+ + + K +G+V 
Sbjct: 32 ILYELFLQAGPLTK---------------------------VTICKDR-EGKPKSFGFVC 63

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          F   E    A+A +NG  L GR I V 
Sbjct: 64 FKHPESVSYAIALLNGIRLYGRPINVS 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 70.3 bits (173), Expect = 8e-17
 Identities = 18/94 (19%), Positives = 31/94 (32%), Gaps = 27/94 (28%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   F   G +                               I+ D     S GY +V 
Sbjct: 19 ELYALFRAIGPINT---------------------------CRIMRDYKTGYSYGYAFVD 51

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          F++E ++Q+A+  +NG  +  + + V   RP   
Sbjct: 52 FTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE 85

>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 = 64.5 bits (158), Expect = 1e-14
 Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 27/82 (32%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   F ++G + +                             I+ DK   R +G  +V 
Sbjct: 105 QLDTIFGKYGSIVQ---------------------------KNILRDKLTGRPRGVAFVR 137

Query: 61  FSTEEEAQKALADMNGKLLDGR 82
           ++  EEAQ+A++ +N  + +G 
Sbjct: 138 YNKREEAQEAISALNNVIPEGG 159

>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 = 69.3 bits (170), Expect = 9e-17
 Identities = 19/93 (20%), Positives = 31/93 (33%), Gaps = 28/93 (30%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + + F++FG + +                           A +  D+   RS G   V 
Sbjct: 51  DIQELFAEFGTLKK---------------------------AAVDYDR-SGRSLGTADVH 82

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
           F    +A KA+    G  LDGR + +  V    
Sbjct: 83  FERRADALKAMKQYKGVPLDGRPMDIQLVASQI 115

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 68.4 bits (168), Expect = 1e-16
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 27/91 (29%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + D F+++G++                               + +D+     KGY  V 
Sbjct: 39  DIHDKFAEYGEIKN---------------------------IHLNLDRRTGYLKGYTLVE 71

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           + T +EAQ A+  +NG+ L G+ I VD    
Sbjct: 72  YETYKEAQAAMEGLNGQDLMGQPISVDWCFV 102

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 68.1 bits (167), Expect = 1e-16
 Identities = 14/93 (15%), Positives = 28/93 (30%), Gaps = 28/93 (30%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L +     G V +                             ++ ++   + KG  YV +
Sbjct: 34 LEEICKAHGTVKD---------------------------LRLVTNRAG-KPKGLAYVEY 65

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            E +A +A+  M+G  +   +I V        
Sbjct: 66 ENESQASQAVMKMDGMTIKENIIKVAISNSGPS 98

>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 = 68.4 bits (168), Expect = 1e-16
 Identities = 21/93 (22%), Positives = 35/93 (37%), Gaps = 27/93 (29%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L D FS+ G V                               ++ D+   + KGYG+  +
Sbjct: 25 LKDIFSEVGPVVS---------------------------FRLVYDRETGKPKGYGFCEY 57

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            +E A  A+ ++NG+   GR + VDN    + 
Sbjct: 58 QDQETALSAMRNLNGREFSGRALRVDNAASEKN 90

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 68.6 bits (168), Expect = 1e-16
 Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 27/86 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            LA  F  FG V                             A + +DK  + SK +G+V+
Sbjct: 56  DLASTFLPFGNVIS---------------------------AKVFIDKQTSLSKCFGFVS 88

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFV 86
           F   + AQ A+  MNG  +  + + V
Sbjct: 89  FDNPDSAQVAIKAMNGFQVGTKRLKV 114

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 68.1 bits (167), Expect = 1e-16
 Identities = 15/91 (16%), Positives = 30/91 (32%), Gaps = 29/91 (31%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L  A S+                                    ++D     ++ +GYV 
Sbjct: 33 ELKVAISELFAKN----------------------------DLAVVDVRTGTNRKFGYVD 64

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          F + E+ +KAL ++ G  + G  I ++  + 
Sbjct: 65 FESAEDLEKAL-ELTGLKVFGNEIKLEKPKG 94

>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 = 67.6 bits (166), Expect = 2e-16
 Identities = 13/99 (13%), Positives = 26/99 (26%), Gaps = 34/99 (34%)

Query: 2  LADAFSQFG--QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYV 59
          L +A    G   + E                                ++   +SKG+  V
Sbjct: 18 LTEAVHSLGVNDILE---------------------------IKFFENRANGQSKGFALV 50

Query: 60 TFSTEEEAQKALADMNGKLLDGRVIFVD-----NVRPSR 93
             +E  ++K +  +  + L G+   V            
Sbjct: 51 GVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHHHHH 89

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 68.1 bits (167), Expect = 2e-16
 Identities = 22/97 (22%), Positives = 31/97 (31%), Gaps = 33/97 (34%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L +   QFG +                               +++      SKG  +  
Sbjct: 31  ALGEVLQQFGDLKY---------------------------VRVVLHPDTEHSKGCAFAQ 63

Query: 61  FSTEEEAQKALADMN------GKLLDGRVIFVDNVRP 91
           F T+E AQK LA  +      G  LDGR + VD    
Sbjct: 64  FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 67.7 bits (166), Expect = 2e-16
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 31/96 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L + F +   +                                +      +SKGY ++ 
Sbjct: 31 TLQEVFEKATFI-------------------------------KVPQNQNGKSKGYAFIE 59

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
          F++ E+A++AL   N + ++GR I ++   P    N
Sbjct: 60 FASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPN 95

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 69.2 bits (170), Expect = 2e-16
 Identities = 14/45 (31%), Positives = 24/45 (53%)

Query: 43  TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
            I +     +SKG  Y+ F +E +A+K L +  G  +DGR + + 
Sbjct: 125 EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169

>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 = 68.0 bits (167), Expect = 8e-16
 Identities = 16/100 (16%), Positives = 31/100 (31%), Gaps = 29/100 (29%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L  A S+                                    ++D     ++ +GYV 
Sbjct: 29  ELKVAISELFAKN----------------------------DLAVVDVRTGTNRKFGYVD 60

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           F + E+ +KAL ++ G  + G  I ++  +        A 
Sbjct: 61  FESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAA 99

>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 = 66.8 bits (164), Expect = 3e-16
 Identities = 23/92 (25%), Positives = 32/92 (34%), Gaps = 28/92 (30%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F   G V                              TI+ DK     KG+ Y+ F
Sbjct: 23 LEAHFHGCGSVNR---------------------------VTILCDKFSGHPKGFAYIEF 55

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          S +E  + +LA ++  L  GR I V   R +R
Sbjct: 56 SDKESVRTSLA-LDESLFRGRQIKVIPKRTNR 86

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 68.8 bits (169), Expect = 3e-16
 Identities = 22/99 (22%), Positives = 35/99 (35%), Gaps = 27/99 (27%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
               F   G++                               ++ DK   +S GYG+V 
Sbjct: 18 EFRSLFGSIGEIES---------------------------CKLVRDKITGQSLGYGFVN 50

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA 99
          +   ++A+KA+  +NG  L  + I V   RPS     DA
Sbjct: 51 YIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDA 89

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 64.9 bits (159), Expect = 9e-15
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 27/82 (32%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   FSQ+G++                             + I++D+    S+G G++ 
Sbjct: 104 ELEQLFSQYGRIIT---------------------------SRILVDQVTGVSRGVGFIR 136

Query: 61  FSTEEEAQKALADMNGKLLDGR 82
           F    EA++A+  +NG+   G 
Sbjct: 137 FDKRIEAEEAIKGLNGQKPSGA 158

>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 = 66.9 bits (164), Expect = 6e-16
 Identities = 15/91 (16%), Positives = 24/91 (26%), Gaps = 28/91 (30%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L +    FGQV                               I+ D     S+G G+  
Sbjct: 41  ELENMLKPFGQVIS---------------------------TRILRDS-SGTSRGVGFAR 72

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
             + E+ +  +   NGK +           P
Sbjct: 73  MESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 103

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 70.0 bits (172), Expect = 7e-16
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 27/87 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
              +    FG +                               ++  +   +SKGYG+  
Sbjct: 111 QFEELVRPFGSLER---------------------------CFLVYSERTGQSKGYGFAE 143

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           +  ++ A +A +D+ GK L  R ++V 
Sbjct: 144 YMKKDSAARAKSDLLGKPLGPRTLYVH 170

>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 = 65.0 bits (159), Expect = 4e-14
 Identities = 19/108 (17%), Positives = 31/108 (28%), Gaps = 30/108 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L  A S     T                              +   +   + KG+  + +
Sbjct: 202 LCRALSAVHSPTF---------------------------CQLACGQ-DGQLKGFAVLEY 233

Query: 62  STEEEAQKALADMNGKLLDGRVIFVD--NVRPSRRYNTDAPLARQSAQ 107
            T E A++A    +G  L G  + V      P  R    A +A Q+  
Sbjct: 234 ETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281

>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 = 59.2 bits (144), Expect = 6e-12
 Identities = 11/48 (22%), Positives = 21/48 (43%)

Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          L +   +     ++ KG  +VT    E+A+ A+   +   L  R + V
Sbjct: 42 LLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 89

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 68.0 bits (167), Expect = 9e-16
 Identities = 14/87 (16%), Positives = 27/87 (31%), Gaps = 27/87 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + +  + FG +                            A  ++ D     SKGY +  
Sbjct: 110 QVKELLTSFGPLK---------------------------AFNLVKDSATGLSKGYAFCE 142

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           +       +A+A +NG  L  + + V 
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQ 169

>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 = 64.2 bits (157), Expect = 2e-14
 Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 10/90 (11%)

Query: 11  QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
            +TE+ +  +F +          +          ++    N+ K + ++ F + +E  +A
Sbjct: 15  GITEEAMMDFFNA-------QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67

Query: 71  LADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           +A  +G +  G+ + +   RP         
Sbjct: 68  MA-FDGIIFQGQSLKIR--RPHDYQPLPGA 94

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

 Score = 66.7 bits (163), Expect = 9e-16
 Identities = 18/96 (18%), Positives = 29/96 (30%), Gaps = 19/96 (19%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           +AD F Q G +  +                            +  D+   + KG   V+
Sbjct: 23 SVADYFKQIGIIKTNKKTGQPM-------------------INLYTDRETGKLKGEATVS 63

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
          F     A+ A+   +GK   G  I V        +N
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

>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 = 65.8 bits (161), Expect = 2e-15
 Identities = 22/86 (25%), Positives = 33/86 (38%), Gaps = 28/86 (32%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F  FG + E                           A +I D+   +S+GYG+VT 
Sbjct: 34 LRKYFEGFGDIEE---------------------------AVVITDRQTGKSRGYGFVTM 66

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
          +    A++A  D N   +DGR   V+
Sbjct: 67 ADRAAAERACKDPNPI-IDGRKANVN 91

>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 = 65.1 bits (159), Expect = 2e-15
 Identities = 21/99 (21%), Positives = 31/99 (31%), Gaps = 19/99 (19%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           LAD F Q G V  +                            I +DK   + KG   V++
Sbjct: 32  LADFFKQCGVVKMNKRTGQPM-------------------IHIYLDKETGKPKGDATVSY 72

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
                A+ A+   +GK   G  + V   R     N+   
Sbjct: 73  EDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPS 111

>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 = 65.0 bits (159), Expect = 2e-15
 Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 29/96 (30%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + + F  +G++                               + +D+    SKGY  V 
Sbjct: 42  EIQEKFCDYGEIKN---------------------------IHLNLDRRTGFSKGYALVE 74

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD--NVRPSRR 94
           + T ++A  A   +NG  + G+ I VD   V+  +R
Sbjct: 75  YETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110

>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 = 66.6 bits (163), Expect = 4e-15
 Identities = 14/87 (16%), Positives = 27/87 (31%), Gaps = 27/87 (31%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + +  + FG +                            A  ++ D     SKGY +  
Sbjct: 130 QVKELLTSFGPLK---------------------------AFNLVKDSATGLSKGYAFCE 162

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           +       +A+A +NG  L  + + V 
Sbjct: 163 YVDINVTDQAIAGLNGMQLGDKKLLVQ 189

>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 = 66.2 bits (162), Expect = 6e-15
 Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 10/102 (9%)

Query: 11  QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
            +TE+ +  +F +Q         +          ++    N+ K + ++ F + +E  +A
Sbjct: 15  GITEEAMMDFFNAQ-------MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67

Query: 71  LADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEEN 112
           +A  +G +  G+ + +   RP             S   P   
Sbjct: 68  MA-FDGIIFQGQSLKIR--RPHDYQPLPGMSENPSVYVPGVV 106

>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 = 64.2 bits (157), Expect = 6e-15
 Identities = 17/100 (17%), Positives = 35/100 (35%), Gaps = 28/100 (28%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L   F++F +                                I       R +G  ++T
Sbjct: 41  DLVSLFARFQEKKG---------------------------PPIQFRMMTGRMRGQAFIT 73

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAP 100
           F  +E A +AL  +NG  L G+++ ++  +  ++  +  P
Sbjct: 74  FPNKEIAWQALHLVNGYKLYGKILVIEFGKN-KKQRSSGP 112

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 67.3 bits (165), Expect = 6e-15
 Identities = 11/106 (10%), Positives = 29/106 (27%), Gaps = 27/106 (25%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + D       V   +                            +     N S+ + Y+ 
Sbjct: 133 NIRDLLQDINVVALSIR---------------------------LPSLRFNTSRRFAYID 165

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSA 106
            +++E+A+  +  +NG  ++G  +      P  +         +  
Sbjct: 166 VTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR 211

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 17/88 (19%), Positives = 30/88 (34%), Gaps = 29/88 (32%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMD-KGKNRSKGYGYV 59
           +L ++F  FG + +                             I    K  + +    ++
Sbjct: 227 LLRESFEGFGSIEK---------------------------INIPAGQKEHSFNNCCAFM 259

Query: 60  TFSTEEEAQKALADMNGKLLDGRVIFVD 87
            F  ++ A++AL  MN  LL  R I V 
Sbjct: 260 VFENKDSAERALQ-MNRSLLGNREISVS 286

>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 = 55.8 bits (135), Expect = 1e-10
 Identities = 8/86 (9%), Positives = 19/86 (22%), Gaps = 30/86 (34%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            +   F   G +                               +     K  +  +  + 
Sbjct: 57  KVYKYFKHCGPIIH---------------------------VDVADSLKK--NFRFARIE 87

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFV 86
           F+  + A  A+   +   +    I V
Sbjct: 88  FARYDGALAAITKTHKV-VGQNEIIV 112

>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 = 66.7 bits (162), Expect = 7e-15
 Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 42  ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPL 101
                ++   +SKG+  V   +E  ++K +  +  + L G+   V  V   +  +     
Sbjct: 100 IKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK-QFLSQFEMQ 158

Query: 102 ARQSAQSPEEN 112
           +R++ QS + +
Sbjct: 159 SRKTTQSGQMS 169

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 65.2 bits (159), Expect = 7e-15
 Identities = 20/104 (19%), Positives = 36/104 (34%), Gaps = 29/104 (27%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           + + F  +G++                               + +D+    SKGY  V +
Sbjct: 89  IQEKFCDYGEIKN---------------------------IHLNLDRRTGFSKGYALVEY 121

Query: 62  STEEEAQKALADMNGKLLDGRVIFVD--NVRPSRRYNTDAPLAR 103
            T ++A  A   +NG  + G+ I VD   V+  +R        R
Sbjct: 122 ETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 65.6 bits (160), Expect = 8e-15
 Identities = 19/93 (20%), Positives = 31/93 (33%), Gaps = 28/93 (30%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + + F++FG + +                           A +  D+   RS G   V 
Sbjct: 104 DIQELFAEFGTLKK---------------------------AAVDYDR-SGRSLGTADVH 135

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
           F    +A KA+    G  LDGR + +  V    
Sbjct: 136 FERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168

>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 = 63.1 bits (154), Expect = 1e-14
 Identities = 17/86 (19%), Positives = 27/86 (31%), Gaps = 19/86 (22%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          +AD F Q G +  +                            +  D+   + KG   V+F
Sbjct: 30 VADYFKQIGIIKTNKKTGQPM-------------------INLYTDRETGKLKGEATVSF 70

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
               A+ A+   +GK   G  I V 
Sbjct: 71 DDPPSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 62.2 bits (152), Expect = 2e-14
 Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 28/90 (31%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          + + FSQFG+V                               +I D+   + KG+G+V  
Sbjct: 18 VKELFSQFGKVFN---------------------------VKLIYDRETKKPKGFGFVEM 50

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
            EE   +A+A ++     GR I V    P
Sbjct: 51 Q-EESVSEAIAKLDNTDFMGRTIRVTEANP 79

>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 = 62.0 bits (151), Expect = 5e-14
 Identities = 21/90 (23%), Positives = 28/90 (31%), Gaps = 28/90 (31%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L   FS  G +                              TI+ DK     KGY Y+ F
Sbjct: 53  LEAHFSSCGSINR---------------------------ITILCDKFSGHPKGYAYIEF 85

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           +       A+A M+  +  GR I V   R 
Sbjct: 86  AERNSVDAAVA-MDETVFRGRTIKVLPKRT 114

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 63.8 bits (156), Expect = 5e-14
 Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 29/87 (33%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L D FS FG +                               ++ D+    SKGYG+V 
Sbjct: 119 ALYDTFSAFGNILS---------------------------CKVVCDEN--GSKGYGFVH 149

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           F T+E A++A+  MNG LL+ R +FV 
Sbjct: 150 FETQEAAERAIEKMNGMLLNDRKVFVG 176

>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 = 61.5 bits (150), Expect = 4e-13
 Identities = 22/103 (21%), Positives = 36/103 (34%), Gaps = 29/103 (28%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           ML + FS  G +                            +  +  D    RS GY YV 
Sbjct: 31  MLYEKFSPAGPIL---------------------------SIRVCRDMITRRSLGYAYVN 63

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD--NVRPSRRYNTDAPL 101
           F    +A++AL  MN  ++ G+ + +      PS R +    +
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNI 106

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 61.6 bits (150), Expect = 5e-14
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 4/50 (8%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK----LLDGRVIFVD 87
            +I DK   +++G+ +V  S+  +A + L  +        +DG+ I VD
Sbjct: 41 IRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVD 90

>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 = 61.2 bits (149), Expect = 9e-14
 Identities = 18/97 (18%), Positives = 31/97 (31%), Gaps = 30/97 (30%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   F +FG++ E                            T++ D+     KG  ++T
Sbjct: 29 DLKPLFEEFGKIYE---------------------------LTVLKDRFTGMHKGCAFLT 61

Query: 61 FSTEEEAQKALADMNGKLL---DGRVIFVDNVRPSRR 94
          +   E A KA + ++ +       R I V       R
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR 98

>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 = 60.7 bits (148), Expect = 1e-13
 Identities = 17/91 (18%), Positives = 31/91 (34%), Gaps = 30/91 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           +   F+++G V E                             II D+    SKGYG+V+
Sbjct: 25 EIRSFFARYGSVKE---------------------------VKIITDR-TGVSKGYGFVS 56

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          F  + + QK +   +     G+ + +     
Sbjct: 57 FYNDVDVQKIV--ESQINFHGKKLKLGPAIR 85

>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 = 62.1 bits (151), Expect = 1e-13
 Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 27/94 (28%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            + + FS+ G + +                             + +DK K  + G+ +V 
Sbjct: 55  QIYELFSKSGDIKK---------------------------IIMGLDKMKKTACGFCFVE 87

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           + +  +A+ A+  +NG  LD R+I  D     + 
Sbjct: 88  YYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 121

>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 = 59.9 bits (146), Expect = 1e-13
 Identities = 23/86 (26%), Positives = 33/86 (38%), Gaps = 28/86 (32%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L D F++FG+V +                            TI MD    RS+G+G++ F
Sbjct: 28 LKDYFTKFGEVVD---------------------------CTIKMDPNTGRSRGFGFILF 60

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
                +K L     + LDGRVI   
Sbjct: 61 KDAASVEKVLDQKEHR-LDGRVIDPK 85

>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 = 60.0 bits (146), Expect = 2e-13
 Identities = 18/57 (31%), Positives = 29/57 (50%)

Query: 53  SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSP 109
            K Y ++ F   + A KA+ +MNGK L+G  I +   +P  +   +    RQ+A  P
Sbjct: 44  LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>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 = 59.9 bits (146), Expect = 2e-13
 Identities = 18/83 (21%), Positives = 29/83 (34%), Gaps = 29/83 (34%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + FS FG+V                               +  D     SKG+G+V F
Sbjct: 32 LKEYFSTFGEVLM---------------------------VQVKKDLKTGHSKGFGFVRF 64

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
          +  E   K ++  +  ++DGR  
Sbjct: 65 TEYETQVKVMSQRH--MIDGRWC 85

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 59.4 bits (145), Expect = 2e-13
 Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + F QFG+V E                             ++ D    RS+G+G+VTF
Sbjct: 17 LREYFGQFGEVKE---------------------------CLVMRDPLTKRSRGFGFVTF 49

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
            +    K LA  +   LD + I
Sbjct: 50 MDQAGVDKVLA-QSRHELDSKTI 71

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 60.0 bits (146), Expect = 2e-13
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          ++ DK  ++ KG+ YV F   +  ++AL   +G LL  R + VD     ++
Sbjct: 46 LVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQ 95

>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 = 59.9 bits (146), Expect = 2e-13
 Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 28/90 (31%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + F +FG VTE                             +I D  K R +G+G++TF
Sbjct: 27 LREYFKKFGVVTE---------------------------VVMIYDAEKQRPRGFGFITF 59

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
            E+   +A+  M+   + G+ + V    P
Sbjct: 60 EDEQSVDQAVN-MHFHDIMGKKVEVKRAEP 88

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 61.5 bits (150), Expect = 3e-13
 Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 29/95 (30%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK--GKNRSKGYGYV 59
          L + F Q+G V E                             ++ D+     +SKG  +V
Sbjct: 20 LRELFEQYGAVYE---------------------------INVLRDRSQNPPQSKGCCFV 52

Query: 60 TFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          TF T + A +A   ++   +   +     ++P+  
Sbjct: 53 TFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADS 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 = 56.5 bits (137), Expect = 2e-11
 Identities = 17/77 (22%), Positives = 25/77 (32%), Gaps = 28/77 (36%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            +   FS FGQ+ E                             I+       S+G  +VT
Sbjct: 111 DIRVMFSSFGQIEE---------------------------CRILRGP-DGLSRGCAFVT 142

Query: 61  FSTEEEAQKALADMNGK 77
           F+T   AQ A+  M+  
Sbjct: 143 FTTRAMAQTAIKAMHQA 159

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 58.6 bits (143), Expect = 3e-13
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          +   F QFG+V +                           A ++ DK  NR +G+G+VTF
Sbjct: 16 VKHYFEQFGKVDD---------------------------AMLMFDKTTNRHRGFGFVTF 48

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
           +E+  +K    ++   ++ +++
Sbjct: 49 ESEDIVEKVCE-IHFHEINNKMV 70

>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 = 59.2 bits (144), Expect = 4e-13
 Identities = 16/43 (37%), Positives = 26/43 (60%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          + + Y +V FS  E+A +A+  +NGK+LDG  I V   +P  +
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 91

>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 = 59.6 bits (145), Expect = 4e-13
 Identities = 22/83 (26%), Positives = 30/83 (36%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   FSQ+G+V +                             I+ DK  N+S+G+G+V F
Sbjct: 33 LRSYFSQYGEVVD---------------------------CVIMKDKTTNQSRGFGFVKF 65

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
                   LA      LDGR I
Sbjct: 66 KDPNCVGTVLA-SRPHTLDGRNI 87

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 59.4 bits (144), Expect = 4e-13
 Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 27/88 (30%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   FS+ G+V                                 +D+   ++KG+ +V 
Sbjct: 28 ALTSLFSKAGKVVN---------------------------MEFPIDEATGKTKGFLFVE 60

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDN 88
            +  +A+K +   +GK LD +      
Sbjct: 61 CGSMNDAKKIIKSFHGKRLDLKHRLFLY 88

>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 = 58.4 bits (142), Expect = 8e-13
 Identities = 18/99 (18%), Positives = 30/99 (30%), Gaps = 29/99 (29%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           ++   FSQ G                                 +I +   N    Y +V 
Sbjct: 31  LILQLFSQIGPCKS---------------------------CKMITEHTSNDP--YCFVE 61

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDA 99
           F    +A  ALA MNG+ + G+ + V+         +  
Sbjct: 62  FYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGP 100

>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 = 58.5 bits (142), Expect = 8e-13
 Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 26/86 (30%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           ++ AF+  G+                           + +  II ++      GY +V 
Sbjct: 25 FISRAFATMGET--------------------------VMSVKIIRNRLTGIPAGYCFVE 58

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFV 86
          F+    A+K L  +NGK L G     
Sbjct: 59 FADLATAEKCLHKINGKPLPGATPAK 84

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 60.4 bits (147), Expect = 9e-13
 Identities = 24/104 (23%), Positives = 40/104 (38%), Gaps = 30/104 (28%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L   F Q+G +T+                             ++ D    RS+G+G+VT+
Sbjct: 30  LRSHFEQWGTLTD---------------------------CVVMRDPNTKRSRGFGFVTY 62

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQS 105
           +T EE   A+       +DGRV+     R   R ++  P A  +
Sbjct: 63  ATVEEVDAAMN-ARPHKVDGRVVEPK--RAVSREDSQRPGAHLT 103

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 57.7 bits (140), Expect = 8e-12
 Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 28/87 (32%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
            L D F Q+G++                               I+ D+G  + +G+ +VT
Sbjct: 120 HLRDYFEQYGKIEV---------------------------IEIMTDRGSGKKRGFAFVT 152

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           F   +   K +       ++G    V 
Sbjct: 153 FDDHDSVDKIVI-QKYHTVNGHNCEVR 178

>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 = 58.4 bits (142), Expect = 1e-12
 Identities = 20/83 (24%), Positives = 35/83 (42%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + + Q+G++T+                             ++ D    RS+G+G+VTF
Sbjct: 44 LRNYYEQWGKLTD---------------------------CVVMRDPASKRSRGFGFVTF 76

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
          S+  E   A+A      +DGRV+
Sbjct: 77 SSMAEVDAAMA-ARPHSIDGRVV 98

>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 = 58.4 bits (142), Expect = 1e-12
 Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + F QFG+V E                             ++ D    RS+G+G+VTF
Sbjct: 42 LREYFGQFGEVKE---------------------------CLVMRDPLTKRSRGFGFVTF 74

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
            +    K LA  +   LD + I
Sbjct: 75 MDQAGVDKVLA-QSRHELDSKTI 96

>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 = 2e-12
 Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL-LDGRVIFVDNVRPSRR 94
          + +        GY +V +  +  A +A+  ++GK+ L G+++ VD     + 
Sbjct: 34 LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 85

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 59.1 bits (144), Expect = 2e-12
 Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 28/87 (32%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
              + FSQ+G + +                           A +++DK   +S+G+G+VT
Sbjct: 103 EFEEFFSQWGTIID---------------------------AQLMLDKDTGQSRGFGFVT 135

Query: 61  FSTEEEAQKALADMNGKLLDGRVIFVD 87
           + + +   +            R I + 
Sbjct: 136 YDSADAVDRVCQ-NKFIDFKDRKIEIK 161

>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 = 59.1 bits (144), Expect = 2e-12
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 29/86 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + F ++G VT+                             I+ D    RS+G+G+++F
Sbjct: 20 LREYFGKYGTVTD---------------------------LKIMKDPATGRSRGFGFLSF 52

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
                 + +   +  +LDG+VI   
Sbjct: 53 EKPSSVDEVVKTQH--ILDGKVIDPK 76

>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 = 56.9 bits (138), Expect = 3e-12
 Identities = 16/98 (16%), Positives = 34/98 (34%), Gaps = 29/98 (29%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK-GKNRSKGYGYVT 60
           + + FS FG++                               +     G    +G+G+V 
Sbjct: 32  IRELFSTFGELKT---------------------------VRLPKKMTGTGAHRGFGFVD 64

Query: 61  FSTEEEAQKALADM-NGKLLDGRVIFVDNVRPSRRYNT 97
           F T+++A+KA   + +   L GR + ++         +
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 56.9 bits (138), Expect = 3e-12
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 13/76 (17%)

Query: 12 VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKAL 71
          V + ++Y +F         Y            +++D+    SKGYG+V F+ E E ++AL
Sbjct: 21 VDDGMLYEFFVK------VYPSCRG-----GKVVLDQ-TGVSKGYGFVKFTDELEQKRAL 68

Query: 72 ADMNGK-LLDGRVIFV 86
           +  G   L  + + +
Sbjct: 69 TECQGAVGLGSKPVRL 84

>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 = 56.9 bits (138), Expect = 3e-12
 Identities = 14/93 (15%), Positives = 28/93 (30%), Gaps = 33/93 (35%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          +   F ++G+  E                             I       + KG+G++  
Sbjct: 32 MRKLFEKYGKAGE---------------------------VFIH------KDKGFGFIRL 58

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           T   A+ A  +++   L G+ + V     S  
Sbjct: 59 ETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 91

>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 = 56.5 bits (137), Expect = 5e-12
 Identities = 12/52 (23%), Positives = 26/52 (50%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
          I+D   +  +   +VT+   E A +A+A++NG  ++   + V+  R     +
Sbjct: 40 IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLD 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 56.7 bits (137), Expect = 5e-12
 Identities = 16/98 (16%), Positives = 35/98 (35%), Gaps = 30/98 (30%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           ++   FS+FG++T                                  +   ++KGY ++ 
Sbjct: 37  VIHKIFSKFGKITN-----------------------------DFYPEEDGKTKGYIFLE 67

Query: 61  FSTEEEAQKALADMNGKLLDGR-VIFVDNVRPSRRYNT 97
           +++   A  A+ + +G  LD +    V+      +Y T
Sbjct: 68  YASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMT 105

>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 = 56.1 bits (136), Expect = 6e-12
 Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 2/51 (3%)

Query: 44 IIMDKG-KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          +  +     R KG+GY  F   +    AL+ +N + L  R I VD    ++
Sbjct: 50 LPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQ 99

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.5 bits (134), Expect = 8e-12
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 29/88 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          ++   FS+FG++T                                  +   ++KGY ++ 
Sbjct: 23 VIHKIFSKFGKITN-----------------------------DFYPEEDGKTKGYIFLE 53

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDN 88
          +++   A  A+ + +G  LD +  F  N
Sbjct: 54 YASPAHAVDAVKNADGYKLDKQHTFRVN 81

>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 = 56.1 bits (136), Expect = 8e-12
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 44 IIMDKGK-NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          +  +     R KG+GY  F   +    AL+ +N + L  + I VD    ++ 
Sbjct: 46 LPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQD 96

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 58.2 bits (141), Expect = 1e-11
 Identities = 23/114 (20%), Positives = 41/114 (35%), Gaps = 30/114 (26%)

Query: 1   MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           +L  AFSQFG V +                           A +++D  + R+ G G+V 
Sbjct: 112 LLEQAFSQFGPVEK---------------------------AVVVVDD-RGRATGKGFVE 143

Query: 61  FSTEEEAQKALADMNGK-LLDGRVIFVDNVRP-SRRYNTDAPLARQSAQSPEEN 112
           F+ +  A+KAL        L         V P  +  + D    +   ++ + +
Sbjct: 144 FAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYH 197

>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 = 56.2 bits (136), Expect = 6e-11
 Identities = 13/86 (15%), Positives = 30/86 (34%), Gaps = 33/86 (38%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
               F ++G+ +E  +                                 NR +G+G++ 
Sbjct: 38 DFKRLFERYGEPSEVFI---------------------------------NRDRGFGFIR 64

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFV 86
            +   A+ A A+++G +L  R + +
Sbjct: 65 LESRTLAEIAKAELDGTILKSRPLRI 90

>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 = 56.4 bits (136), Expect = 1e-11
 Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 11  QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
            V E  + + F         Y   S         I    + R KG  ++    E+ A KA
Sbjct: 56  HVQEKDLKYIFGR-------YVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKA 108

Query: 71  LADMNGKLLDGRVIFVD 87
           L + NG +L G+ + V 
Sbjct: 109 LKEANGYVLFGKPMVVQ 125

>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 = 54.6 bits (132), Expect = 2e-11
 Identities = 10/44 (22%), Positives = 19/44 (43%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           +    K    G   V F + +EA  A+ D+N + +  R + + 
Sbjct: 47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV 90

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 54.2 bits (131), Expect = 3e-11
 Identities = 10/43 (23%), Positives = 19/43 (44%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           +    K    G   V F + +EA  A+ D+N + +  R + +
Sbjct: 47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 89

>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 = 54.6 bits (132), Expect = 3e-11
 Identities = 21/92 (22%), Positives = 33/92 (35%), Gaps = 33/92 (35%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
          ++   FS FGQ+ E                             +  +KG      Y +V 
Sbjct: 41 LMRQTFSPFGQIME---------------------------IRVFPEKG------YSFVR 67

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          FST E A  A+  +NG  ++G V+     + S
Sbjct: 68 FSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99

>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 = 54.5 bits (131), Expect = 3e-11
 Identities = 11/42 (26%), Positives = 19/42 (45%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
             G        YVT+   E+A +A+  +N  ++DGR +   
Sbjct: 55 SYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS 96

>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 = 53.7 bits (130), Expect = 4e-11
 Identities = 13/83 (15%), Positives = 25/83 (30%), Gaps = 28/83 (33%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          + + F  FG+V                               + MD   N+ +G+ ++TF
Sbjct: 16 IREYFGGFGEVES---------------------------IELPMDNKTNKRRGFCFITF 48

Query: 62 STEEEAQKALADMNGKLLDGRVI 84
            EE  +K +       +     
Sbjct: 49 KEEEPVKKIME-KKYHNVGLSKC 70

>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 = 53.4 bits (129), Expect = 5e-11
 Identities = 18/93 (19%), Positives = 32/93 (34%), Gaps = 35/93 (37%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F + G+V E                             ++        K Y +V  
Sbjct: 26 LRSLFERRGRVIE---------------------------CDVV--------KDYAFVHM 50

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            E +A+ A+A +NGK + G+ I V+     ++
Sbjct: 51 EKEADAKAAIAQLNGKEVKGKRINVELSTKGQK 83

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.5 bits (129), Expect = 1e-10
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 54  KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            G+ +V F   E A KA+ +++GK    + + V   +   +
Sbjct: 65  NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105

>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 = 53.3 bits (128), Expect = 1e-10
 Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 1/65 (1%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQ 104
           I      ++ G G+V F  E + + AL   + + +  R I V  +           + ++
Sbjct: 58  IAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITKKGMLEKIDMIRKR 116

Query: 105 SAQSP 109
               P
Sbjct: 117 LQSGP 121

>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 = 52.8 bits (127), Expect = 2e-10
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQ 104
           ++     +  G   V F  E++A+K+   ++ K L+GR  F   V      +        
Sbjct: 48  VLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAF---VHVVTLEDMREIEKNP 103

Query: 105 SAQS 108
            AQ 
Sbjct: 104 PAQG 107

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.5 bits (126), Expect = 2e-10
 Identities = 17/51 (33%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 47  DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV---DNVRPSRR 94
                   G G + F +EE   +AL  +N     G VI V   DN  P RR
Sbjct: 60  SVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPIRR 110

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 52.3 bits (126), Expect = 2e-10
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 50  KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP-SRRYNTDAPLARQS 105
                G+ +V F    +A+ A+  ++GK++ G  + V+      RR   D P AR+ 
Sbjct: 33  ARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPARRK 89

>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 = 52.0 bits (125), Expect = 3e-10
 Identities = 12/42 (28%), Positives = 23/42 (54%)

Query: 53  SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            KGY +V +S E  A+ A+   NG++L G+ + ++     + 
Sbjct: 61  HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKP 102

>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 = 51.6 bits (124), Expect = 4e-10
 Identities = 11/47 (23%), Positives = 20/47 (42%)

Query: 48  KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           K +     + +V F    +A+ A+   +G   DG  + V+  R  R 
Sbjct: 55  KNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 101

>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 = 52.6 bits (126), Expect = 4e-10
 Identities = 10/45 (22%), Positives = 21/45 (46%)

Query: 50  KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
                G+ +V F    +A  A+ +++G+ L G  + V+     +R
Sbjct: 106 ARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKR 150

>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 = 51.0 bits (123), Expect = 4e-10
 Identities = 17/93 (18%), Positives = 30/93 (32%), Gaps = 35/93 (37%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          +   F Q+G+V E                             II        K YG+V  
Sbjct: 25 IRSLFEQYGKVLE---------------------------CDII--------KNYGFVHI 49

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            +  A+ A+ +++   L G  I V+  +   +
Sbjct: 50 EDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK 82

>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 = 50.7 bits (122), Expect = 6e-10
 Identities = 15/93 (16%), Positives = 26/93 (27%), Gaps = 35/93 (37%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F ++G V E                             I+        K Y +V  
Sbjct: 27 LRAKFEEYGPVIE---------------------------CDIV--------KDYAFVHM 51

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
             E+A +A+  ++     G+ + V       R
Sbjct: 52 ERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 49.9 bits (120), Expect = 1e-09
 Identities = 6/46 (13%), Positives = 20/46 (43%)

Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD 98
             +G++ F   +  + A+   + ++  G+ + ++    + R   D
Sbjct: 44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFD 89

>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 = 50.4 bits (121), Expect = 1e-09
 Identities = 16/76 (21%), Positives = 25/76 (32%), Gaps = 28/76 (36%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          +   F  FG + E                            T++       SKG  +V F
Sbjct: 32 VLRLFQPFGVIDE---------------------------CTVLRGP-DGSSKGCAFVKF 63

Query: 62 STEEEAQKALADMNGK 77
          S+  EAQ A+  ++G 
Sbjct: 64 SSHTEAQAAIHALHGS 79

>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 = 50.4 bits (121), Expect = 1e-09
 Identities = 13/95 (13%), Positives = 30/95 (31%), Gaps = 30/95 (31%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          + D F ++G + +                              I       ++G  YV +
Sbjct: 25 MYDIFGKYGPIRQ------------------------------IRVGNTPETRGTAYVVY 54

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
              +A+ A+  ++G  +  R + V     +R + 
Sbjct: 55 EDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQ 89

>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 = 50.1 bits (120), Expect = 1e-09
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
           ++ D    R+ G G V F + ++  +AL   N  L+  R + V      
Sbjct: 46 HLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER 93

>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 = 49.9 bits (120), Expect = 2e-09
 Identities = 15/86 (17%), Positives = 25/86 (29%), Gaps = 30/86 (34%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   FS+FGQ+ +                              I+     + +G  +V F
Sbjct: 29 LHAIFSRFGQILD------------------------------ILVSRSLKMRGQAFVIF 58

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
               A  AL  M G     + + + 
Sbjct: 59 KEVSSATNALRSMQGFPFYDKPMRIQ 84

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 50.2 bits (120), Expect = 2e-09
 Identities = 9/58 (15%), Positives = 16/58 (27%)

Query: 52  RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSP 109
              G G V F  +E+   A+  ++             +R            R  +  P
Sbjct: 48  YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGP 105

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 49.4 bits (118), Expect = 2e-09
 Identities = 14/86 (16%), Positives = 26/86 (30%), Gaps = 30/86 (34%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L     Q+G V                                +             VT+
Sbjct: 32 LDSLLVQYGVVES---------------------------CEQVNTD---SETAVVNVTY 61

Query: 62 STEEEAQKALADMNGKLLDGRVIFVD 87
          S++++A++AL  +NG  L+   + V 
Sbjct: 62 SSKDQARQALDKLNGFQLENFTLKVA 87

>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 = 48.5 bits (116), Expect = 6e-09
 Identities = 5/41 (12%), Positives = 19/41 (46%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            +G++ F   +  + A+   + ++  G+ + ++    + R
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 48.5 bits (116), Expect = 6e-09
 Identities = 7/33 (21%), Positives = 14/33 (42%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
            KG  ++ + T E+A   +  +      GR +
Sbjct: 61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 48.1 bits (115), Expect = 7e-09
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          I+        GY +V FS EEE ++AL   N + + GR I V   +  
Sbjct: 41 IVRNAHGNKTGYIFVDFSNEEEVKQAL-KCNREYMGGRYIEVFREKSG 87

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 48.7 bits (116), Expect = 8e-09
 Identities = 19/64 (29%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQ 104
            +     R  G  +V F+ EE AQ AL   +  LL  R I    +  S        L R 
Sbjct: 59  FVTYPDGRPTGDAFVLFACEEYAQNALR-KHKDLLGKRYI---ELFRSTAAEVQQVLNRF 114

Query: 105 SAQS 108
           S+ S
Sbjct: 115 SSAS 118

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 48.3 bits (115), Expect = 1e-08
 Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 41  AATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
               +    + +  G  +V F+++E A+KAL   + + +  R I V
Sbjct: 71  NGITLPVDPEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEV 115

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 49.9 bits (118), Expect = 1e-08
 Identities = 16/87 (18%), Positives = 25/87 (28%), Gaps = 30/87 (34%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   FSQFGQ+ +                              I+     + +G  +V 
Sbjct: 29 SLYAIFSQFGQILD------------------------------ILVSRSLKMRGQAFVI 58

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVD 87
          F     A  AL  M G     + + + 
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQ 85

>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 = 37.5 bits (86), Expect = 3e-04
 Identities = 7/45 (15%), Positives = 14/45 (31%), Gaps = 1/45 (2%)

Query: 43  TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLLDGRVIFV 86
                +         +V F  E +A  A   + G K+     + +
Sbjct: 233 GFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI 277

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          I      R  G   V F+T E+A  A+A  +   +  R + +
Sbjct: 46 IEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVEL 86

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 48.3 bits (115), Expect = 2e-08
 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           I      R  G   V F+T EEA  A++  +   +  R I +
Sbjct: 77  IEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANMQHRYIEL 117

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 47.5 bits (113), Expect = 2e-08
 Identities = 9/58 (15%), Positives = 17/58 (29%)

Query: 52  RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSP 109
              G G V F  +E+   A+  ++             +R            R  ++S 
Sbjct: 49  YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSR 106

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 6/43 (13%), Positives = 18/43 (41%)

Query: 42  ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
            ++ +  GK+     G + + ++ +A + L  +N   +     
Sbjct: 153 TSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNG 195

>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 = 36.2 bits (83), Expect = 8e-04
 Identities = 6/35 (17%), Positives = 13/35 (37%)

Query: 53 SKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
            G   V  +      +A+  +N   + G+ + V 
Sbjct: 41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVC 75

>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 = 46.2 bits (110), Expect = 3e-08
 Identities = 10/36 (27%), Positives = 18/36 (50%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +R+K   +VT    E+AQ A+   +     G+ + V
Sbjct: 37 DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIV 72

>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 = 46.7 bits (111), Expect = 3e-08
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           +    + RS G  +V F+++E A+KAL   + + +  R I +
Sbjct: 47 TLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEI 88

>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 = 46.5 bits (111), Expect = 4e-08
 Identities = 20/88 (22%), Positives = 28/88 (31%), Gaps = 35/88 (39%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          LA  F +FG +                               I   KG      + Y+ +
Sbjct: 34 LAREFDRFGSIRT-----------------------------IDHVKGD----SFAYIQY 60

Query: 62 STEEEAQKALADMNGKLLDG--RVIFVD 87
           + + AQ A A M G  L G  R + VD
Sbjct: 61 ESLDAAQAACAKMRGFPLGGPDRRLRVD 88

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 46.3 bits (110), Expect = 4e-08
 Identities = 14/81 (17%), Positives = 35/81 (43%), Gaps = 10/81 (12%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
           +TE+ +  +F +Q         +          ++    N+ K + ++ F + +E  +A
Sbjct: 17 GITEEAMMDFFNAQ-------MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 69

Query: 71 LADMNGKLLDGRVIFVDNVRP 91
          +A  +G +  G+ + +   RP
Sbjct: 70 MA-FDGIIFQGQSLKIR--RP 87

>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 = 48.0 bits (114), Expect = 5e-08
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 29  LHYFLISDSFLFAA-----TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 83
           L+   ++   LF        +   K     K    V  +   +AQ A++ +NG  L G+ 
Sbjct: 11  LNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKP 70

Query: 84  IFVDNVRPSRRYNTDAPLARQSAQSPEEN 112
           I    +  S+  N   P   Q  Q   ++
Sbjct: 71  I---RITLSKHQNVQLPREGQEDQGLTKD 96

>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 = 44.1 bits (104), Expect = 1e-06
 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 40  FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLLDGRVIFVD 87
               +   K   + +    +   + EEA +AL D++   L +   + V 
Sbjct: 144 NGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 45.7 bits (108), Expect = 1e-07
 Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 4/65 (6%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQ 104
            +   + R  G  +V   +E++ + AL   + + +  R I    V  S R   D  L   
Sbjct: 52  FIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYI---EVFKSHRTEMDWVLKHS 107

Query: 105 SAQSP 109
              S 
Sbjct: 108 GPNSA 112

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 45.7 bits (108), Expect = 1e-07
 Identities = 13/86 (15%), Positives = 24/86 (27%), Gaps = 30/86 (34%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L    S  G + +                              I+    + + G  Y+ F
Sbjct: 50  LYALASSQGDILD------------------------------IVVDLSDDNSGKAYIVF 79

Query: 62  STEEEAQKALADMNGKLLDGRVIFVD 87
           +T+E AQ  +    G    G  + + 
Sbjct: 80  ATQESAQAFVEAFQGYPFQGNPLVIT 105

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 44.8 bits (106), Expect = 1e-07
 Identities = 8/44 (18%), Positives = 17/44 (38%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
             +   ++ +     AQ+A++ + G  L    + V   R  R 
Sbjct: 53 QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 44.5 bits (105), Expect = 2e-07
 Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 4/65 (6%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLAR 103
             +     + +G   +   +E++ QKAL   +   +  R +    V      + DA +  
Sbjct: 45  HFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE---VYEINNEDVDALMKS 100

Query: 104 QSAQS 108
              +S
Sbjct: 101 LQVKS 105

>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 = 45.4 bits (107), Expect = 4e-07
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 10/91 (10%)

Query: 29  LHYFLISDSFLFAA-----TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRV 83
           L+   ++   LF        +   K     K    V  +   +AQ A++ +NG  L G+ 
Sbjct: 42  LNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKP 101

Query: 84  IFV-----DNVRPSRRYNTDAPLARQSAQSP 109
           I +      NV+  R    D  L +    SP
Sbjct: 102 IRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 1/49 (2%)

Query: 40  FAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLLDGRVIFVD 87
               +   K   + +    +   + EEA +AL D++   L +   + V 
Sbjct: 175 NGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 223

>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 = 43.7 bits (103), Expect = 4e-07
 Identities = 14/44 (31%), Positives = 24/44 (54%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
            + D   +   G  YV F  EE+A+KA+ D+N +  +G+ I  +
Sbjct: 58  NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 43.1 bits (102), Expect = 6e-07
 Identities = 17/103 (16%), Positives = 30/103 (29%), Gaps = 36/103 (34%)

Query: 2   LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
           L++ F  FG V                               ++MDK K     +  V  
Sbjct: 25  LSEYFLAFGPVAS-----------------------------VVMDKDKGV---FAIVEM 52

Query: 62  STEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQ 104
                 +  L+  +   L G  +    VRP  +    +P ++ 
Sbjct: 53  GDVGAREAVLS-QSQHSLGGHRL---RVRPREQKEFQSPASKS 91

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.2 bits (102), Expect = 8e-07
 Identities = 8/42 (19%), Positives = 17/42 (40%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +        KG  +V F + E A+K +     K  +  ++ +
Sbjct: 43 MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLIL 84

>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 = 42.6 bits (101), Expect = 9e-07
 Identities = 15/90 (16%), Positives = 29/90 (32%), Gaps = 34/90 (37%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L + FSQ+G V +                              I        + + +VTF
Sbjct: 22 LREFFSQYGDVMD----------------------------VFIP----KPFRAFAFVTF 49

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          + ++ AQ    +    ++ G  + + N  P
Sbjct: 50 ADDQIAQSLCGEDL--IIKGISVHISNAEP 77

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 43.1 bits (101), Expect = 1e-06
 Identities = 9/42 (21%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
            +   + R  G  +V   +E++ + AL   + + +  R I V
Sbjct: 79  FIYTREGRQSGEAFVELGSEDDVKMAL-KKDRESMGHRYIEV 119

>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 = 41.7 bits (98), Expect = 2e-06
 Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 2/55 (3%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGK--LLDGRVIFVDNVRPSRRYNTD 98
              K +++G+ +V + +   A  A   +      L G  I VD   P    + D
Sbjct: 44 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDED 98

>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 Length = 112

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 11/46 (23%), Positives = 17/46 (36%)

Query: 50  KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRY 95
                G   V+F   EEA   +  ++G+   GR I       +  Y
Sbjct: 60  DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 105

>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 = 41.3 bits (97), Expect = 3e-06
 Identities = 9/60 (15%), Positives = 17/60 (28%), Gaps = 1/60 (1%)

Query: 52  RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSPEE 111
                  V F    EA+KA   +         ++++   P   +           + P E
Sbjct: 44  EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA-PIGVFGAAPQKKDSQHEQPAE 102

>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 = 40.3 bits (95), Expect = 6e-06
 Identities = 14/90 (15%), Positives = 28/90 (31%), Gaps = 34/90 (37%)

Query: 2  LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTF 61
          L   F Q+G+V +                              I        + + +VTF
Sbjct: 28 LQQFFCQYGEVVD----------------------------VFIP----KPFRAFAFVTF 55

Query: 62 STEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          + ++ AQ    +    ++ G  + + N  P
Sbjct: 56 ADDKVAQSLCGEDL--IIKGISVHISNAEP 83

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 40.3 bits (95), Expect = 6e-06
 Identities = 7/35 (20%), Positives = 18/35 (51%), Gaps = 1/35 (2%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADM-NGKLLDGRVI 84
           + +   ++ F+T + A+ A     N  +++GR +
Sbjct: 45 VQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL 79

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 40.7 bits (95), Expect = 7e-06
 Identities = 13/79 (16%), Positives = 23/79 (29%), Gaps = 33/79 (41%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L     + G V                               ++M   K     Y +  
Sbjct: 43 QLLPVLEKCGLVDA-----------------------------LLMPPNK----PYSFAR 69

Query: 61 FSTEEEAQKALADMNGKLL 79
          + T EE+++A   +NGK +
Sbjct: 70 YRTTEESKRAYVTLNGKEV 88

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 40.6 bits (94), Expect = 2e-05
 Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 1/42 (2%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           +        KG  +V F + E A+K +     K      + +
Sbjct: 141 MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK-YKETDLLI 181

>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 = 40.6 bits (94), Expect = 3e-05
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 44  IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
           ++  K   + +GY ++ +  E +   A    +GK +DGR + VD  R      
Sbjct: 134 MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKG 186

>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 = 38.2 bits (89), Expect = 5e-05
 Identities = 9/31 (29%), Positives = 17/31 (54%)

Query: 54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
           G  +V F++  + QKA+  + G+    RV+
Sbjct: 59 CGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 89

>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 = 6e-05
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 50 KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          KN ++G  YV   +   A  A+  ++G+   G++I    V    
Sbjct: 51 KNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPT 94

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 38.2 bits (89), Expect = 7e-05
 Identities = 10/30 (33%), Positives = 15/30 (50%)

Query: 55  GYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
              +V FS   E  KA+  +NG+   GR +
Sbjct: 72  VKIFVEFSIASETHKAIQALNGRWFAGRKV 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	112
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.72
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.68
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.68
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.66
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.66
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.66
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.65
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.65
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.64
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.64
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.64
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.64
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.64
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.64
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.64
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.63
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.63
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.63
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.63
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.63
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.62
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.62
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.61
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.61
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.61
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.61
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.61
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.61
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.61
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.61
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.61
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.6
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.6
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.6
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.6
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.6
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.59
2div_A	99	TRNA selenocysteine associated protein; structural	99.59
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.59
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.59
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.59
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.59
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.59
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.58
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.58
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.58
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.58
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.57
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.57
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.57
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.57
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.57
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.57
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.57
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.57
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.57
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.57
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.56
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.56
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.56
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.56
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.55
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.55
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.55
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.54
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.54
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.54
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.54
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.54
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.54
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.53
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.53
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.53
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.53
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.52
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.52
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.52
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.51
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.51
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.51
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.51
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.5
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.5
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.5
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.5
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.5
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.5
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.5
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.49
1x5p_A	97	Negative elongation factor E; structure genomics,	99.49
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.49
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.49
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.48
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.48
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.48
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.48
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.47
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.47
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.47
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.47
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.47
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.47
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.46
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.46
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.46
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.46
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.45
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.45
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.44
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.44
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.43
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.43
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.43
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.43
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.43
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.42
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.42
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.42
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.42
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.42
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.42
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.42
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.41
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.41
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.4
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.4
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.4
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.4
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.4
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.39
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.39
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.39
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.39
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.39
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.38
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.38
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.38
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.38
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.38
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.38
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.38
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.38
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.37
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.37
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.37
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.37
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.37
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.37
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.37
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.37
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.37
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.36
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.36
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.36
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.36
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.35
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.35
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.35
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.34
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.34
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.34
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.34
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.33
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.32
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.32
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.32
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.31
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.31
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.31
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.31
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.3
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.29
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.28
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.27
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.27
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.27
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.26
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.26
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.22
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.22
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.21
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.18
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.18
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.17
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.16
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.16
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.13
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.13
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.11
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.1
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.09
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.03
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.03
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.02
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.99
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.99
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.94
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.9
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.83
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.79
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.2
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.36
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	97.13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.93
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.69
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.43
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.37
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	92.87
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	90.66
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	83.38

>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=99.72  E-value=2.5e-17  Score=107.10  Aligned_cols=64  Identities=39%  Similarity=0.650  Sum_probs=61.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++++|+.+|+++|||||+|.++++|++|+..|||..++|
T Consensus        36 L~~~F~~~G~I~~---------------------------v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   88 (99)
T 4fxv_A           36 LRSLFSSIGEVES---------------------------AKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS   88 (99)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------eEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|++|+|+
T Consensus        89 r~l~V~~AkPS   99 (99)
T 4fxv_A           89 KTIKVSYARPS   99 (99)
T ss_dssp             EECEEEECCBC
T ss_pred             EEEEEEEeeCC
Confidence            99999999763

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.68  E-value=1.9e-16  Score=104.90  Aligned_cols=65  Identities=18%  Similarity=0.351  Sum_probs=62.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++|++|+.|++++|||||+|.+.++|++|+..|||..++|
T Consensus        23 L~~~F~~~G~i~~---------------------------v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~g   75 (110)
T 3s8s_A           23 LKDMCRKYGEVEE---------------------------VEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG   75 (110)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++....
T Consensus        76 r~i~V~~a~~~~   87 (110)
T 3s8s_A           76 NIIHAQLDIKGQ   87 (110)
T ss_dssp             EECEEEECSTTH
T ss_pred             eEEEEEECCCCc
Confidence            999999997543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.9e-16  Score=99.78  Aligned_cols=71  Identities=35%  Similarity=0.590  Sum_probs=65.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        22 l~~~f~~~G~v~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   74 (95)
T 2dnz_A           22 LRGIFEPFGKIDN---------------------------IVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG   74 (95)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             HHHHHHhcCCEeE---------------------------EEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTDA   99 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~~   99 (112)
                      +.|.|++++++...+.++
T Consensus        75 ~~l~V~~a~~~~~~~~~~   92 (95)
T 2dnz_A           75 RPMRVGHVTERLDGGSGP   92 (95)
T ss_dssp             SCCEEEESSCCCCCCCCC
T ss_pred             cEEEEEEcccccCCCCCC
Confidence            999999998776655443

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.66  E-value=7.1e-16  Score=101.54  Aligned_cols=70  Identities=30%  Similarity=0.467  Sum_probs=65.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|++++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        42 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   94 (115)
T 2cpz_A           42 LLQMFMPFGNVVS---------------------------AKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   94 (115)
T ss_dssp             HHHHHGGGSCCSE---------------------------EEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++++.....+.
T Consensus        95 ~~l~V~~a~~~~~~~~~  111 (115)
T 2cpz_A           95 KRLKVQLKRSKNDSKSG  111 (115)
T ss_dssp             EECEEECCCCSCCCCCC
T ss_pred             EEEEEEEcCCCCcCCCC
Confidence            99999999877665443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=5e-16  Score=98.88  Aligned_cols=69  Identities=30%  Similarity=0.515  Sum_probs=64.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAA-TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||.|..                           + +|++|+.++.++|||||+|.++++|++|+..|||..++
T Consensus        22 l~~~F~~~G~i~~---------------------------~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~   74 (96)
T 1x5t_A           22 LYDTFSAFGVILQ---------------------------TPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC   74 (96)
T ss_dssp             HHHHHHTTSCBSS---------------------------CCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            7899999999999                           8 99999889999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~~   97 (112)
                      |+.|.|+++.+...+..
T Consensus        75 g~~l~v~~a~~~~~~~~   91 (96)
T 1x5t_A           75 NRPITVSYAFKKDSKGS   91 (96)
T ss_dssp             TEECEEEESCCCCCCCC
T ss_pred             CEEEEEEEecccCCCCC
Confidence            99999999987665543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.66  E-value=1.8e-15  Score=99.38  Aligned_cols=68  Identities=31%  Similarity=0.588  Sum_probs=63.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|++++.++.++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (115)
T 2dgo_A           32 IKAAFAPFGRISD---------------------------ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   84 (115)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++++.....
T Consensus        85 ~~l~V~~a~~~~~~~   99 (115)
T 2dgo_A           85 RQIRTNWATRKPPAP   99 (115)
T ss_dssp             EECEEEESSCCCCCS
T ss_pred             EEEEEEEccCCCCCC
Confidence            999999998765543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=4.8e-16  Score=100.09  Aligned_cols=70  Identities=33%  Similarity=0.556  Sum_probs=64.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.|+.+++++|||||+|.++++|++|+..|||..++|
T Consensus        29 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   81 (102)
T 2cqb_A           29 LHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG   81 (102)
T ss_dssp             HHHHHTTTSCCCC---------------------------EECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHhhccCCEEE---------------------------EEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++++...+.+.
T Consensus        82 ~~l~V~~a~~~~~~~~~   98 (102)
T 2cqb_A           82 RTIRVNLAKPMRIKESG   98 (102)
T ss_dssp             EEEEEEECCCCCCCCCC
T ss_pred             cEEEEEeCCCCCCCCCC
Confidence            99999999877665543

>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=99.65  E-value=1e-15  Score=94.91  Aligned_cols=65  Identities=29%  Similarity=0.587  Sum_probs=61.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.+++++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        18 l~~~f~~~G~i~~---------------------------~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g   70 (83)
T 3md1_A           18 LRNAFKDFPSYLS---------------------------GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG   70 (83)
T ss_dssp             HHHHHTTSTTEEE---------------------------EEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++++++
T Consensus        71 ~~l~v~~a~~~~   82 (83)
T 3md1_A           71 RPLRINWAAKLE   82 (83)
T ss_dssp             EECEEEECCCCC
T ss_pred             cEEEEEecCcCC
Confidence            999999998754

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=9e-16  Score=99.11  Aligned_cols=69  Identities=28%  Similarity=0.531  Sum_probs=64.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   84 (103)
T 2cq0_A           32 LQELFRPFGSISR---------------------------IYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH   84 (103)
T ss_dssp             HHTTSTTTCCEEE---------------------------EEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             HHHHHHhCCCeEE---------------------------EEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            7889999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++.....+
T Consensus        85 ~~l~v~~a~~~~~~~~  100 (103)
T 2cq0_A           85 LILNVEWAKPSTNSGP  100 (103)
T ss_dssp             EECEEEESSCCCCSCC
T ss_pred             cEEEEEECCCCCCCCC
Confidence            9999999987665543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=9.1e-16  Score=98.44  Aligned_cols=69  Identities=30%  Similarity=0.577  Sum_probs=63.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.|+.+++++|||||+|.+.++|++|+. ||+..++|
T Consensus        27 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g   78 (99)
T 2dgs_A           27 LREYFKKFGVVTE---------------------------VVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMG   78 (99)
T ss_dssp             HHHHHSSSSCEEE---------------------------EEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999 99999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++.+.......
T Consensus        79 ~~l~V~~a~~~~~~~~~   95 (99)
T 2dgs_A           79 KKVEVKRAEPRDSKSSG   95 (99)
T ss_dssp             CBCEEEECCCCCCCCCC
T ss_pred             eEEEEEECCCCcccCCC
Confidence            99999999876655443

>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=99.64  E-value=9.9e-16  Score=98.13  Aligned_cols=68  Identities=29%  Similarity=0.523  Sum_probs=63.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        25 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (99)
T 1whw_A           25 LEKLFSAYGPLSE---------------------------LHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG   77 (99)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS
T ss_pred             HHHHHHhcCCEeE---------------------------EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++++.....
T Consensus        78 ~~l~V~~a~~~~~~~   92 (99)
T 1whw_A           78 RMLHVLPSTIKKEAS   92 (99)
T ss_dssp             CEEEEEECCCCSTTC
T ss_pred             cEEEEEEcCCCcccc
Confidence            999999998766543

>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=99.64  E-value=1.6e-16  Score=100.78  Aligned_cols=66  Identities=20%  Similarity=0.352  Sum_probs=58.3

Q ss_pred             HHHHhhccC--cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFG--QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G--~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||  .|.+                           ++++.|+.+|+++|||||+|.+.++|++|+..|||..+
T Consensus        18 l~~~F~~~G~~~v~~---------------------------v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~   70 (90)
T 3p5t_L           18 LTEAVHSLGVNDILE---------------------------IKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL   70 (90)
T ss_dssp             HHHHHHTTTCCCCCC---------------------------EEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCS
T ss_pred             HHHHHHHhCCCceEE---------------------------EEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCee
Confidence            789999999  9999                           99999999999999999999999999999999999999


Q ss_pred             CCeeEEEEeccCCCC
Q 033734           80 DGRVIFVDNVRPSRR   94 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~   94 (112)
                      +|+.|.|+.+.+...
T Consensus        71 ~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           71 HGQNPVVTPSNKLEH   85 (90)
T ss_dssp             SSCCCEECCC-----
T ss_pred             CCEEEEEEECCCCcc
Confidence            999999999976544

>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=99.64  E-value=1.1e-15  Score=95.45  Aligned_cols=64  Identities=34%  Similarity=0.665  Sum_probs=60.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        23 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   75 (87)
T 3bs9_A           23 IAAAFAPFGRISD---------------------------ARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   75 (87)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEeE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|++++++
T Consensus        76 ~~l~v~~a~~k   86 (87)
T 3bs9_A           76 RQIRTNWATRK   86 (87)
T ss_dssp             EECEEEEEC--
T ss_pred             eEEEEEecCCC
Confidence            99999999764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.64  E-value=2e-16  Score=101.17  Aligned_cols=67  Identities=18%  Similarity=0.379  Sum_probs=60.6

Q ss_pred             HHHHhhccC-cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC-Ccee
Q 033734            2 LADAFSQFG-QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN-GKLL   79 (112)
Q Consensus         2 l~~~f~~~G-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~-g~~l   79 (112)
                      |+++|++|| +|.+                           ++|++|+.+++++|||||+|.++++|++|+..++ +..+
T Consensus        18 l~~~F~~~G~~v~~---------------------------v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~   70 (91)
T 2lxi_A           18 IRGQLQSHGVQARE---------------------------VRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNI   70 (91)
T ss_dssp             HHHHHHHHTCCCSB---------------------------CCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEE
T ss_pred             HHHHHHHhCCEeEE---------------------------EEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEE
Confidence            789999999 7999                           9999999999999999999999999999999874 5679


Q ss_pred             CCeeEEEEeccCCCCC
Q 033734           80 DGRVIFVDNVRPSRRY   95 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~   95 (112)
                      +|++|.|++|.++...
T Consensus        71 ~gr~i~V~~a~~~~~~   86 (91)
T 2lxi_A           71 LGQKVSMHYSDPKPKI   86 (91)
T ss_dssp             TTEEEEEECCCSCCCC
T ss_pred             CCEEEEEEEcCCCCCC
Confidence            9999999999876543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=6.7e-16  Score=99.40  Aligned_cols=69  Identities=39%  Similarity=0.729  Sum_probs=64.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        29 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   81 (102)
T 1x5s_A           29 LEQVFSKYGQISE---------------------------VVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG   81 (102)
T ss_dssp             HHHHHHHHSCCCE---------------------------EEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++......
T Consensus        82 ~~l~v~~a~~~~~~~~   97 (102)
T 1x5s_A           82 RQIRVDQAGKSSDNRS   97 (102)
T ss_dssp             CCCEEEEEECCCCCCC
T ss_pred             eEEEEEECCCCCCCCC
Confidence            9999999987665544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.64  E-value=2.5e-16  Score=102.04  Aligned_cols=64  Identities=25%  Similarity=0.480  Sum_probs=61.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.|++++|||||+|.++++|++|+..|||..++|
T Consensus        29 L~~~F~~~G~i~~---------------------------v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   81 (100)
T 3ns6_A           29 LTSLFSKAGKVVN---------------------------MEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL   81 (100)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHHhcCCEeE---------------------------EEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             -eeEEEEeccCC
Q 033734           82 -RVIFVDNVRPS   92 (112)
Q Consensus        82 -~~i~V~~a~~~   92 (112)
                       +.|.|+++.+.
T Consensus        82 ~r~l~V~~a~~~   93 (100)
T 3ns6_A           82 KHRLFLYTMKDV   93 (100)
T ss_dssp             SCBCEEEESHHH
T ss_pred             CeEEEEEECchh
Confidence             99999999764

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.63  E-value=1.3e-15  Score=97.40  Aligned_cols=69  Identities=30%  Similarity=0.479  Sum_probs=62.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCC---CCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKG---KNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~---t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|++||+|..                           +.++.++.   +++++|||||+|.+.++|++|+..|||..
T Consensus        22 l~~~F~~~G~i~~---------------------------v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~   74 (98)
T 2cpf_A           22 LKGVFSKVGAIKS---------------------------CTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT   74 (98)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCe
Confidence            7899999999999                           99999886   66899999999999999999999999999


Q ss_pred             eCCeeEEEEeccCCCCCCC
Q 033734           79 LDGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        79 l~g~~i~V~~a~~~~~~~~   97 (112)
                      ++|+.|.|+++.+......
T Consensus        75 ~~g~~l~V~~a~~~~~~~~   93 (98)
T 2cpf_A           75 VDGHKLEVRISERATKPAS   93 (98)
T ss_dssp             ETTEECEEECSSCSSCCCC
T ss_pred             eCCeEEEEEEccCCCCCCC
Confidence            9999999999987665444

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=1.3e-15  Score=99.84  Aligned_cols=69  Identities=30%  Similarity=0.400  Sum_probs=63.8

Q ss_pred             HHHHhhccCcce--------ecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHh
Q 033734            2 LADAFSQFGQVT--------EDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALAD   73 (112)
Q Consensus         2 l~~~f~~~G~i~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~   73 (112)
                      |+++|++||.|.        .                           ++|+.|+.+++++|||||+|.++++|++|+..
T Consensus        32 l~~~F~~~G~i~~~~~~~~~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~   84 (113)
T 2cpe_A           32 LADFFKQCGVVKMNKRTGQPM---------------------------IHIYLDKETGKPKGDATVSYEDPPTAKAAVEW   84 (113)
T ss_dssp             HHHHHTTTSCBCBCSSSCCBS---------------------------EECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH
T ss_pred             HHHHHHhcCCEeEccccCccC---------------------------EEEEEeCCCCCeeeEEEEEECCHHHHHHHHHH
Confidence            789999999998        6                           89999988999999999999999999999999


Q ss_pred             hCCceeCCeeEEEEeccCCCCCCC
Q 033734           74 MNGKLLDGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        74 l~g~~l~g~~i~V~~a~~~~~~~~   97 (112)
                      |||..++|+.|.|+++++......
T Consensus        85 l~g~~~~g~~l~V~~a~~~~~~~~  108 (113)
T 2cpe_A           85 FDGKDFQGSKLKVSLARKKPPMNS  108 (113)
T ss_dssp             HTTCEETTEECEEECSSCCCCSTT
T ss_pred             cCCCccCCCEEEEEECCCCCCCCC
Confidence            999999999999999987665544

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=6.4e-16  Score=99.81  Aligned_cols=69  Identities=32%  Similarity=0.518  Sum_probs=64.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        30 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   82 (103)
T 2dnm_A           30 LRRVFEKYGRVGD---------------------------VYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG   82 (103)
T ss_dssp             HHHHHTTTSCEEE---------------------------EECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++......
T Consensus        83 ~~l~V~~a~~~~~~~~   98 (103)
T 2dnm_A           83 RELRVQVARYGRRDLS   98 (103)
T ss_dssp             BCCEEEECSSCCSCCC
T ss_pred             cEEEEEECCcCCCCCC
Confidence            9999999987655444

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.63  E-value=4e-16  Score=101.27  Aligned_cols=63  Identities=25%  Similarity=0.476  Sum_probs=58.5

Q ss_pred             HHHHhhccCc--ceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCc--
Q 033734            2 LADAFSQFGQ--VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK--   77 (112)
Q Consensus         2 l~~~f~~~G~--i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~--   77 (112)
                      |+++|++||.  +.+                           +++++|+.+++++|||||+|.++++|++|+..|||.  
T Consensus        26 L~~~F~~~G~i~v~~---------------------------v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~   78 (95)
T 2lkz_A           26 IMTALSPYASLAVNN---------------------------IRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHP   78 (95)
T ss_dssp             HHHHSTTTCCCCGGG---------------------------EECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSS
T ss_pred             HHHHHHhhCCccEEE---------------------------EEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCC
Confidence            7899999995  567                           999999999999999999999999999999999997  


Q ss_pred             --eeCCeeEEEEeccC
Q 033734           78 --LLDGRVIFVDNVRP   91 (112)
Q Consensus        78 --~l~g~~i~V~~a~~   91 (112)
                        .++|++|.|++|++
T Consensus        79 ~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           79 PLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CEEETTEEEEEEECCC
T ss_pred             CceECCEEEEEEEccC
Confidence              48999999999975

>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=99.63  E-value=1.1e-15  Score=99.02  Aligned_cols=70  Identities=26%  Similarity=0.383  Sum_probs=64.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+++|++||.|..                           ++|+.|+.+++++|||||+|.+.++|++|+..|||..+  
T Consensus        30 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~   82 (106)
T 2dgp_A           30 LKPLFEEFGKIYE---------------------------LTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLP   82 (106)
T ss_dssp             HHHHHHHHSCCCE---------------------------EECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCT
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccC
Confidence            7899999999999                           99999999999999999999999999999999999998  


Q ss_pred             -CCeeEEEEeccCCCCCCCC
Q 033734           80 -DGRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        80 -~g~~i~V~~a~~~~~~~~~   98 (112)
                       +|+.|.|+++.+......+
T Consensus        83 ~~g~~l~v~~a~~~~~~~~~  102 (106)
T 2dgp_A           83 GMNRPIQVKPADSESRGGSG  102 (106)
T ss_dssp             TCSSCCEEEECCCCSCCCCC
T ss_pred             CCCceEEEEECCcccccCCC
Confidence             8999999999876665443

>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=99.62  E-value=1.3e-15  Score=98.52  Aligned_cols=69  Identities=29%  Similarity=0.420  Sum_probs=64.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (105)
T 1x5u_A           32 LWELFLQAGPVVN---------------------------THMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG   84 (105)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++.+......
T Consensus        85 ~~l~v~~a~~~~~~~~  100 (105)
T 1x5u_A           85 KPIRVNKASAHNKNLS  100 (105)
T ss_dssp             CBCEEEETTTTSCCCC
T ss_pred             eEEEEEECCCCCcCCC
Confidence            9999999987665443

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.62  E-value=2.1e-15  Score=97.67  Aligned_cols=69  Identities=23%  Similarity=0.511  Sum_probs=63.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEee-CCCCCcccEEEEEeCCHHHHHHHHHhh-CCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMD-KGKNRSKGYGYVTFSTEEEAQKALADM-NGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d-~~t~~~rG~afV~f~~~~~a~~Ai~~l-~g~~l   79 (112)
                      |+++|++||.|..                           ++|+.+ +.+++++|||||+|.++++|++|+..| ||..+
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~   84 (107)
T 2cph_A           32 IRELFSTFGELKT---------------------------VRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL   84 (107)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS
T ss_pred             HHHHHHccCCeEE---------------------------EEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeE
Confidence            7899999999999                           999999 789999999999999999999999999 99999


Q ss_pred             CCeeEEEEeccCCCCCCC
Q 033734           80 DGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~~~   97 (112)
                      +|+.|.|+++++......
T Consensus        85 ~g~~l~v~~a~~~~~~~~  102 (107)
T 2cph_A           85 YGRRLVLEWADSEVTVQS  102 (107)
T ss_dssp             SSCBCEEEECCCCCCCCC
T ss_pred             CCCEEEEEeCCCCCCCCC
Confidence            999999999987665544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.61  E-value=3.6e-15  Score=100.90  Aligned_cols=69  Identities=26%  Similarity=0.501  Sum_probs=64.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|..                           ++|++++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        59 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  111 (139)
T 1u6f_A           59 LRQLFERYGPIES---------------------------VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN  111 (139)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++...+..
T Consensus       112 ~~l~v~~a~~~~~~~~  127 (139)
T 1u6f_A          112 KRLKVALAASGHQRPG  127 (139)
T ss_dssp             CEEEEEESSCCCCCCC
T ss_pred             eEEEEEECCCCCCCCC
Confidence            9999999987655433

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2e-15  Score=97.79  Aligned_cols=65  Identities=31%  Similarity=0.491  Sum_probs=61.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        40 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   92 (106)
T 1p27_B           40 IHDKFAEYGEIKN---------------------------IHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG   92 (106)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHhccCCeEE---------------------------EEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++.+..
T Consensus        93 ~~l~V~~a~~~~  104 (106)
T 1p27_B           93 QPISVDWCFVRG  104 (106)
T ss_dssp             SBCEEEESEESS
T ss_pred             cEEEEEeecCCC
Confidence            999999997654

>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=99.61  E-value=2.8e-15  Score=97.63  Aligned_cols=69  Identities=32%  Similarity=0.506  Sum_probs=64.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC------
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN------   75 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~------   75 (112)
                      |+++|++||.|..                           ++|++|+.++.++|||||+|.+.++|++|+..||      
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~   84 (111)
T 1x4h_A           32 LGEVLQQFGDLKY---------------------------VRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGG   84 (111)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTC
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccC
Confidence            7899999999999                           9999999999999999999999999999999999      


Q ss_pred             CceeCCeeEEEEeccCCCCCCC
Q 033734           76 GKLLDGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        76 g~~l~g~~i~V~~a~~~~~~~~   97 (112)
                      |..++|+.|.|+++.++.....
T Consensus        85 ~~~~~g~~l~v~~a~~~~~~~~  106 (111)
T 1x4h_A           85 GLKLDGRQLKVDLAVTRDEAAS  106 (111)
T ss_dssp             CEESSSCEEEEECCCCCCCCCC
T ss_pred             CcEEcCEEEEEEECCCCccCCC
Confidence            9999999999999987655443

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=3.3e-15  Score=95.96  Aligned_cols=66  Identities=21%  Similarity=0.429  Sum_probs=61.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++ +++++|||||+|.++++|++|+..|||..++|
T Consensus        34 l~~~F~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   85 (100)
T 2do4_A           34 LEEICKAHGTVKD---------------------------LRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKE   85 (100)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSS
T ss_pred             HHHHHHhCCCeEE---------------------------EEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999998 89999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++...+
T Consensus        86 ~~l~v~~a~~~~~~   99 (100)
T 2do4_A           86 NIIKVAISNSGPSS   99 (100)
T ss_dssp             CEEEEEECCCCSCC
T ss_pred             EEEEEEECCCCCCC
Confidence            99999999876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=8.9e-15  Score=95.78  Aligned_cols=68  Identities=35%  Similarity=0.453  Sum_probs=62.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++ +++++|||||+|.+.++|++|+..|||..++|
T Consensus        32 l~~~f~~~G~i~~---------------------------~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   83 (114)
T 2do0_A           32 LKEVFSMAGVVVR---------------------------ADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD   83 (114)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           9999998 69999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|++++....+..
T Consensus        84 ~~l~v~~a~~~~~~~~   99 (114)
T 2do0_A           84 RPMHVKMDERALPKGD   99 (114)
T ss_dssp             EECEEEECSCCCCCSC
T ss_pred             CEEEEEEcccCCCCCC
Confidence            9999999976554433

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.61  E-value=3.9e-15  Score=96.21  Aligned_cols=67  Identities=24%  Similarity=0.483  Sum_probs=61.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++|| |..                           ++|++|+.+++++|||||+|.++++|++|+ .|||..++|
T Consensus        32 l~~~F~~~g-i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   82 (103)
T 2dng_A           32 IDAIFKDLS-IRS---------------------------VRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD   82 (103)
T ss_dssp             HHHHTTTSC-EEE---------------------------EEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             HHHHHHhCC-ceE---------------------------EEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECC
Confidence            788999997 888                           999999999999999999999999999999 899999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++.+......
T Consensus        83 ~~l~V~~a~~~~~~~~   98 (103)
T 2dng_A           83 RSLRVDIAEGRKQDKS   98 (103)
T ss_dssp             EECEEEECCCCCCCCS
T ss_pred             eEEEEEEecCCCCCCC
Confidence            9999999987665444

>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=99.61  E-value=2.6e-15  Score=95.92  Aligned_cols=66  Identities=27%  Similarity=0.449  Sum_probs=62.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        19 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   71 (96)
T 2x1f_A           19 ILDLCSNVGPVIN---------------------------LKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS   71 (96)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+...
T Consensus        72 ~~l~V~~a~~~~~   84 (96)
T 2x1f_A           72 RFLKCGYSSNSDI   84 (96)
T ss_dssp             EECEEEECSCSSG
T ss_pred             eEEEEEEcCCCCC
Confidence            9999999987543

>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=99.61  E-value=2.1e-15  Score=93.86  Aligned_cols=62  Identities=34%  Similarity=0.580  Sum_probs=59.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.+++++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        24 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   76 (85)
T 3mdf_A           24 LHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG   76 (85)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhccCCEEE---------------------------EEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999998899999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|.|++++
T Consensus        77 ~~l~v~~ak   85 (85)
T 3mdf_A           77 RTIRVNLAK   85 (85)
T ss_dssp             EECEEEECC
T ss_pred             cEEEEEEcC
Confidence            999999874

>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=99.61  E-value=3.8e-15  Score=98.99  Aligned_cols=66  Identities=32%  Similarity=0.630  Sum_probs=61.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++ +++++|||||+|.+.++|++|+..|||..++|
T Consensus        24 l~~~F~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g   75 (116)
T 2fy1_A           24 LKAVFGKHGPISE---------------------------VLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHG   75 (116)
T ss_dssp             HHHHHHTSSCCSE---------------------------EEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999998 99999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus        76 ~~l~V~~a~~~~~~   89 (116)
T 2fy1_A           76 KAIKVEQAKKPSFQ   89 (116)
T ss_dssp             SBCEEEECCCSSCS
T ss_pred             EEEEEEECCCCCCC
Confidence            99999999765543

>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=99.60  E-value=3.5e-15  Score=96.60  Aligned_cols=68  Identities=21%  Similarity=0.403  Sum_probs=62.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCC-CCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGK-NRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t-~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| |..                           ++|++++.+ ++++|||||+|.++++|++|+ .|||..++
T Consensus        32 l~~~F~~~G-i~~---------------------------v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~   82 (104)
T 1wi8_A           32 IKEFFRGLN-ISA---------------------------VRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG   82 (104)
T ss_dssp             HHHHTTTSC-EEE---------------------------EECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET
T ss_pred             HHHHHHHCC-ceE---------------------------EEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeC
Confidence            789999999 999                           999999987 999999999999999999999 89999999


Q ss_pred             CeeEEEEeccCCCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~~~   98 (112)
                      |+.|.|++++++....++
T Consensus        83 g~~l~V~~a~~~~~~~~~  100 (104)
T 1wi8_A           83 NKRIRVDVADQAQDKDSG  100 (104)
T ss_dssp             TEECEEEECCCCCCCCCC
T ss_pred             CcEEEEEEccCCCCCCCC
Confidence            999999999887665543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=4.3e-15  Score=94.19  Aligned_cols=63  Identities=33%  Similarity=0.638  Sum_probs=60.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~f~~~G~v~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   84 (95)
T 2cqc_A           32 LREVFSKYGPIAD---------------------------VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG   84 (95)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|+++++
T Consensus        85 ~~l~v~~a~~   94 (95)
T 2cqc_A           85 RRIRVSGPSS   94 (95)
T ss_dssp             EEEEEECCSC
T ss_pred             EEEEEEecCC
Confidence            9999999875

>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=99.60  E-value=3.1e-15  Score=97.57  Aligned_cols=66  Identities=26%  Similarity=0.445  Sum_probs=62.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        43 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   95 (110)
T 1oo0_B           43 IQEKFCDYGEIKN---------------------------IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG   95 (110)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+...
T Consensus        96 ~~l~V~~a~~~~~  108 (110)
T 1oo0_B           96 QTIQVDWCFVKGP  108 (110)
T ss_dssp             EECEEEESEESSC
T ss_pred             cEEEEEEcccCCC
Confidence            9999999986554

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.3e-15  Score=95.87  Aligned_cols=68  Identities=38%  Similarity=0.724  Sum_probs=62.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.+  ++.++|||||+|.+.++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   82 (103)
T 2d9p_A           32 LRKAFSPFGTITS---------------------------AKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT   82 (103)
T ss_dssp             HHHTTTTTSCEEE---------------------------EEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           999998  89999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++++...+...
T Consensus        83 ~~l~V~~a~~~~~~~~~   99 (103)
T 2d9p_A           83 KPLYVALAQRKEERQSG   99 (103)
T ss_dssp             SBCEEEECSSCCCCCCC
T ss_pred             cEEEEEEecccccCCCC
Confidence            99999999876665443

>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=99.60  E-value=5.4e-15  Score=92.69  Aligned_cols=64  Identities=34%  Similarity=0.555  Sum_probs=60.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+++++|||||+|.++++|++|+ .|||..++|
T Consensus        23 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g   74 (89)
T 3ucg_A           23 LEAHFHGCGSVNR---------------------------VTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRG   74 (89)
T ss_dssp             HHHHHGGGCCEEE---------------------------EEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECC
Confidence            7899999999999                           999999989999999999999999999999 899999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++++..
T Consensus        75 ~~l~V~~a~~~~   86 (89)
T 3ucg_A           75 RQIKVIPKRTNR   86 (89)
T ss_dssp             EECEEEETTTTS
T ss_pred             cEEEEEEccCCC
Confidence            999999997643

>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=99.59  E-value=5.3e-15  Score=97.93  Aligned_cols=65  Identities=42%  Similarity=0.789  Sum_probs=59.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|++|+  +.++|||||+|.++++|++||..|||..++|
T Consensus        22 L~~~F~~~G~v~~---------------------------v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g   72 (115)
T 4f25_A           22 LYDTFSAFGNILS---------------------------CKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLND   72 (115)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhccCCEEE---------------------------EEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999996  4589999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++.++..+
T Consensus        73 ~~i~V~~a~~~~~~   86 (115)
T 4f25_A           73 RKVFVGRFKSRKER   86 (115)
T ss_dssp             EECEEEESSCCCC-
T ss_pred             EEEEEEECCCcccc
Confidence            99999999765443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4e-15  Score=95.28  Aligned_cols=66  Identities=27%  Similarity=0.442  Sum_probs=61.9

Q ss_pred             HHHHhhccCcce-ecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVT-EDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||+|. .                           +++++|+.+++++|||||+|.++++|++|+..|||..++
T Consensus        26 l~~~F~~~G~i~~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~   78 (99)
T 2div_A           26 ISRAFATMGETVMS---------------------------VKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLP   78 (99)
T ss_dssp             HHHHHHHTTCCCCE---------------------------EEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEES
T ss_pred             HHHHHHHhCCcceE---------------------------EEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccC
Confidence            789999999999 9                           999999999999999999999999999999999999999


Q ss_pred             Cee----EEEEeccCCCC
Q 033734           81 GRV----IFVDNVRPSRR   94 (112)
Q Consensus        81 g~~----i~V~~a~~~~~   94 (112)
                      |+.    |+|+++++...
T Consensus        79 g~~~~~~l~v~~a~~~~~   96 (99)
T 2div_A           79 GATPAKRFKLNYATYSGP   96 (99)
T ss_dssp             SCSSCEECCEEETTCCSS
T ss_pred             CCCcceeEEEeecCCCCC
Confidence            999    99999976543

>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=99.59  E-value=5.4e-15  Score=94.83  Aligned_cols=64  Identities=16%  Similarity=0.199  Sum_probs=58.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|+.|+.+   +|||||+|.++++|++|+..|||..++|
T Consensus        30 l~~~F~~~G~v~~---------------------------v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g   79 (96)
T 2dgx_A           30 LQEAFARHGKVKS---------------------------VELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGS   79 (96)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHhccccCcEEE---------------------------EEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4499999999999                           999999865   8999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|+++++....
T Consensus        80 r~l~V~~a~~~~~~   93 (96)
T 2dgx_A           80 KKILVSLATGASGP   93 (96)
T ss_dssp             EEEEEEECCCSSCC
T ss_pred             eEEEEEEcCCCCCC
Confidence            99999999876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=4.8e-15  Score=93.93  Aligned_cols=62  Identities=35%  Similarity=0.529  Sum_probs=59.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        33 l~~~f~~~G~v~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   85 (94)
T 2e5h_A           33 LYRIFSKYGKVVK---------------------------VTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG   85 (94)
T ss_dssp             HHHHTTTTSCEEE---------------------------EEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|.|++|+
T Consensus        86 ~~l~v~~ak   94 (94)
T 2e5h_A           86 RVIKASIAI   94 (94)
T ss_dssp             EEEEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=6.6e-15  Score=96.98  Aligned_cols=69  Identities=29%  Similarity=0.560  Sum_probs=63.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++.+++++|||||+|.++++|++|+.. ++..++|
T Consensus        44 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g   95 (116)
T 1x4b_A           44 LRNYYEQWGKLTD---------------------------CVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDG   95 (116)
T ss_dssp             HHHHHTSSCCCSE---------------------------EEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECC
Confidence            7899999999999                           99999999999999999999999999999997 9999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++.++....++
T Consensus        96 ~~l~V~~a~~~~~~~~~  112 (116)
T 1x4b_A           96 RVVEPKRAVAREESGSG  112 (116)
T ss_dssp             EEEEEECCSSCCCCCCS
T ss_pred             EEEEEEECCCCccCCCC
Confidence            99999999877665443

>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=99.59  E-value=6.2e-16  Score=99.74  Aligned_cols=67  Identities=31%  Similarity=0.641  Sum_probs=62.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        25 l~~~f~~~G~i~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (104)
T 1p1t_A           25 LKDIFSEVGPVVS---------------------------FRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG   77 (104)
T ss_dssp             HHHHHHTTSCCSE---------------------------EEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++.+....
T Consensus        78 ~~l~v~~a~~~~~~   91 (104)
T 1p1t_A           78 RALRVDNAASEKNK   91 (104)
T ss_dssp             SCBEEEETTCTTHH
T ss_pred             cEEEEEeCCCccch
Confidence            99999999876543

>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=99.59  E-value=7.8e-15  Score=94.81  Aligned_cols=68  Identities=25%  Similarity=0.413  Sum_probs=62.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++ +++++|||||+|.+.++|++|+..|||..+.|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   83 (105)
T 2dnh_A           32 VLRLFQPFGVIDE---------------------------CTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMP   83 (105)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCC
Confidence            7899999999999                           9999998 89999999999999999999999999999998


Q ss_pred             ---eeEEEEeccCCCCCCC
Q 033734           82 ---RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ---~~i~V~~a~~~~~~~~   97 (112)
                         +.|.|+++++...+.+
T Consensus        84 g~~~~l~V~~a~~~~~~~~  102 (105)
T 2dnh_A           84 GASSSLVVKFADTDKESGP  102 (105)
T ss_dssp             TCSSCCEEEESCSSCCCSC
T ss_pred             CCCccEEEEECccCcccCC
Confidence               9999999987665443

>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=99.58  E-value=3.9e-15  Score=92.99  Aligned_cols=66  Identities=32%  Similarity=0.577  Sum_probs=60.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCC-cccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNR-SKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~-~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||.|..                           +.++.++.++. ++|||||+|.++++|++|+..|||..++
T Consensus        21 l~~~F~~~G~i~~---------------------------~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~   73 (88)
T 4a8x_A           21 IMEIFSTYGKIKM---------------------------IDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQID   73 (88)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeEC
Confidence            7899999999999                           99999987766 8999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      |+.|.|+++.+...
T Consensus        74 g~~l~v~~a~~~~~   87 (88)
T 4a8x_A           74 GQEITATAVLAPWP   87 (88)
T ss_dssp             TEECEEEEECCCCC
T ss_pred             CeEEEEEECCCCCC
Confidence            99999999976543

>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=99.58  E-value=1e-14  Score=100.66  Aligned_cols=66  Identities=26%  Similarity=0.430  Sum_probs=62.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           |.|+.++.+++++|||||+|.++++|++||..||+..++|
T Consensus        56 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  108 (156)
T 1h2v_Z           56 IYELFSKSGDIKK---------------------------IIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD  108 (156)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++++...
T Consensus       109 ~~l~V~~a~~~~~  121 (156)
T 1h2v_Z          109 RIIRTDWDAGFKE  121 (156)
T ss_dssp             EECEEEEESCCCT
T ss_pred             eEEEEEECCCCCC
Confidence            9999999976544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.4e-15  Score=96.11  Aligned_cols=68  Identities=34%  Similarity=0.539  Sum_probs=62.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++.+++++|||||+|.++++|++|+.. |+..++|
T Consensus        33 l~~~F~~~G~v~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g   84 (105)
T 2dh8_A           33 LRSYFSQYGEVVD---------------------------CVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDG   84 (105)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECC
Confidence            7899999999999                           99999999999999999999999999999998 9999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++.+......
T Consensus        85 ~~l~V~~a~~~~~~~~  100 (105)
T 2dh8_A           85 RNIDPKPCTPRGMQPS  100 (105)
T ss_dssp             EEEBCCCSCCSSCCTT
T ss_pred             EEEEEEEccCCCCCCC
Confidence            9999999987665443

>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=99.58  E-value=5.1e-15  Score=101.94  Aligned_cols=67  Identities=31%  Similarity=0.575  Sum_probs=63.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.|+.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        87 l~~~F~~~G~v~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  139 (158)
T 2kn4_A           87 LRRVFEKYGRVGD---------------------------VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  139 (158)
T ss_dssp             HHHHHHHHSCEEE---------------------------EECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus       140 ~~l~v~~a~~~~~~  153 (158)
T 2kn4_A          140 RELRVQMARYGRPP  153 (158)
T ss_dssp             SEEEEEEECCSSCC
T ss_pred             eEEEEEECCCCCCC
Confidence            99999999876544

>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=99.57  E-value=4.1e-15  Score=99.14  Aligned_cols=67  Identities=30%  Similarity=0.456  Sum_probs=62.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+.++.++.++|||||+|.++++|++|+..|||..++|
T Consensus        39 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   91 (126)
T 3ex7_B           39 IHDKFAEYGEIKN---------------------------IHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG   91 (126)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++.+....
T Consensus        92 ~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           92 QPISVDWCFVRGPP  105 (126)
T ss_dssp             SBCEEEESEESSSC
T ss_pred             eEEEEEEecCCCCC
Confidence            99999999765544

>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=99.57  E-value=6e-15  Score=96.92  Aligned_cols=65  Identities=42%  Similarity=0.687  Sum_probs=61.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +++++++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        43 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g   95 (108)
T 2jrs_A           43 LRGIFEPFGRIES---------------------------IQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG   95 (108)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|++++++.
T Consensus        96 ~~l~V~~a~~k~  107 (108)
T 2jrs_A           96 RPMKVGHVTERT  107 (108)
T ss_dssp             SCCEEECSCSSC
T ss_pred             EEEEEEEcccCC
Confidence            999999998653

>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=99.57  E-value=1.3e-14  Score=95.41  Aligned_cols=65  Identities=22%  Similarity=0.335  Sum_probs=58.9

Q ss_pred             HHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            4 DAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKN---RSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         4 ~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~---~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      ++|++||+|.+                           +.|++++.++   +++|||||+|.++++|++|+..|||..++
T Consensus        37 ~~F~~~G~i~~---------------------------v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           37 EYFGKFGKIHK---------------------------VVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             TTTTTTSCEEE---------------------------EEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             HHhhccCCEEE---------------------------EEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            89999999999                           9999998754   56699999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCC
Q 033734           81 GRVIFVDNVRPSRRY   95 (112)
Q Consensus        81 g~~i~V~~a~~~~~~   95 (112)
                      |+.|.|+++.++...
T Consensus        90 gr~l~V~~a~~k~~~  104 (111)
T 2cpi_A           90 GRTLKASLGTTKYCS  104 (111)
T ss_dssp             TEEEEEESCCCCSCS
T ss_pred             CEEEEEEeccccccc
Confidence            999999999876543

>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=99.57  E-value=2e-14  Score=92.75  Aligned_cols=67  Identities=25%  Similarity=0.429  Sum_probs=60.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++.  .++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cqi_A           32 ILQLFSQIGPCKS---------------------------CKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILG   82 (103)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhcCCEeE---------------------------EEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCC
Confidence            7899999999999                           99999964  378999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++......
T Consensus        83 ~~l~V~~a~~~~~~~~   98 (103)
T 2cqi_A           83 KEVKVNWATTPSSQKS   98 (103)
T ss_dssp             EEEEEEECCCTTCCCC
T ss_pred             CeEEEEECCCCccccc
Confidence            9999999987655443

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.57  E-value=1.3e-14  Score=95.57  Aligned_cols=63  Identities=24%  Similarity=0.359  Sum_probs=58.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCC-CCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGK-NRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t-~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||+|.+                           +.|++++.+ ++++|++||+|.++++|++|+..|||+.++
T Consensus        30 l~~~f~~~G~V~~---------------------------v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~   82 (105)
T 2pe8_A           30 TKEECEKYGKVGK---------------------------CVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG   82 (105)
T ss_dssp             HHHHGGGGSCEEE---------------------------EEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             HHHHHHhcCCEEE---------------------------EEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            7889999999999                           999998754 689999999999999999999999999999


Q ss_pred             CeeEEEEeccC
Q 033734           81 GRVIFVDNVRP   91 (112)
Q Consensus        81 g~~i~V~~a~~   91 (112)
                      |+.|.|.++.+
T Consensus        83 Gr~i~v~~a~~   93 (105)
T 2pe8_A           83 GRVVKACFYNL   93 (105)
T ss_dssp             TEECEEEECCH
T ss_pred             CcEEEEEEcCH
Confidence            99999999864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=6.5e-15  Score=95.03  Aligned_cols=68  Identities=25%  Similarity=0.502  Sum_probs=62.6

Q ss_pred             HHHHhhc-cCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce-e
Q 033734            2 LADAFSQ-FGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL-L   79 (112)
Q Consensus         2 l~~~f~~-~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~-l   79 (112)
                      |+++|++ ||.|..                           ++|+.|+ +++++|||||+|.+.++|++|+..|||.. +
T Consensus        26 l~~~F~~~~G~v~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~   77 (104)
T 2dhg_A           26 LYEFFVKVYPSCRG---------------------------GKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGL   77 (104)
T ss_dssp             HHHHHHHHCTTEEE---------------------------EEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSS
T ss_pred             HHHHHHHhCCCeEE---------------------------EEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCccc
Confidence            7899999 999999                           9999998 99999999999999999999999999999 9


Q ss_pred             CCeeEEEEeccCCCCCCC
Q 033734           80 DGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~~~   97 (112)
                      +|+.|.|+++.+......
T Consensus        78 ~g~~l~v~~a~~~~~~~~   95 (104)
T 2dhg_A           78 GSKPVRLSVAIPKASRVK   95 (104)
T ss_dssp             SSSCCCCCBCCCCCSCCC
T ss_pred             CCEeEEEEEccCCCcCCC
Confidence            999999999976655433

>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=99.57  E-value=6e-15  Score=99.99  Aligned_cols=66  Identities=35%  Similarity=0.624  Sum_probs=62.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++++|+.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        63 L~~~F~~~G~I~~---------------------------v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g  115 (129)
T 2kxn_B           63 LREVFSKYGPIAD---------------------------VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG  115 (129)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+.++
T Consensus       116 ~~l~V~~a~~~~p  128 (129)
T 2kxn_B          116 RRIRVDFSITKRP  128 (129)
T ss_dssp             SCCEESCCSSSSC
T ss_pred             EEEEEEEecCCCC
Confidence            9999999987653

>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=99.57  E-value=2.7e-14  Score=92.11  Aligned_cols=67  Identities=34%  Similarity=0.658  Sum_probs=60.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++.  .++|||||+|.+.++|++|+..|||..++|
T Consensus        32 l~~~f~~~G~v~~---------------------------v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cq3_A           32 LRQMFGQFGKILD---------------------------VEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEG   82 (103)
T ss_dssp             HHHHGGGTSCEEE---------------------------EEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           99999863  389999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++.+......
T Consensus        83 ~~l~v~~a~~~~~~~~   98 (103)
T 2cq3_A           83 RKIEVNNATARVMTNS   98 (103)
T ss_dssp             EECEEEECCSSCCCCC
T ss_pred             EEEEEEEcccCCCCCC
Confidence            9999999987665544

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.57  E-value=1.8e-14  Score=95.75  Aligned_cols=65  Identities=31%  Similarity=0.504  Sum_probs=61.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+++++|||||+|.+.++|++|+ .|||..++|
T Consensus        53 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  104 (124)
T 2jwn_A           53 LEAHFSSCGSINR---------------------------ITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRG  104 (124)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECC
Confidence            7899999999999                           999999989999999999999999999999 799999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++++...
T Consensus       105 ~~l~V~~a~~~~~  117 (124)
T 2jwn_A          105 RTIKVLPKRTNMP  117 (124)
T ss_dssp             EECEEEESSCCCS
T ss_pred             eEEEEEECCCCCC
Confidence            9999999976544

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.57  E-value=2.7e-15  Score=101.30  Aligned_cols=68  Identities=24%  Similarity=0.433  Sum_probs=62.3

Q ss_pred             HHHHhhccCcc--eecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCc--
Q 033734            2 LADAFSQFGQV--TEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK--   77 (112)
Q Consensus         2 l~~~f~~~G~i--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~--   77 (112)
                      |+++|++||.|  ..                           ++|++|+.+++++|||||+|.+. +|.+|+..|||.  
T Consensus        40 L~~~F~~~G~v~~~~---------------------------v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~   91 (131)
T 2m2b_A           40 ILGALAPYAVLSSSN---------------------------VRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHP   91 (131)
T ss_dssp             HHHHHGGGCCCCTTT---------------------------EECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCC
T ss_pred             HHHHHHHhCCcceee---------------------------EEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCC
Confidence            78999999999  55                           89999999999999999999999 999999999999  


Q ss_pred             --eeCCeeEEEEeccCCCCCCC
Q 033734           78 --LLDGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        78 --~l~g~~i~V~~a~~~~~~~~   97 (112)
                        .++|+.|.|+++++..+...
T Consensus        92 ~~~~~gr~l~V~~a~~~~~~~~  113 (131)
T 2m2b_A           92 PLTIDGKTINVEFAKGSKRDMA  113 (131)
T ss_dssp             SCCGGGCCCCCEECCCSCCCCC
T ss_pred             CccCCCEEEEEEECCCCCCCCC
Confidence              99999999999987765543

>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=99.56  E-value=7.5e-15  Score=93.82  Aligned_cols=64  Identities=19%  Similarity=0.273  Sum_probs=60.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~v~~---------------------------~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   84 (98)
T 2cqp_A           32 ILDFFYGYQVIPG---------------------------SVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS   84 (98)
T ss_dssp             HHHHTTTSCCCTT---------------------------TCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT
T ss_pred             HHHHHHHcCCccc---------------------------eEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            7899999999988                           8888898899999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++...
T Consensus        85 ~~l~V~~a~~~   95 (98)
T 2cqp_A           85 RKVKLVLGSGP   95 (98)
T ss_dssp             EECEEEESSCS
T ss_pred             eEEEEEEcCCC
Confidence            99999998754

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.6e-14  Score=94.06  Aligned_cols=64  Identities=34%  Similarity=0.593  Sum_probs=60.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|++++.+++++|||||+|.++++|++|+..+++ .++|
T Consensus        34 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g   85 (116)
T 2cqd_A           34 LRKYFEGFGDIEE---------------------------AVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG   85 (116)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT
T ss_pred             HHHHHHhCCCeeE---------------------------EEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCC
Confidence            7899999999999                           99999999999999999999999999999999998 8999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++.+..
T Consensus        86 ~~l~V~~a~~~~   97 (116)
T 2cqd_A           86 RKANVNLAYLGA   97 (116)
T ss_dssp             EECEEEESTTTC
T ss_pred             EEEEEEEcccCC
Confidence            999999997543

>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=99.56  E-value=1.7e-14  Score=93.49  Aligned_cols=61  Identities=33%  Similarity=0.553  Sum_probs=58.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+.++ +++++|||||+|.++++|++|+..|||..++|
T Consensus        46 l~~~F~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   97 (107)
T 3ulh_A           46 IQELFAEFGTLKK---------------------------AAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDG   97 (107)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           9999998 99999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|.|+++.
T Consensus        98 ~~l~V~~a~  106 (107)
T 3ulh_A           98 RPMNIQLVT  106 (107)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEeC
Confidence            999999985

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.56  E-value=9.9e-15  Score=102.08  Aligned_cols=63  Identities=27%  Similarity=0.437  Sum_probs=60.6

Q ss_pred             HHHHhhccC--cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFG--QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G--~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||  .|.+                           ++|+.|+.+|+++|||||+|.+.++|++||..|||..+
T Consensus        72 L~~~F~~~G~i~v~~---------------------------v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~  124 (156)
T 3n9u_C           72 LIQVIRSIGVYDVVE---------------------------LKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL  124 (156)
T ss_dssp             HHHHHHHTTCCCEEE---------------------------EEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEE
T ss_pred             HHHHHHHHCCccEEE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            789999999  8999                           99999999999999999999999999999999999999


Q ss_pred             CCeeEEEEeccC
Q 033734           80 DGRVIFVDNVRP   91 (112)
Q Consensus        80 ~g~~i~V~~a~~   91 (112)
                      +|+.|.|+++.+
T Consensus       125 ~Gr~l~V~~a~~  136 (156)
T 3n9u_C          125 NGEKVDVRPATR  136 (156)
T ss_dssp             TTEECEEEECCH
T ss_pred             CCeEeEEEEcCC
Confidence            999999999864

>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=99.55  E-value=4.1e-14  Score=91.22  Aligned_cols=67  Identities=27%  Similarity=0.455  Sum_probs=61.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|+.++.+++++|||||+|.+.++|++|+.  ++..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g   82 (103)
T 2cqg_A           32 LKEYFSTFGEVLM---------------------------VQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDG   82 (103)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCC
Confidence            7899999999999                           9999999999999999999999999999998  4789999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++.++.....
T Consensus        83 ~~l~v~~a~~~~~~~~   98 (103)
T 2cqg_A           83 RWCDCKLPNSKQSQDS   98 (103)
T ss_dssp             EEEEEECCCTTCCCCC
T ss_pred             eEEEEEecCCCCcCCC
Confidence            9999999987655443

>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=99.55  E-value=1.9e-14  Score=91.33  Aligned_cols=62  Identities=35%  Similarity=0.501  Sum_probs=58.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|+.++. ++++|||||+|.++++|++|+..|||..++|
T Consensus        33 l~~~F~~~G~i~~---------------------------v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (95)
T 2ywk_A           33 LYELFLQAGPLTK---------------------------VTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYG   84 (95)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           99999985 9999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|++++.
T Consensus        85 ~~l~V~~a~~   94 (95)
T 2ywk_A           85 RPINVSGPSS   94 (95)
T ss_dssp             EECEEECCCC
T ss_pred             CEEEEEEcCC
Confidence            9999999864

>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=99.55  E-value=1e-14  Score=92.51  Aligned_cols=63  Identities=19%  Similarity=0.330  Sum_probs=59.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   84 (95)
T 2ek1_A           32 ILDFFYGYQVIPG---------------------------SVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS   84 (95)
T ss_dssp             HHHHTTTSCBCTT---------------------------CCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCccc---------------------------eEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            7899999999998                           8889999899999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|+++.+
T Consensus        85 r~l~v~~a~s   94 (95)
T 2ek1_A           85 RKVKLSGPSS   94 (95)
T ss_dssp             EECEEECCC-
T ss_pred             cEEEEEeccC
Confidence            9999998864

>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=99.54  E-value=2.5e-15  Score=98.77  Aligned_cols=65  Identities=34%  Similarity=0.545  Sum_probs=61.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.|+.+++++|||||+|.+.++|++|+ .|||..++|
T Consensus        42 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   93 (114)
T 2cq4_A           42 LEDFFSAVGKVRD---------------------------VRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLG   93 (114)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETT
T ss_pred             HHHHHHhCCCEeE---------------------------EEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCC
Confidence            7899999999999                           999999999999999999999999999999 899999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++++...
T Consensus        94 ~~l~V~~a~~~~~  106 (114)
T 2cq4_A           94 VPIIVQASQAEKN  106 (114)
T ss_dssp             EEEEEEEHHHHHH
T ss_pred             eEEEEEecCCCcc
Confidence            9999999976443

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.54  E-value=3.5e-14  Score=94.58  Aligned_cols=66  Identities=29%  Similarity=0.465  Sum_probs=61.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++ +++++|||||+|.+.++|++|+..|||..++|
T Consensus        52 l~~~F~~~G~v~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  103 (124)
T 2kt5_A           52 IQELFAEFGTLKK---------------------------AAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDG  103 (124)
T ss_dssp             HHHHHHTTSCCSE---------------------------EEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSS
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999998 99999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|++|.+....
T Consensus       104 ~~l~V~~a~~~~~~  117 (124)
T 2kt5_A          104 RPMDIQLVASQIDL  117 (124)
T ss_dssp             CEEEEEEECCTTCC
T ss_pred             cEEEEEEeCCCCCC
Confidence            99999999765443

>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=99.54  E-value=2.1e-14  Score=100.25  Aligned_cols=68  Identities=25%  Similarity=0.423  Sum_probs=62.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+.++.++.++|||||+|.+.++|++||..|||..|.|
T Consensus        89 L~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  141 (165)
T 1rk8_A           89 IQEKFCDYGEIKN---------------------------IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG  141 (165)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHhhcCCCEEE---------------------------EEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|.++.+.....
T Consensus       142 ~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A          142 QTIQVDWCFVKGPKR  156 (165)
T ss_dssp             EECEEEESEECC---
T ss_pred             EEEEEEEecCCCCCC
Confidence            999999997655443

>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=99.54  E-value=3.1e-15  Score=94.26  Aligned_cols=66  Identities=30%  Similarity=0.616  Sum_probs=58.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.+++++.+++++|||||+|.+.+ |++|+..|||..++|
T Consensus        18 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g   69 (90)
T 2ki2_A           18 VKELFSQFGKVFN---------------------------VKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMG   69 (90)
T ss_dssp             HTTTHHHHTCCSE---------------------------EEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECC
Confidence            6789999999999                           999999999999999999999999 999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|++|.+....
T Consensus        70 ~~l~V~~a~~~~~~   83 (90)
T 2ki2_A           70 RTIRVTEANPKKSL   83 (90)
T ss_dssp             SSCSEEEC------
T ss_pred             eEEEEEEcCCCCCC
Confidence            99999999765443

>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=99.54  E-value=2.4e-14  Score=93.05  Aligned_cols=67  Identities=18%  Similarity=0.304  Sum_probs=61.0

Q ss_pred             HHHHhhccCc-ceecceeeeccCCCCCcccccccccccceEEEEE-eeCCCCCcccEEEEEeCCHHHHHHHHHhhC--Cc
Q 033734            2 LADAFSQFGQ-VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATII-MDKGKNRSKGYGYVTFSTEEEAQKALADMN--GK   77 (112)
Q Consensus         2 l~~~f~~~G~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~--g~   77 (112)
                      |+++|++||. |..                           +.++ .++.+++++|||||+|.++++|++|+..||  +.
T Consensus        25 l~~~f~~~G~~v~~---------------------------v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~   77 (109)
T 2dis_A           25 ILEEIAKVTEGVLD---------------------------VIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI   77 (109)
T ss_dssp             HHHHHHHHSTTEEE---------------------------EECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCS
T ss_pred             HHHHHHHhcCCceE---------------------------EEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCc
Confidence            7899999998 999                           8888 888889999999999999999999999996  58


Q ss_pred             eeCCeeEEEEeccCCCCC
Q 033734           78 LLDGRVIFVDNVRPSRRY   95 (112)
Q Consensus        78 ~l~g~~i~V~~a~~~~~~   95 (112)
                      .++|+.|.|+++.+....
T Consensus        78 ~~~g~~l~V~~a~~~~~~   95 (109)
T 2dis_A           78 QLWGHQIAVDWAEPEIDV   95 (109)
T ss_dssp             CBTTBCCEEEESCSSCST
T ss_pred             eecCCeEEEEEcCCCCCc
Confidence            999999999999876553

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.54  E-value=8.9e-15  Score=96.47  Aligned_cols=62  Identities=34%  Similarity=0.543  Sum_probs=59.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|++++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        57 l~~~F~~~G~i~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  109 (118)
T 2khc_A           57 LASTFLPFGNVIS---------------------------AKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGT  109 (118)
T ss_dssp             HHHHTTTSCEEEE---------------------------EEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|+|++++
T Consensus       110 ~~l~V~~ak  118 (118)
T 2khc_A          110 KRLKVQLKK  118 (118)
T ss_dssp             EECCEEEC-
T ss_pred             EEEEEEecC
Confidence            999999874

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.53  E-value=6e-15  Score=90.04  Aligned_cols=60  Identities=28%  Similarity=0.607  Sum_probs=57.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.++.+++++|||||+|.++++|++|+. +||..++|
T Consensus        16 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g   67 (75)
T 2mss_A           16 VKHYFEQFGKVDD---------------------------AMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINN   67 (75)
T ss_dssp             HHHHHHTTSCCSE---------------------------ECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECC
Confidence            7899999999999                           9999999899999999999999999999998 99999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|++|
T Consensus        68 ~~l~v~~A   75 (75)
T 2mss_A           68 KMVECKKA   75 (75)
T ss_dssp             CCCEEECC
T ss_pred             EEEEEEeC
Confidence            99999875

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.53  E-value=2.7e-14  Score=90.10  Aligned_cols=65  Identities=40%  Similarity=0.494  Sum_probs=59.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++++  +++++|||||+|.+.++|++|+..|||..++|
T Consensus        25 l~~~f~~~G~v~~---------------------------~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g   75 (92)
T 2dgv_A           25 LKDKFNECGHVLY---------------------------ADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSG   75 (92)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           888875  78999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus        76 ~~l~v~~a~~~~~~   89 (92)
T 2dgv_A           76 REIDVRIDRNASGP   89 (92)
T ss_dssp             BCCCCEECSCCSSC
T ss_pred             cEEEEEEcCCCCCC
Confidence            99999999876543

>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=99.53  E-value=7e-14  Score=91.09  Aligned_cols=67  Identities=19%  Similarity=0.376  Sum_probs=59.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|..+   +.++|||||+|.+.++|++|+..||+..++|
T Consensus        39 l~~~F~~~G~v~~---------------------------~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   88 (109)
T 1x4a_A           39 IEDVFYKYGAIRD---------------------------IDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG   88 (109)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           887544   5589999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++++.....++
T Consensus        89 ~~l~V~~a~~~~~~~~~  105 (109)
T 1x4a_A           89 YRLRVEFPRSGRGTGSG  105 (109)
T ss_dssp             EECEEECCCCCCCCCCC
T ss_pred             eEEEEEEcccCCCCCCC
Confidence            99999999876655443

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.53  E-value=2.2e-14  Score=94.18  Aligned_cols=60  Identities=27%  Similarity=0.485  Sum_probs=55.5

Q ss_pred             HHHHh-hccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAF-SQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f-~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++| ++||+|.+                           +.|+++. +++++|||||+|.++++|++|+..|||+.++
T Consensus        43 l~~~f~~~~G~V~~---------------------------v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~   94 (104)
T 1jmt_A           43 VFTEMEEKYGEVEE---------------------------MNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFN   94 (104)
T ss_dssp             HHHHHHHHTCCEEE---------------------------EEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEET
T ss_pred             HHHHhhccCCceEE---------------------------EEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            55677 99999999                           9999887 5799999999999999999999999999999


Q ss_pred             CeeEEEEec
Q 033734           81 GRVIFVDNV   89 (112)
Q Consensus        81 g~~i~V~~a   89 (112)
                      |+.|.|+++
T Consensus        95 Gr~i~v~~s  103 (104)
T 1jmt_A           95 GQPIHAELS  103 (104)
T ss_dssp             TEECCEEEC
T ss_pred             CEEEEEEEc
Confidence            999999886

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.52  E-value=4.9e-14  Score=92.54  Aligned_cols=65  Identities=35%  Similarity=0.558  Sum_probs=60.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|++++.+++++|||||+|.+.++|++|+..+ +..++|
T Consensus        42 L~~~F~~~G~i~~---------------------------v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g   93 (109)
T 2rs2_A           42 LREYFGQFGEVKE---------------------------CLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDS   93 (109)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETT
T ss_pred             HHHHHHccCCeEE---------------------------EEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCC
Confidence            7899999999999                           999999999999999999999999999999976 589999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.++..
T Consensus        94 ~~l~V~~a~~~~~  106 (109)
T 2rs2_A           94 KTIDPKVAFPRRA  106 (109)
T ss_dssp             EEEEEEECCCCCC
T ss_pred             EEEEEEEccCCCC
Confidence            9999999986544

>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=99.52  E-value=4.7e-14  Score=88.25  Aligned_cols=60  Identities=38%  Similarity=0.681  Sum_probs=56.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +++++++.+++++|||||+|.+.++|++|+. +++..++|
T Consensus        28 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g   79 (87)
T 3s7r_A           28 LKDYFTKFGEVVD---------------------------CTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDG   79 (87)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECC
Confidence            7899999999999                           9999999999999999999999999999997 58899999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|++|
T Consensus        80 ~~i~v~~A   87 (87)
T 3s7r_A           80 RVIDPKKA   87 (87)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEEEeC
Confidence            99999875

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.52  E-value=1.8e-14  Score=93.86  Aligned_cols=65  Identities=23%  Similarity=0.455  Sum_probs=58.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+  +.+|+++|||||+|.+.++|++|+..|||..++|
T Consensus        38 l~~~F~~~G~v~~---------------------------v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g   88 (105)
T 2nlw_A           38 IHKIFSKFGKITN---------------------------DFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   88 (105)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST
T ss_pred             HHHHHhcCCCEEE---------------------------EEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            7899999999999                           8887  3589999999999999999999999999999999


Q ss_pred             e-eEEEEeccCCCCC
Q 033734           82 R-VIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~-~i~V~~a~~~~~~   95 (112)
                      + .|.|+++....+.
T Consensus        89 ~~~l~V~~a~~~~k~  103 (105)
T 2nlw_A           89 QHTFRVNLFTDFDKY  103 (105)
T ss_dssp             TCEEEEECSCCCCCC
T ss_pred             CceEEEEEcchHhhh
Confidence            8 9999999765543

>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=99.51  E-value=1.3e-14  Score=93.58  Aligned_cols=63  Identities=24%  Similarity=0.431  Sum_probs=58.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeC-CCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK-GKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~-~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| |..                           ++|++++ .+++++|||||+|.+.++|++|+ .|||..++
T Consensus        36 l~~~F~~~G-i~~---------------------------v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~   86 (100)
T 2j76_E           36 IKEFFRGLN-ISA---------------------------VRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG   86 (100)
T ss_dssp             HHHHSCSSC-EEE---------------------------EECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBT
T ss_pred             HHHHHHhcC-CeE---------------------------EEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEEC
Confidence            789999999 999                           9999998 68999999999999999999999 89999999


Q ss_pred             CeeEEEEeccCCC
Q 033734           81 GRVIFVDNVRPSR   93 (112)
Q Consensus        81 g~~i~V~~a~~~~   93 (112)
                      |+.|.|++++++.
T Consensus        87 g~~l~V~~a~~~~   99 (100)
T 2j76_E           87 NRRIRVDVADQAQ   99 (100)
T ss_dssp             TBCCCCEECCCSC
T ss_pred             CeEEEEEeccCCC
Confidence            9999999998754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=8.6e-14  Score=89.42  Aligned_cols=57  Identities=32%  Similarity=0.564  Sum_probs=52.3

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCCCCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~~~~~   98 (112)
                      +.++.++.+++++|||||+|.++++|++|+..|||..++|+.|.|++++++...+++
T Consensus        42 ~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~   98 (102)
T 2fc8_A           42 ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSG   98 (102)
T ss_dssp             EEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCSSSCS
T ss_pred             EEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCCCCCC
Confidence            888999889999999999999999999999999999999999999999887665443

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

Probab=99.51  E-value=3.2e-14  Score=95.69  Aligned_cols=61  Identities=34%  Similarity=0.575  Sum_probs=58.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +++++++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        80 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  132 (140)
T 2ku7_A           80 LHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG  132 (140)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|+|++|
T Consensus       133 ~~l~v~~A  140 (140)
T 2ku7_A          133 RTIRVNLA  140 (140)
T ss_dssp             EEEEEEC-
T ss_pred             EEEEEEeC
Confidence            99999875

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=8.8e-14  Score=87.80  Aligned_cols=63  Identities=25%  Similarity=0.417  Sum_probs=58.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.| .|..                           ++|+++ .+++++|||||+|.+.++|++|+. |||..++|
T Consensus        27 l~~~F~~~-~i~~---------------------------v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~g   76 (91)
T 2dgw_A           27 VMEFLAPL-KPVA---------------------------IRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGG   76 (91)
T ss_dssp             HHHHHTTS-CCSE---------------------------EEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETT
T ss_pred             HHHHHhhC-CceE---------------------------EEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCC
Confidence            78899999 8888                           999999 689999999999999999999999 99999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|.++.++..
T Consensus        77 r~i~v~~a~~~~~   89 (91)
T 2dgw_A           77 RYIEVFREKSGPS   89 (91)
T ss_dssp             EEEEEEEESSCCC
T ss_pred             cEEEEEECCcCCC
Confidence            9999999987643

>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=99.50  E-value=5.3e-14  Score=92.58  Aligned_cols=63  Identities=24%  Similarity=0.370  Sum_probs=57.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCC--CCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGK--NRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t--~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||+|.+                           +.|++++.+  ++++|++||+|.++++|++|+..|||+.+
T Consensus        32 l~~~f~k~G~V~~---------------------------v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f   84 (105)
T 3v4m_A           32 VRDECSKYGLVKS---------------------------IEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   84 (105)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHccCCEEE---------------------------EEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            7889999999999                           999998765  36899999999999999999999999999


Q ss_pred             CCeeEEEEeccC
Q 033734           80 DGRVIFVDNVRP   91 (112)
Q Consensus        80 ~g~~i~V~~a~~   91 (112)
                      +||.|.|.++..
T Consensus        85 ~GR~i~v~~~~~   96 (105)
T 3v4m_A           85 ANRVVVTKYCDP   96 (105)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCCEEEEEEeCH
Confidence            999999998753

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.50  E-value=2.3e-14  Score=97.69  Aligned_cols=67  Identities=31%  Similarity=0.575  Sum_probs=62.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        64 L~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g  116 (135)
T 2lea_A           64 LRRVFEKYGRVGD---------------------------VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  116 (135)
T ss_dssp             HHHHHGGGSCCSE---------------------------EECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus       117 ~~l~V~~a~~~~~~  130 (135)
T 2lea_A          117 RELRVQMARYGRPP  130 (135)
T ss_dssp             SCCEEEECCCCCCC
T ss_pred             EEEEEEECCCCCCC
Confidence            99999999865443

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.50  E-value=2.3e-14  Score=87.53  Aligned_cols=60  Identities=35%  Similarity=0.566  Sum_probs=57.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.++.+++++|||||+|.++++|++|+..++ ..++|
T Consensus        17 l~~~F~~~G~v~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g   68 (77)
T 1uaw_A           17 LREYFGQFGEVKE---------------------------CLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDS   68 (77)
T ss_dssp             HHHHHTTTSCCCC---------------------------EEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCC
Confidence            7899999999999                           9999999899999999999999999999999999 99999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|++|
T Consensus        69 ~~l~v~~a   76 (77)
T 1uaw_A           69 KTIDPKVA   76 (77)
T ss_dssp             CCCEEEEC
T ss_pred             EEEEEEec
Confidence            99999886

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.50  E-value=7.8e-14  Score=89.43  Aligned_cols=70  Identities=24%  Similarity=0.302  Sum_probs=59.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.....                   .....++++.|+.+++++|||||+|.+.++|++|+..|||..++|
T Consensus        30 l~~~F~~~G~i~~~~~-------------------~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           30 VADYFKQIGIIKTNKK-------------------TGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             HHHHHTTTSCBCEETT-------------------TTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHHHhCCEeeccc-------------------cccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7899999999875100                   011126889998899999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|+|++|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>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=99.50  E-value=1.9e-14  Score=94.33  Aligned_cols=70  Identities=23%  Similarity=0.397  Sum_probs=58.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+..+..+++++|||||+|.+.++|++|+..|||..++|
T Consensus        42 l~~~f~~~G~v~~---------------------------~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   94 (115)
T 2cpx_A           42 LVSLFARFQEKKG---------------------------PPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG   94 (115)
T ss_dssp             HHHHTHHHHHSSS---------------------------SCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             HHHHHHHhCCccc---------------------------eEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7889999999965                           3222222378999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++++.....+.
T Consensus        95 ~~l~v~~a~~~~~~~~~  111 (115)
T 2cpx_A           95 KILVIEFGKNKKQRSSG  111 (115)
T ss_dssp             CBCEEEECCCCSCCCCC
T ss_pred             cEEEEEEccCCCCCCCC
Confidence            99999999877665443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=6.4e-15  Score=91.91  Aligned_cols=62  Identities=26%  Similarity=0.500  Sum_probs=57.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus        22 l~~~f~~~G~i~~---------------------------~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   74 (85)
T 1x4e_A           22 LVKLCQPYGKIVS---------------------------TKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA   74 (85)
T ss_dssp             HHTTSTTTSCEEE---------------------------EEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCE
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEee
Confidence            7889999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.+++++++
T Consensus        75 ~~~~~~~~~   83 (85)
T 1x4e_A           75 QMAKQSGPS   83 (85)
T ss_dssp             ESCCSSCCC
T ss_pred             EEEeecCCC
Confidence            988776654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.50  E-value=6.5e-14  Score=90.62  Aligned_cols=56  Identities=25%  Similarity=0.372  Sum_probs=52.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|.+||+|..                           ++++.      ++|||||+|.++++|.+|++.||+..++|
T Consensus        24 L~~lF~q~G~V~~---------------------------~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~g   70 (89)
T 2wbr_A           24 LRTLCMQHGPLVS---------------------------FHPYL------NQGIALCKYTTREEANKAQMALNNCVLAN   70 (89)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhhCCEEE---------------------------EEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECC
Confidence            7899999999999                           88754      68999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|+|++|.
T Consensus        71 r~I~V~~A~   79 (89)
T 2wbr_A           71 TTIFAESPS   79 (89)
T ss_dssp             EEEEEECCC
T ss_pred             cEEEEEECC
Confidence            999999984

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=3.3e-14  Score=93.10  Aligned_cols=61  Identities=18%  Similarity=0.182  Sum_probs=57.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|++|+. ++++|||||+|.++++|++|+. ++|..++|
T Consensus        28 L~~~F~~~G~v~~---------------------------v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~g   78 (103)
T 1s79_A           28 IKEWLEDKGQVLN---------------------------IQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKE   78 (103)
T ss_dssp             HHHHHHTSSCEEE---------------------------EEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTT
T ss_pred             HHHHHhhcCCEEE---------------------------EEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECC
Confidence            7899999999999                           99999986 9999999999999999999999 99999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|.++..
T Consensus        79 r~l~V~~~~~   88 (103)
T 1s79_A           79 TDLLILFKDD   88 (103)
T ss_dssp             TTCEEEEHHH
T ss_pred             EEEEEEEchH
Confidence            9999998753

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=2.3e-13  Score=87.01  Aligned_cols=63  Identities=25%  Similarity=0.473  Sum_probs=56.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|.      +++|||||+|.+.++|++|+..|||..++|
T Consensus        30 l~~~F~~~G~i~~---------------------------v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   76 (97)
T 1x5p_A           30 LRGAFSPFGNIID---------------------------LSMD------PPRNCAFVTYEKMESADQAVAELNGTQVES   76 (97)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETT
T ss_pred             HHHHHhhCCCEEE---------------------------EEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            7899999999999                           8773      578999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++.....+
T Consensus        77 ~~l~v~~a~~~~~~~~   92 (97)
T 1x5p_A           77 VQLKVNIARKQPMLDS   92 (97)
T ss_dssp             EEEEEECCSSCCCCCS
T ss_pred             eEEEEEECCCCCCCCC
Confidence            9999999987655444

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.49  E-value=1.3e-13  Score=93.52  Aligned_cols=63  Identities=30%  Similarity=0.615  Sum_probs=60.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.++.++|+|||+|.++++|.+|+..|||..++|
T Consensus       104 l~~~f~~~G~i~~---------------------------~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  156 (166)
T 3md3_A          104 LRNAFKDFPSYLS---------------------------GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG  156 (166)
T ss_dssp             HHHHHTTSTTEEE---------------------------EEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhccCCeeE---------------------------EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|++|++
T Consensus       157 ~~i~v~~a~~  166 (166)
T 3md3_A          157 RPLRINWAAK  166 (166)
T ss_dssp             EECEEEESCC
T ss_pred             cEEEEEecCC
Confidence            9999999863

>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=99.49  E-value=5.9e-14  Score=91.49  Aligned_cols=65  Identities=20%  Similarity=0.214  Sum_probs=57.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||. +.                           ++|++|+ +++++|||||+|.++++|++||. +|+..+++
T Consensus        32 l~~~F~~~G~-~~---------------------------v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g   81 (102)
T 1wez_A           32 IYNFFSPLNP-MR---------------------------VHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQH   81 (102)
T ss_dssp             HHHSSCSCCC-SE---------------------------EEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSS
T ss_pred             HHHHHHHcCc-eE---------------------------EEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECC
Confidence            7889999994 48                           9999998 89999999999999999999995 89999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|..+.+.....
T Consensus        82 r~i~V~~~~~~~~~~   96 (102)
T 1wez_A           82 RYVELFLNSTAGTSG   96 (102)
T ss_dssp             SCCEEEEECCCCCCC
T ss_pred             cEEEEEECCCCCCCC
Confidence            999999987665443

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.48  E-value=1.6e-13  Score=97.29  Aligned_cols=66  Identities=26%  Similarity=0.490  Sum_probs=62.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+++++|||||+|.+.++|.+|+..|||..++|
T Consensus       142 l~~~f~~~G~v~~---------------------------v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g  194 (216)
T 2qfj_A          142 IKSVFEAFGKIKS---------------------------ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG  194 (216)
T ss_dssp             HHHHHTTSSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHhccCCeeE---------------------------EEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+...
T Consensus       195 ~~i~V~~a~~~~~  207 (216)
T 2qfj_A          195 QYLRVGKAVTPPM  207 (216)
T ss_dssp             SBCEEEECSSCSS
T ss_pred             cEEEEEEecCCCC
Confidence            9999999987543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=1.1e-13  Score=88.92  Aligned_cols=62  Identities=26%  Similarity=0.468  Sum_probs=57.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.+     ++|||||+|.++++|++|+..|||..++|
T Consensus        17 l~~~F~~~G~i~~---------------------------v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g   64 (101)
T 2hvz_A           17 LERAFSYYGPLRT---------------------------VWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICG   64 (101)
T ss_dssp             HHHHHHHHCCCSE---------------------------EEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECC
Confidence            7899999999999                           988877     78999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus        65 ~~l~V~~a~~~~~~   78 (101)
T 2hvz_A           65 SRVRVELSTGMPRR   78 (101)
T ss_dssp             CCCEEEESSSCCCS
T ss_pred             cEEEEEEccCCCCc
Confidence            99999999876544

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=2.1e-13  Score=85.98  Aligned_cols=61  Identities=28%  Similarity=0.516  Sum_probs=55.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++        +|||||+|.++++|++|+..|||..++|
T Consensus        25 l~~~F~~~G~i~~---------------------------v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g   69 (90)
T 2dnq_A           25 IRSLFEQYGKVLE---------------------------CDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHG   69 (90)
T ss_dssp             HHHHHHTSSCEEE---------------------------EEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHHhCCCEEE---------------------------EEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCC
Confidence            7899999999999                           8876        6899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++++.....+
T Consensus        70 ~~l~v~~a~~~~~~~~   85 (90)
T 2dnq_A           70 VNINVEASKNKSKASS   85 (90)
T ss_dssp             CBCEEECSSCCCCCCS
T ss_pred             cEEEEEECCCCCCCCC
Confidence            9999999987665544

>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=99.48  E-value=2.9e-13  Score=89.13  Aligned_cols=64  Identities=27%  Similarity=0.493  Sum_probs=56.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +.| .|+   .++|||||+|.++++|++|+..|||..++|
T Consensus        43 l~~~f~~~G~v~~---------------------------v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   91 (112)
T 2dit_A           43 LRVECSKFGQIRK---------------------------LLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGG   91 (112)
T ss_dssp             HHHHGGGTSCCSE---------------------------EEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             HHHHHHccCCEeE---------------------------EEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            6889999999999                           854 554   389999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++.+.....
T Consensus        92 r~l~v~~a~~~~~~~  106 (112)
T 2dit_A           92 RQITAQAWDGTTDYQ  106 (112)
T ss_dssp             EECEEEECCSCCCSS
T ss_pred             cEEEEEEeCCCCCcc
Confidence            999999998765543

>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=99.47  E-value=2.1e-13  Score=88.91  Aligned_cols=62  Identities=34%  Similarity=0.591  Sum_probs=56.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.+      +|||||+|.+.++|++|+..|||..++|
T Consensus        42 l~~~F~~~G~i~~---------------------------v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g   88 (109)
T 1x4g_A           42 MRQTFSPFGQIME---------------------------IRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEG   88 (109)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           888776      6899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++++.....
T Consensus        89 ~~l~v~~a~~~~~~~  103 (109)
T 1x4g_A           89 HVVKCYWGKESPDMT  103 (109)
T ss_dssp             EECEEECCCCCCSSC
T ss_pred             cEEEEEecCCCCCCC
Confidence            999999998765543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=7.3e-14  Score=94.96  Aligned_cols=62  Identities=19%  Similarity=0.322  Sum_probs=55.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|++||.|.+                           +.+.   .+++++|||||+|.+.++|+.|+..|||..+.|
T Consensus        50 L~~~F~~~G~I~~---------------------------v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g   99 (127)
T 2a3j_A           50 LYALASSQGDILD---------------------------IVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQG   99 (127)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT
T ss_pred             HHHHhccCCCeEE---------------------------EEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            4579999999988                           7663   267899999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++++..
T Consensus       100 r~l~V~~a~~~~  111 (127)
T 2a3j_A          100 NPLVITFSETPQ  111 (127)
T ss_dssp             SCCEEEECCCCC
T ss_pred             CEEEEEEccCcc
Confidence            999999997653

>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=99.47  E-value=1.5e-13  Score=90.05  Aligned_cols=63  Identities=25%  Similarity=0.528  Sum_probs=58.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+++|++||.|..                           ++|+.++ ++.++|||||+|.+.++|++|+..|||..+  
T Consensus        42 l~~~F~~~G~i~~---------------------------~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~   93 (114)
T 1x5o_A           42 LENMLKPFGQVIS---------------------------TRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKT   93 (114)
T ss_dssp             HHHTTTTTSCEEE---------------------------EEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCC
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcC
Confidence            7899999999999                           9999998 999999999999999999999999999999  


Q ss_pred             ------CCeeEEEEeccCC
Q 033734           80 ------DGRVIFVDNVRPS   92 (112)
Q Consensus        80 ------~g~~i~V~~a~~~   92 (112)
                            .+++|.|+++.+.
T Consensus        94 ~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           94 PPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             CTTSCCCSSCBEEEECCCS
T ss_pred             CccccCCCCceeEEccCCC
Confidence                  5778999998754

>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=99.47  E-value=4.4e-14  Score=104.13  Aligned_cols=62  Identities=23%  Similarity=0.408  Sum_probs=59.8

Q ss_pred             HHHHhhccC--cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFG--QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G--~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||  .|.+                           |+|++|+.+++++|||||+|.+.++|++||..|||..|
T Consensus        85 L~~~F~~~G~~~v~~---------------------------v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~  137 (229)
T 3q2s_C           85 LTEAVHSLGVNDILE---------------------------IKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL  137 (229)
T ss_dssp             HHHHHHTTTCCCEEE---------------------------EEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCB
T ss_pred             HHHHHHHHCCcceEE---------------------------EEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeE
Confidence            789999999  9999                           99999999999999999999999999999999999999


Q ss_pred             CCeeEEEEecc
Q 033734           80 DGRVIFVDNVR   90 (112)
Q Consensus        80 ~g~~i~V~~a~   90 (112)
                      +|+.|.|++++
T Consensus       138 ~Gr~l~V~~a~  148 (229)
T 3q2s_C          138 HGQNPVVTPVN  148 (229)
T ss_dssp             TTBCCEEEECC
T ss_pred             CCEEeEEEECC
Confidence            99999999874

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.47  E-value=8.5e-14  Score=96.09  Aligned_cols=63  Identities=13%  Similarity=0.197  Sum_probs=56.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCC----HHH----HHHHHH-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFST----EEE----AQKALA-   72 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~----~~~----a~~Ai~-   72 (112)
                      |+.+|+.||+|.+                           +.++.|++||+++|||||+|.+    +++    |.+|+. 
T Consensus        23 Lk~~Fs~fGeV~~---------------------------~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~   75 (136)
T 2j8a_A           23 IKNYFKKYGEISH---------------------------FEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRK   75 (136)
T ss_dssp             HHHHHHTTSCCSE---------------------------EEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHH
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHH
Confidence            7899999999999                           9999999999999999999996    433    889988 


Q ss_pred             -hhCCceeCCeeEEEEeccC
Q 033734           73 -DMNGKLLDGRVIFVDNVRP   91 (112)
Q Consensus        73 -~l~g~~l~g~~i~V~~a~~   91 (112)
                       .+||..|+|+.|+|.+.+.
T Consensus        76 ~~lng~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           76 HESSGCFIMGFKFEVILNKH   95 (136)
T ss_dssp             TTTTCEEETTEEEEEEECCT
T ss_pred             hhhcCCeecCcEEEEEECcc
Confidence             8899999999999998764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=2.4e-13  Score=87.31  Aligned_cols=55  Identities=27%  Similarity=0.503  Sum_probs=47.4

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCCCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~~~~   97 (112)
                      ++++.+ .+++++|||||+|.++++|++|+..|||..++|+.|.|+++++......
T Consensus        42 v~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~   96 (101)
T 2fc9_A           42 IKVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNS   96 (101)
T ss_dssp             EECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCCCC
T ss_pred             EEEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCCCC
Confidence            344555 5889999999999999999999999999999999999999987655443

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=1.5e-13  Score=90.16  Aligned_cols=62  Identities=35%  Similarity=0.719  Sum_probs=57.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++  +.++|||||+|.+.++|++|+..|||..++|
T Consensus        46 l~~~F~~~G~i~~---------------------------v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   96 (109)
T 2err_A           46 LRQMFGQFGKILD---------------------------VEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEG   96 (109)
T ss_dssp             HHHHGGGTCCCSC---------------------------EEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999985  4589999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|++++++
T Consensus        97 ~~l~V~~a~~~  107 (109)
T 2err_A           97 RKIEVNNATAR  107 (109)
T ss_dssp             EECEEEECCCS
T ss_pred             EEEEEEECCCC
Confidence            99999999764

>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=99.46  E-value=4e-13  Score=87.69  Aligned_cols=60  Identities=25%  Similarity=0.328  Sum_probs=55.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.|+.|       |||||+|.++++|++||..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g   77 (108)
T 1x4c_A           32 LKDHMREAGDVCY---------------------------ADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRS   77 (108)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEEC
T ss_pred             HHHHHHhcCCEeE---------------------------EEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccC
Confidence            7899999999999                           988776       899999999999999999999999999


Q ss_pred             -----eeEEEEeccCCCCC
Q 033734           82 -----RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 -----~~i~V~~a~~~~~~   95 (112)
                           +.|.|+++.++.+.
T Consensus        78 ~~~~~~~i~V~~a~~~~~~   96 (108)
T 1x4c_A           78 HEGETAYIRVKVDGPRSPS   96 (108)
T ss_dssp             TTSCEEEEEEEESSCCSCC
T ss_pred             CcCcceEEEEEeCCCCCCC
Confidence                 99999999876544

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.46  E-value=2.7e-14  Score=88.68  Aligned_cols=56  Identities=25%  Similarity=0.494  Sum_probs=51.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++  +.+|+++|||||+|.++++|++|+..|||..++|
T Consensus        24 l~~~F~~~G~i~~---------------------------v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g   74 (81)
T 2krb_A           24 IHKIFSKFGKITN---------------------------DFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK   74 (81)
T ss_dssp             HHHHHHTTCCEEE---------------------------EECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSS
T ss_pred             HHHHHhhcCCeEE---------------------------EEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCC
Confidence            7899999999999                           8877  3589999999999999999999999999999999


Q ss_pred             e-eEEE
Q 033734           82 R-VIFV   86 (112)
Q Consensus        82 ~-~i~V   86 (112)
                      + .|+|
T Consensus        75 ~~~l~V   80 (81)
T 2krb_A           75 QHTFRV   80 (81)
T ss_dssp             SSCCCC
T ss_pred             ceeEEe
Confidence            9 8876

>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=99.46  E-value=1.7e-13  Score=92.23  Aligned_cols=63  Identities=24%  Similarity=0.406  Sum_probs=57.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCC----CCCcccEEEEEeCCHHHHHHHHHhhCCc
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKG----KNRSKGYGYVTFSTEEEAQKALADMNGK   77 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~----t~~~rG~afV~f~~~~~a~~Ai~~l~g~   77 (112)
                      |+++|++||+|.+                           +.|++++.    +++++|++||+|.++++|++|+..|||+
T Consensus        42 l~eef~k~G~V~~---------------------------v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr   94 (118)
T 3ue2_A           42 VTEECGKFGAVNR---------------------------VIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR   94 (118)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             HHHHHhccCCEeE---------------------------EEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCC
Confidence            6889999999999                           99999865    4578899999999999999999999999


Q ss_pred             eeCCeeEEEEeccC
Q 033734           78 LLDGRVIFVDNVRP   91 (112)
Q Consensus        78 ~l~g~~i~V~~a~~   91 (112)
                      .++|+.|.|.++..
T Consensus        95 ~f~GR~i~v~~~~~  108 (118)
T 3ue2_A           95 WFAGRKVVAEVYDQ  108 (118)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EECCcEEEEEEcCh
Confidence            99999999998753

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.45  E-value=2.2e-13  Score=95.38  Aligned_cols=66  Identities=20%  Similarity=0.456  Sum_probs=62.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.++.++|||||+|.++++|++|+..|||..++|
T Consensus       131 l~~~f~~~G~v~~---------------------------~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  183 (198)
T 2yh0_A          131 VKELLTSFGPLKA---------------------------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD  183 (198)
T ss_dssp             HHHHHHTBSCEEE---------------------------EEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETT
T ss_pred             HHHHHHHcCCccE---------------------------EEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++++++..
T Consensus       184 ~~l~v~~a~~~~~  196 (198)
T 2yh0_A          184 KKLLVQRASVGAK  196 (198)
T ss_dssp             EECEEEESCCCCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999987654

>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=99.45  E-value=2.8e-13  Score=94.68  Aligned_cols=68  Identities=22%  Similarity=0.490  Sum_probs=58.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.|+.++.++|||||+|.++++|.+|+.. +|..++|
T Consensus       121 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G  172 (196)
T 1l3k_A          121 LRDYFEQYGKIEV---------------------------IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNG  172 (196)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETT
T ss_pred             HHHHHhcCCCeEE---------------------------EEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECC
Confidence            7899999999999                           99999998999999999999999999999986 7999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|.|+++.++.....
T Consensus       173 ~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          173 HNCEVRKALSKQEMAS  188 (196)
T ss_dssp             EECEEEECC-------
T ss_pred             EEEEEEecCChhHhcc
Confidence            9999999987665543

>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=99.44  E-value=3.8e-14  Score=86.30  Aligned_cols=60  Identities=22%  Similarity=0.396  Sum_probs=56.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.++.+++++|||||+|.++++|++|+. +++..++|
T Consensus        16 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g   67 (75)
T 1iqt_A           16 IREYFGGFGEVES---------------------------IELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGL   67 (75)
T ss_dssp             HHHHHHHHSCCSE---------------------------ECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECC
Confidence            7899999999999                           9999999899999999999999999999999 58999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|++|
T Consensus        68 ~~l~v~~a   75 (75)
T 1iqt_A           68 SKCEIKVA   75 (75)
T ss_dssp             BCCCEEEC
T ss_pred             EEEEEEEC
Confidence            99999875

>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=99.44  E-value=2.7e-13  Score=93.03  Aligned_cols=61  Identities=21%  Similarity=0.490  Sum_probs=59.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.+++++|||||+|.++++|++|+..|||..++|
T Consensus       111 l~~~f~~~G~v~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  163 (172)
T 2g4b_A          111 VKELLTSFGPLKA---------------------------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD  163 (172)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCceE---------------------------EEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999998899999999999999999999999999999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|++|
T Consensus       164 ~~l~V~~A  171 (172)
T 2g4b_A          164 KKLLVQRA  171 (172)
T ss_dssp             EECEEEEC
T ss_pred             eEEEEEeC
Confidence            99999987

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

Probab=99.16  E-value=8.7e-15  Score=96.51  Aligned_cols=81  Identities=22%  Similarity=0.288  Sum_probs=64.4

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|++||.|....                   ......++|+.|+.+++++|||||+|.+.++|++|+..|||..++
T Consensus        23 ~l~~~F~~~G~i~~~~-------------------~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A           23 SVADYFKQIGIIKTNK-------------------KTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            3788999999986510                   000111578888889999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYNTDAP  100 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~~~~~  100 (112)
                      |+.|.|++++++....++..
T Consensus        84 g~~l~V~~a~~~~~~~~ggg  103 (116)
T 2lcw_A           84 GNPIKVSFATRRADFNRGGG  103 (116)
Confidence            99999999987766554433

>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=99.43  E-value=6.4e-13  Score=90.22  Aligned_cols=66  Identities=30%  Similarity=0.568  Sum_probs=62.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||+|..                           +++++++.+++++|||||+|.++++|++|+..|||..+.|
T Consensus        19 l~~~f~~~G~i~~---------------------------v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g   71 (167)
T 1fxl_A           19 FRSLFGSIGEIES---------------------------CKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT   71 (167)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|.++.+...
T Consensus        72 ~~l~v~~~~~~~~   84 (167)
T 1fxl_A           72 KTIKVSYARPSSA   84 (167)
T ss_dssp             EECEEEECCCCCG
T ss_pred             ceEEEEecCCCcc
Confidence            9999999976543

>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=99.43  E-value=1.5e-13  Score=90.60  Aligned_cols=63  Identities=22%  Similarity=0.326  Sum_probs=58.4

Q ss_pred             HHHHhhccCcc-eecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQV-TEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|+.||.| ..                           ++|++|+ +++++|||||+|.+.++|++||.. |+..++
T Consensus        32 l~~~F~~~g~v~~~---------------------------v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~   82 (114)
T 2cpy_A           32 VLQFLEGIPVDENA---------------------------VHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLN   82 (114)
T ss_dssp             HHHHTTTSCCCSTT---------------------------EEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEET
T ss_pred             HHHHHHhCCCcCCe---------------------------EEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccC
Confidence            78999999999 88                           9999998 999999999999999999999996 999999


Q ss_pred             CeeEEEEeccCCC
Q 033734           81 GRVIFVDNVRPSR   93 (112)
Q Consensus        81 g~~i~V~~a~~~~   93 (112)
                      |+.|.|.++.+..
T Consensus        83 gr~i~v~~a~~~~   95 (114)
T 2cpy_A           83 GREAFVHVVTLED   95 (114)
T ss_dssp             TEEEEEEEECHHH
T ss_pred             CeEEEEEECCHHH
Confidence            9999999986543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=9.1e-13  Score=83.35  Aligned_cols=62  Identities=24%  Similarity=0.480  Sum_probs=55.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++        ++||||+|.++++|++|+..|||..++|
T Consensus        27 l~~~F~~~G~v~~---------------------------v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g   71 (92)
T 2dgt_A           27 LRAKFEEYGPVIE---------------------------CDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQG   71 (92)
T ss_dssp             HHHHHHTTSCCCE---------------------------EEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            7899999999999                           8875        3499999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|+++++.....++
T Consensus        72 ~~l~V~~a~~~~~~~~~   88 (92)
T 2dgt_A           72 KRMHVQLSTSRLRTASG   88 (92)
T ss_dssp             EEEEEEESSCCCSCCCC
T ss_pred             cEEEEEEccCCCCCCCC
Confidence            99999999876655443

>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=99.43  E-value=3.7e-13  Score=85.93  Aligned_cols=60  Identities=27%  Similarity=0.460  Sum_probs=54.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |+++|++||.|..                           +.++.+      +|||||+|.++++|++|+..|||..++ 
T Consensus        34 l~~~F~~~G~v~~---------------------------v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~   80 (97)
T 1why_A           34 LAREFDRFGSIRT---------------------------IDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGG   80 (97)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHHhcCCeeE---------------------------EEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            7899999999999                           877643      689999999999999999999999999 


Q ss_pred             -CeeEEEEeccCCCC
Q 033734           81 -GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 -g~~i~V~~a~~~~~   94 (112)
                       |+.|.|++++++..
T Consensus        81 ~g~~l~V~~a~~~~~   95 (97)
T 1why_A           81 PDRRLRVDFAKSGPS   95 (97)
T ss_dssp             SSCBCEEEECCCCCC
T ss_pred             CCcEEEEEECCCCCC
Confidence             99999999987654

>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=99.43  E-value=1.8e-13  Score=93.53  Aligned_cols=63  Identities=24%  Similarity=0.536  Sum_probs=59.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.|+.++.++|||||+|.++++|++|+. ++|..++|
T Consensus       104 l~~~F~~~G~i~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g  155 (167)
T 2cjk_A          104 FEEFFSQWGTIID---------------------------AQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKD  155 (167)
T ss_dssp             HHHHHHTTSCCSE---------------------------EECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSS
T ss_pred             HHHHHHhCccEEE---------------------------EEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCC
Confidence            7899999999999                           9999998899999999999999999999998 89999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++.++
T Consensus       156 ~~i~V~~a~pk  166 (167)
T 2cjk_A          156 RKIEIKRAEPR  166 (167)
T ss_dssp             SCEEEEECCCC
T ss_pred             eEEEEeecCCC
Confidence            99999999875

>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=99.42  E-value=4.4e-13  Score=85.87  Aligned_cols=62  Identities=24%  Similarity=0.417  Sum_probs=55.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++++++      +|||||+|.+.++|++|+..|||..++|
T Consensus        32 l~~~F~~~G~i~~---------------------------v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g   78 (99)
T 2cpj_A           32 MRKLFEKYGKAGE---------------------------VFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRG   78 (99)
T ss_dssp             HHHHTSTTCCCSE---------------------------EEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTT
T ss_pred             HHHHHhhcCCeEE---------------------------EEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           888644      6899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++++.....
T Consensus        79 ~~l~v~~a~~~~~~~   93 (99)
T 2cpj_A           79 KQLRVRFACHSASLT   93 (99)
T ss_dssp             BCCEEEESSCCSCCC
T ss_pred             ceEEEEEcCCCCCCC
Confidence            999999998765543

>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=99.42  E-value=1.3e-12  Score=84.39  Aligned_cols=60  Identities=35%  Similarity=0.617  Sum_probs=53.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++        +|||||+|.++++|++|+..|||..++|
T Consensus        28 l~~~F~~~G~i~~---------------------------v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g   72 (103)
T 2dgu_A           28 LEKAFSQFGKLER---------------------------VKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEG   72 (103)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCC
Confidence            7899999999999                           8775        4699999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++++.....
T Consensus        73 ~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           73 ENIEIVFAKPPDQKR   87 (103)
T ss_dssp             EEEEEEECCCCCCCC
T ss_pred             CEEEEEEcCCCcccc
Confidence            999999998665543

>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=99.42  E-value=5.5e-13  Score=87.03  Aligned_cols=59  Identities=27%  Similarity=0.580  Sum_probs=53.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+        ++|||||+|.++++|++|+..|||..++|
T Consensus        45 l~~~F~~~G~v~~---------------------------v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g   89 (110)
T 1wf1_A           45 VETIFSKYGRVAG---------------------------CSV--------HKGYAFVQYSNERHARAAVLGENGRVLAG   89 (110)
T ss_dssp             HHHHHGGGSCCSE---------------------------EEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhCCCeEE---------------------------EEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           877        57999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus        90 ~~l~V~~a~~~~~~  103 (110)
T 1wf1_A           90 QTLDINMAGEPKPD  103 (110)
T ss_dssp             EECCEEESCCCCSC
T ss_pred             eEEEEEECCCCCCC
Confidence            99999999754443

>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=99.42  E-value=6.4e-13  Score=90.66  Aligned_cols=66  Identities=27%  Similarity=0.485  Sum_probs=62.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++++++.+++++|||||+|.++++|++|+..|+|..+.|
T Consensus        20 l~~~f~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g   72 (168)
T 1b7f_A           20 LYALFRAIGPINT---------------------------CRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN   72 (168)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|.++.+...
T Consensus        73 ~~l~v~~~~~~~~   85 (168)
T 1b7f_A           73 KRLKVSYARPGGE   85 (168)
T ss_dssp             EECEEEECCCCSS
T ss_pred             cEEEEEecCCCcc
Confidence            9999999976544

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.42  E-value=4.2e-13  Score=89.29  Aligned_cols=62  Identities=19%  Similarity=0.286  Sum_probs=57.5

Q ss_pred             HHHHhhccCc---ceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQ---VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~---i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|+.||.   |..                           ++|++|+. ++++|||||+|.++++|++||. +||..
T Consensus        34 l~~~F~~~G~~~~v~~---------------------------v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~   84 (118)
T 2db1_A           34 VQNFLSDCTIHDGVAG---------------------------VHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRES   84 (118)
T ss_dssp             HHHHTTTSCBTTGGGG---------------------------EEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEE
T ss_pred             HHHHHHHcCCccCcee---------------------------EEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCe
Confidence            7899999999   788                           99999986 9999999999999999999999 99999


Q ss_pred             eCCeeEEEEeccCC
Q 033734           79 LDGRVIFVDNVRPS   92 (112)
Q Consensus        79 l~g~~i~V~~a~~~   92 (112)
                      ++|+.|.|..+...
T Consensus        85 ~~gr~i~V~~a~~~   98 (118)
T 2db1_A           85 MGHRYIEVFKSHRT   98 (118)
T ss_dssp             ETTEEEEEEEECHH
T ss_pred             ECCeEEEEEECCHH
Confidence            99999999998543

>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=99.42  E-value=1.1e-12  Score=85.78  Aligned_cols=62  Identities=18%  Similarity=0.221  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhh--CCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM--NGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l--~g~~l   79 (112)
                      |+++|++||.|..                           +.++++      +|||||+|.+.++|++|+..|  ++..+
T Consensus        32 L~~~F~~fG~v~~---------------------------v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~   78 (101)
T 2cq1_A           32 VIALGLPFGKVTN---------------------------ILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHL   78 (101)
T ss_dssp             HHHTTTTTSCEEE---------------------------EEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             HHHHHHhcCCEEE---------------------------EEEECC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            7899999999999                           887654      799999999999999999977  46789


Q ss_pred             CCeeEEEEeccCCCCCC
Q 033734           80 DGRVIFVDNVRPSRRYN   96 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~~   96 (112)
                      .|++|.|++++++....
T Consensus        79 ~Gr~l~V~~a~~~~~~~   95 (101)
T 2cq1_A           79 RNQPIYIQYSNHKELKT   95 (101)
T ss_dssp             TTEECEEEECSCSSCCC
T ss_pred             CCcEEEEEEcCcccCcC
Confidence            99999999998765544

>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=99.42  E-value=3.2e-13  Score=88.82  Aligned_cols=61  Identities=21%  Similarity=0.319  Sum_probs=53.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCc--ee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK--LL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~--~l   79 (112)
                      |+++|++||.|.+                           ++|+++      +|||||+|.++++|++|+..||+.  .+
T Consensus        33 L~~lF~~fG~V~~---------------------------v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~   79 (102)
T 1x4d_A           33 LLQLVEPFGVISN---------------------------HLILNK------INEAFIEMATTEDAQAAVDYYTTTPALV   79 (102)
T ss_dssp             HHTTTGGGSCEEE---------------------------EEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceE
Confidence            7899999999999                           888765      389999999999999999999865  49


Q ss_pred             CCeeEEEEeccCCCCC
Q 033734           80 DGRVIFVDNVRPSRRY   95 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~   95 (112)
                      +|++|.|.+++....-
T Consensus        80 ~Gr~l~V~~a~~~~~~   95 (102)
T 1x4d_A           80 FGKPVRVHLSQKYKRI   95 (102)
T ss_dssp             TTEECEEEEECCCTTS
T ss_pred             CCcEEEEEECCCCCCC
Confidence            9999999999865443

>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=99.41  E-value=6.4e-13  Score=106.17  Aligned_cols=66  Identities=24%  Similarity=0.563  Sum_probs=62.1

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+.+|++||.|..                           |.|+.++.+++++|||||+|.++++|++||..|||..|+
T Consensus       118 ~L~~~F~~~G~I~~---------------------------v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~  170 (437)
T 3pgw_S          118 KLRREFEVYGPIKR---------------------------IHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKID  170 (437)
T ss_pred             HHHHHHHHcCCeeE---------------------------EEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEEC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCC
Q 033734           81 GRVIFVDNVRPSR   93 (112)
Q Consensus        81 g~~i~V~~a~~~~   93 (112)
                      |+.|.|.++.+..
T Consensus       171 gr~i~V~~a~~~~  183 (437)
T 3pgw_S          171 GRRVLVDVERGRT  183 (437)
T ss_pred             CEEEEEEEeCCCC
Confidence            9999999997543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.41  E-value=6.1e-14  Score=90.10  Aligned_cols=64  Identities=23%  Similarity=0.383  Sum_probs=55.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                            .++.++.+++++|||||+|.+.++|++|+. |||..++|
T Consensus        34 l~~~F~~~G~v~~----------------------------~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g   84 (101)
T 1fj7_A           34 LKVAISELFAKND----------------------------LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG   84 (101)
T ss_dssp             HHHHHHHHHHHHT----------------------------CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTT
T ss_pred             HHHHHHHhCCcce----------------------------EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECC
Confidence            7889999998866                            234555678999999999999999999999 99999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++++++..
T Consensus        85 ~~l~V~~a~~~~~   97 (101)
T 1fj7_A           85 NEIKLEKPKGRDG   97 (101)
T ss_dssp             BCCEEECCSCCCC
T ss_pred             cEEEEEEcCCCCC
Confidence            9999999986544

>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=99.40  E-value=1.2e-13  Score=92.26  Aligned_cols=63  Identities=22%  Similarity=0.392  Sum_probs=58.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|..                           +.++.+..+++++|||||+|.+.++|++||. |||..++|
T Consensus        42 l~~~F~~~G~v~~---------------------------~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g   93 (124)
T 1wel_A           42 VIDFFKKLDIVED---------------------------SIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN   93 (124)
T ss_dssp             HHHHSCSSCBCTT---------------------------TCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT
T ss_pred             HHHHHHhcCCccc---------------------------eEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECC
Confidence            7899999999988                           7777888899999999999999999999999 99999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.++.+.
T Consensus        94 r~i~V~~a~~~  104 (124)
T 1wel_A           94 RFIQVHPITKK  104 (124)
T ss_dssp             SCBEEEEECHH
T ss_pred             cEEEEEECCHH
Confidence            99999998653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=5.4e-13  Score=88.43  Aligned_cols=61  Identities=20%  Similarity=0.310  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCC--cee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG--KLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g--~~l   79 (112)
                      |+++|++||.|.+                           ++|+++      +|||||+|.++++|++|+..|++  ..+
T Consensus        33 L~~lF~~fG~V~~---------------------------v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l   79 (105)
T 1sjq_A           33 VISLGLPFGKVTN---------------------------LLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVL   79 (105)
T ss_dssp             HHHHHHHHCCEEE---------------------------EEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEE
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            7899999999999                           998865      69999999999999999998864  789


Q ss_pred             CCeeEEEEeccCCCCC
Q 033734           80 DGRVIFVDNVRPSRRY   95 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~   95 (112)
                      +|++|.|++++++...
T Consensus        80 ~Gr~l~V~~A~~~~~~   95 (105)
T 1sjq_A           80 RGQPIYIQFSNHKELK   95 (105)
T ss_dssp             TTEECCBCCCSSSSCC
T ss_pred             CCEEEEEEEcCCCCCC
Confidence            9999999999765544

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.40  E-value=4.1e-13  Score=85.33  Aligned_cols=61  Identities=25%  Similarity=0.431  Sum_probs=53.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +     ..+++++|||||+|.++++|++|+..|||..++|
T Consensus        33 l~~~F~~~g~v~~---------------------------~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   80 (96)
T 1fjc_A           33 LKEVFEDALEIRL---------------------------V-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             HHHHHCSEEEECC---------------------------E-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             HHHHHhhCCcEEE---------------------------e-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            6788999988766                           4     2378899999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.++..
T Consensus        81 ~~l~v~~a~~~~~   93 (96)
T 1fjc_A           81 RSVSLYYTGEKGG   93 (96)
T ss_dssp             EEEEEEECSSSCC
T ss_pred             eEEEEEEcCCCCC
Confidence            9999999977554

>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=99.40  E-value=2.4e-13  Score=86.42  Aligned_cols=62  Identities=23%  Similarity=0.387  Sum_probs=55.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|++||.|..                           +.++.   ++.++|||||+|.+.++|++|+..|||..++|
T Consensus        29 l~~~f~~~G~i~~---------------------------v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (97)
T 1nu4_A           29 LHAIFSRFGQILD---------------------------ILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   78 (97)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            4499999999999                           77753   57789999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++++..
T Consensus        79 ~~l~v~~a~~~~   90 (97)
T 1nu4_A           79 KPMRIQYAKTDS   90 (97)
T ss_dssp             EECEEEECSSCC
T ss_pred             cEEEEEEccCCC
Confidence            999999998654

>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=99.40  E-value=2.2e-13  Score=92.65  Aligned_cols=72  Identities=25%  Similarity=0.427  Sum_probs=55.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..+.+.                   .+..+++   ..+++++|||||+|.+.++|++|+..|||..++|
T Consensus        62 L~~~F~~~G~i~~~~~~-------------------~~~di~~---~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           62 LKYIFGRYVDFSSETQR-------------------IMFDIRL---MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             HHHHHGGGCCTTCHHHH-------------------HHCEEEE---EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             HHHHHHHhCCccccccc-------------------ceeeEEe---ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            78899999998761000                   0000222   2378999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++...+
T Consensus       120 ~~l~V~~a~~~~~~  133 (143)
T 3egn_A          120 KPMVVQFARSARPK  133 (143)
T ss_dssp             EECEEEECCCSCC-
T ss_pred             cEEEEEECCCCCCc
Confidence            99999999876544

>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=99.39  E-value=8.5e-13  Score=83.52  Aligned_cols=62  Identities=19%  Similarity=0.377  Sum_probs=52.6

Q ss_pred             HHHHhhccCc-ceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCC-cee
Q 033734            2 LADAFSQFGQ-VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG-KLL   79 (112)
Q Consensus         2 l~~~f~~~G~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g-~~l   79 (112)
                      |+++|++||. |..                           +.+       .++|||||+|.++++|++|+..||| ..+
T Consensus        25 l~~~F~~~G~vv~~---------------------------~~~-------~~~g~afV~f~~~~~A~~A~~~l~g~~~~   70 (93)
T 2cqh_A           25 LRQLFGDRKLPLAG---------------------------QVL-------LKSGYAFVDYPDQNWAIRAIETLSGKVEL   70 (93)
T ss_dssp             HHHHHHHTTCCCSS---------------------------CEE-------EETTEEEECCSCHHHHHHHHHHHTTTCEE
T ss_pred             HHHHHHHcCCceEE---------------------------EEE-------cCCCEEEEEECCHHHHHHHHHHccCCeeE
Confidence            7899999999 444                           443       2479999999999999999999999 999


Q ss_pred             CCeeEEEEeccCCCCCCC
Q 033734           80 DGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~~~   97 (112)
                      +|+.|.|+++++...+..
T Consensus        71 ~g~~l~v~~a~~~~~~~~   88 (93)
T 2cqh_A           71 HGKIMEVDYSVSKKLRSS   88 (93)
T ss_dssp             TTEECEEEECCCCCCCCC
T ss_pred             CCEEEEEEEccCccccCC
Confidence            999999999987655443

>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=99.39  E-value=4.3e-13  Score=92.17  Aligned_cols=61  Identities=18%  Similarity=0.269  Sum_probs=57.3

Q ss_pred             HHHHhhccCc---ceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQ---VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~---i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|++||.   |..                           ++|++|+. |+++|||||+|.++++|++||. +||..
T Consensus        61 L~~~F~~~G~v~~v~~---------------------------v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~  111 (136)
T 2hgl_A           61 VQNFLSDCTIHDGAAG---------------------------VHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRES  111 (136)
T ss_dssp             HHHHTTTCCCSSSSTT---------------------------EEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEE
T ss_pred             HHHHHHHhCCcCceeE---------------------------EEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCE
Confidence            7899999999   788                           99999986 9999999999999999999999 99999


Q ss_pred             eCCeeEEEEeccC
Q 033734           79 LDGRVIFVDNVRP   91 (112)
Q Consensus        79 l~g~~i~V~~a~~   91 (112)
                      ++|+.|.|..+.+
T Consensus       112 l~gr~i~V~~a~~  124 (136)
T 2hgl_A          112 MGHRYIEVFKSHR  124 (136)
T ss_dssp             SSSSEEEEEECCH
T ss_pred             ECCEEEEEEECCh
Confidence            9999999999854

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.39  E-value=8.6e-13  Score=94.94  Aligned_cols=62  Identities=44%  Similarity=0.820  Sum_probs=57.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|++|.  +.++|||||+|.++++|++|+..|||..++|
T Consensus       120 l~~~F~~~G~i~~---------------------------~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g  170 (213)
T 4f02_A          120 LYDTFSAFGNILS---------------------------CKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLND  170 (213)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhhcCCeEE---------------------------EEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999995  4589999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++.++
T Consensus       171 ~~i~V~~a~~~  181 (213)
T 4f02_A          171 RKVFVGRFKSR  181 (213)
T ss_dssp             EECEEEECCCH
T ss_pred             EEEEEEEcCCC
Confidence            99999999754

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=2.3e-12  Score=82.51  Aligned_cols=61  Identities=31%  Similarity=0.574  Sum_probs=53.4

Q ss_pred             HHHHhhcc--CcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQF--GQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~--G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++|  |.|.+                           +++        .+|||||+|.+.++|++|+..|||..+
T Consensus        32 l~~~F~~~g~g~v~~---------------------------~~~--------~~g~afV~f~~~~~A~~A~~~l~g~~~   76 (99)
T 2cpd_A           32 IEKEFNNIKPGAVER---------------------------VKK--------IRDYAFVHFSNREDAVEAMKALNGKVL   76 (99)
T ss_dssp             HHHHHHTTSTTCEEE---------------------------EEE--------CSSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             HHHHHHhcCCcceEE---------------------------EEE--------eCCeEEEEeCCHHHHHHHHHHhCCCEe
Confidence            78999999  88888                           665        367999999999999999999999999


Q ss_pred             CCeeEEEEeccCCCCCCC
Q 033734           80 DGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~~~   97 (112)
                      +|+.|.|+++++..+...
T Consensus        77 ~g~~l~v~~a~~~~~~~~   94 (99)
T 2cpd_A           77 DGSPIEVTLAKPVDKDSS   94 (99)
T ss_dssp             TTEEEEEECCCCCCCCCC
T ss_pred             CCcEEEEEECCCCCCCCC
Confidence            999999999987655433

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.39  E-value=1.8e-12  Score=93.28  Aligned_cols=64  Identities=28%  Similarity=0.438  Sum_probs=60.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           |+|++|+.+++++|||||+|.++++|++|+..+|+..+.|
T Consensus        32 L~~~F~~~G~I~~---------------------------v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g   84 (213)
T 4f02_A           32 LYEKFSPAGPILS---------------------------IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG   84 (213)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhhCCEEE---------------------------EEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.+++..+...
T Consensus        85 ~~i~~~~~~~~   95 (213)
T 4f02_A           85 KPVRIMWSQRD   95 (213)
T ss_dssp             EECEEEECCCC
T ss_pred             ccccccccccc
Confidence            99999988644

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.38  E-value=6.2e-13  Score=88.52  Aligned_cols=60  Identities=25%  Similarity=0.284  Sum_probs=53.1

Q ss_pred             HHHHhhccC-cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFG-QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| .|..                           +.+..    +.++|||||+|.+.++|++||..|||..++
T Consensus        45 L~~~F~~~G~~v~~---------------------------v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~   93 (111)
T 2jvr_A           45 LKDLARENSLETTF---------------------------SSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFR   93 (111)
T ss_dssp             HHHHHHHHTCCCSE---------------------------EECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEET
T ss_pred             HHHHHHHhCCeeEE---------------------------EEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            789999999 8888                           77643    348899999999999999999999999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|.|++++..
T Consensus        94 Gr~i~V~~a~~~  105 (111)
T 2jvr_A           94 GSVITVERDDNP  105 (111)
T ss_dssp             TEEEEEEESCC-
T ss_pred             CeEEEEEECCCC
Confidence            999999998754

>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=99.38  E-value=1.2e-12  Score=89.36  Aligned_cols=61  Identities=28%  Similarity=0.551  Sum_probs=58.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+++++.+++++|+|||+|.+.++|.+|+..|||..++|
T Consensus       106 l~~~f~~~G~i~~---------------------------~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A          106 LDTIFGKYGSIVQ---------------------------KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG  158 (168)
T ss_dssp             HHHHHTSSSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             HHHhhhcCCcEEE---------------------------EEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecC
Confidence            7899999999999                           9999999899999999999999999999999999999987


Q ss_pred             --eeEEEEec
Q 033734           82 --RVIFVDNV   89 (112)
Q Consensus        82 --~~i~V~~a   89 (112)
                        ++|.|++|
T Consensus       159 ~~~~l~V~~A  168 (168)
T 1b7f_A          159 GSQPLSVRLA  168 (168)
T ss_dssp             CSSCCEEEEC
T ss_pred             CCeEEEEEeC
Confidence              99999875

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.38  E-value=1.4e-12  Score=85.53  Aligned_cols=59  Identities=27%  Similarity=0.535  Sum_probs=53.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++        +|||||+|.+.++|++|+..|||..++|
T Consensus        48 L~~~F~~~G~i~~---------------------------v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (108)
T 2jvo_A           48 LNEIFGPFGPMKE---------------------------VKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFAN   92 (108)
T ss_dssp             HHHHHTTTSCCCE---------------------------EEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           8876        7999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++...+
T Consensus        93 ~~l~V~~a~~~~~r  106 (108)
T 2jvo_A           93 QPLEVVYSKLPAKR  106 (108)
T ss_dssp             EECEEESCSCCC--
T ss_pred             eEEEEEEecCCCCC
Confidence            99999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.38  E-value=3.6e-12  Score=86.38  Aligned_cols=65  Identities=25%  Similarity=0.496  Sum_probs=59.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++++++ +++++|||||+|.++++|++|+..|||..+.|
T Consensus        17 l~~~f~~~G~i~~---------------------------v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g   68 (166)
T 3md3_A           17 LKQYFQVGGPIAN---------------------------IKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIEN   68 (166)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCC
Confidence            7899999999999                           9999997 57899999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|.++.+...
T Consensus        69 ~~i~v~~~~~~~~   81 (166)
T 3md3_A           69 NIVKINWAFQSQQ   81 (166)
T ss_dssp             EECEEEECCCCCC
T ss_pred             CeeEEEEcCCCCC
Confidence            9999999976544

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.38  E-value=2.1e-12  Score=81.37  Aligned_cols=60  Identities=30%  Similarity=0.546  Sum_probs=53.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++        +|||||+|.++++|++|+..|||..++|
T Consensus        26 l~~~F~~~G~v~~---------------------------~~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g   70 (90)
T 2dnp_A           26 LRSLFERRGRVIE---------------------------CDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKG   70 (90)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHcCCCEEE---------------------------EEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           8875        3499999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCC
Q 033734           82 RVIFVDNVRPSRRYN   96 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~   96 (112)
                      +.|.|+++++.....
T Consensus        71 ~~l~v~~a~~~~~~~   85 (90)
T 2dnp_A           71 KRINVELSTKGQKKS   85 (90)
T ss_dssp             EECEEEESCCCCCCC
T ss_pred             cEEEEEECCCCCCCC
Confidence            999999998765443

>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=99.38  E-value=8e-13  Score=90.52  Aligned_cols=60  Identities=22%  Similarity=0.465  Sum_probs=55.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++++.+     ++|||||+|.+.++|++|+..|||..++|
T Consensus        90 l~~~F~~~G~i~~---------------------------v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g  137 (150)
T 2i2y_A           90 LERAFGYYGPLRS---------------------------VWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCG  137 (150)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSS
T ss_pred             HHHHHHhhCCEEE---------------------------EEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           988776     68999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++++++
T Consensus       138 ~~l~v~~a~~~~  149 (150)
T 2i2y_A          138 CRVRVELSNGEK  149 (150)
T ss_dssp             SCCEEEECCCCC
T ss_pred             eEEEEEEcCCCC
Confidence            999999998754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.38  E-value=4.7e-13  Score=86.02  Aligned_cols=63  Identities=27%  Similarity=0.525  Sum_probs=58.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.|+ +++++|||||+|.+.++|++|+.  ++..++|
T Consensus        26 l~~~F~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g   75 (102)
T 2xs2_A           26 IRSFFARYGSVKE---------------------------VKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHG   75 (102)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETT
T ss_pred             HHHHHHhCCCeEE---------------------------EEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECC
Confidence            7899999999999                           9999998 99999999999999999999998  9999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|..+.+...
T Consensus        76 ~~l~v~~a~~~~~   88 (102)
T 2xs2_A           76 KKLKLGPAIRKQN   88 (102)
T ss_dssp             EECEEEEEEECC-
T ss_pred             EEEEEEECCcCcc
Confidence            9999999875543

>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=99.38  E-value=1.2e-12  Score=84.97  Aligned_cols=64  Identities=27%  Similarity=0.355  Sum_probs=56.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                          .++|+.+ .+++++|||||+|.++++|++||.. |+..++|
T Consensus        32 l~~~F~~~G~v~~--------------------------~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~g   83 (104)
T 1wg5_A           32 IVQFFSGLEIVPN--------------------------GMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGH   83 (104)
T ss_dssp             HHHHTTTCCEEEE--------------------------EEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSS
T ss_pred             HHHHHHhcCCcce--------------------------eEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCC
Confidence            7899999999874                          1667788 6899999999999999999999997 9999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|..+.+..
T Consensus        84 r~i~v~~~~~~~   95 (104)
T 1wg5_A           84 RYIEIFKSSRAE   95 (104)
T ss_dssp             SCCEEEEECTTT
T ss_pred             cEEEEEECCHHH
Confidence            999999986543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.37  E-value=8e-13  Score=93.93  Aligned_cols=63  Identities=30%  Similarity=0.501  Sum_probs=59.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           |.|+.++ ++.++|||||+|.+.++|++|+..|||..++|
T Consensus       105 L~~~F~~~G~I~~---------------------------v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~G  156 (177)
T 2f3j_A          105 IQELFAEFGTLKK---------------------------AAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDG  156 (177)
T ss_dssp             HHHHHHHTSCCSE---------------------------EEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999998 99999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++...
T Consensus       157 r~l~V~~a~~~  167 (177)
T 2f3j_A          157 RPMDIQLVASQ  167 (177)
T ss_dssp             SBCEEEEESSG
T ss_pred             EEEEEEEecCC
Confidence            99999999754

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=1.6e-12  Score=86.14  Aligned_cols=60  Identities=25%  Similarity=0.377  Sum_probs=55.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++| .|.+                           ++|++|+. |+++|||||+|.++++|++|| .+|+..++|
T Consensus        33 l~~~F~~~-~v~~---------------------------v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g   82 (109)
T 2dnn_A           33 VRDFFHGL-RVDA---------------------------VHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQ   82 (109)
T ss_dssp             HHHHTTTS-CCCE---------------------------EEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETT
T ss_pred             HHHHhccC-CeeE---------------------------EEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECC
Confidence            78899999 7888                           99999985 999999999999999999999 599999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|..+.+
T Consensus        83 r~i~V~~a~~   92 (109)
T 2dnn_A           83 RYVEVSPATE   92 (109)
T ss_dssp             EEEEEEECCH
T ss_pred             eEEEEEECCc
Confidence            9999988864

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.37  E-value=9.3e-13  Score=84.50  Aligned_cols=57  Identities=19%  Similarity=0.330  Sum_probs=52.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +++.      +++|||||+|.+.++|++|+..|||..++|
T Consensus        44 l~~~f~~~G~i~~---------------------------~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   90 (101)
T 2la4_A           44 LIPLFQNFGFILD---------------------------FKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQG   90 (101)
T ss_dssp             HHHHHHTTSCCSE---------------------------EEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            7899999999999                           8876      467999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|+++++
T Consensus        91 ~~l~V~~a~~  100 (101)
T 2la4_A           91 RNLRTGWGKE  100 (101)
T ss_dssp             EECCCCBCCC
T ss_pred             eEEEEEeccC
Confidence            9999999875

>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=99.37  E-value=2.7e-12  Score=82.53  Aligned_cols=57  Identities=16%  Similarity=0.448  Sum_probs=52.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +++        ++|||||+|.+.++|++|+..|||..++|
T Consensus        40 L~~~F~~~G~v~~---------------------------v~i--------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (97)
T 2xnq_A           40 LFRIFSPYGHIMQ---------------------------INI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFG   84 (97)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEE--------CSSEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           777        37999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++++..
T Consensus        85 ~~l~V~~a~~~~   96 (97)
T 2xnq_A           85 KKLILEVSSSNA   96 (97)
T ss_dssp             EECEEEECCCCC
T ss_pred             EEEEEEecCCCC
Confidence            999999997643

>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=99.37  E-value=1.7e-12  Score=88.14  Aligned_cols=61  Identities=31%  Similarity=0.577  Sum_probs=56.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+|.++|||||+|.+.++|++|+..|||..++|
T Consensus       105 l~~~f~~~G~i~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  157 (167)
T 1fxl_A          105 LEQLFSQYGRIIT---------------------------SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG  157 (167)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             HHHHHHhcCCEeE---------------------------EEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             ee--EEEEec
Q 033734           82 RV--IFVDNV   89 (112)
Q Consensus        82 ~~--i~V~~a   89 (112)
                      +.  |.|++|
T Consensus       158 ~~~~i~v~~A  167 (167)
T 1fxl_A          158 ATEPITVKFA  167 (167)
T ss_dssp             CSSCCEEEEC
T ss_pred             CccceEEEeC
Confidence            65  777765

>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=99.37  E-value=1.5e-12  Score=85.52  Aligned_cols=61  Identities=18%  Similarity=0.279  Sum_probs=53.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce--e
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL--L   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~--l   79 (112)
                      |+++|++||.|..                           +.|+++      +|||||+|.++++|++|+..|++..  +
T Consensus        32 L~~~F~~fG~V~~---------------------------v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i   78 (104)
T 1wex_A           32 LVEALEKFGTICY---------------------------VMMMPF------KRQALVEFENIDSAKECVTFAADVPVYI   78 (104)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBS
T ss_pred             HHHHHHhCCCEEE---------------------------EEEECC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            7899999999999                           887653      6999999999999999999987654  8


Q ss_pred             CCeeEEEEeccCCCCC
Q 033734           80 DGRVIFVDNVRPSRRY   95 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~   95 (112)
                      +|++|.|++++++...
T Consensus        79 ~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           79 AGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             SSSBCEEEECSSSSCC
T ss_pred             CCEEEEEEEccCcccc
Confidence            9999999999876544

>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=99.37  E-value=4.8e-13  Score=88.13  Aligned_cols=59  Identities=17%  Similarity=0.219  Sum_probs=53.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +.|+.      ++|||||+|.+.++|++|+..|||..++|
T Consensus        27 L~~~F~~~G~i~~---------------------------v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   73 (111)
T 1whx_A           27 IQETFSRFGSLGR---------------------------VLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHH   73 (111)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            7899999999998                           77653      57899999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|+++....
T Consensus        74 ~~l~V~~a~~~~   85 (111)
T 1whx_A           74 VPLYLEWAPIGV   85 (111)
T ss_dssp             SBCEEEEEETTT
T ss_pred             eEEEEEECCCCc
Confidence            999999997543

>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=99.37  E-value=1.2e-12  Score=85.84  Aligned_cols=63  Identities=19%  Similarity=0.377  Sum_probs=56.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.+   +.++|||||+|.+.++|++|+..|||..++|
T Consensus        25 l~~~F~~~G~v~~---------------------------v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   74 (115)
T 3lqv_A           25 MYDIFGKYGPIRQ---------------------------IRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSN   74 (115)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           988876   4459999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+...
T Consensus        75 ~~l~v~~a~~~~~   87 (115)
T 3lqv_A           75 RYLVVLYYNANRA   87 (115)
T ss_dssp             CBCEEEECCHHHH
T ss_pred             eEEEEEEecCChh
Confidence            9999999975443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.37  E-value=1.2e-12  Score=83.70  Aligned_cols=59  Identities=17%  Similarity=0.409  Sum_probs=53.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+.        +|||||+|.+.++|++|+..|||..+.|
T Consensus        28 l~~~F~~~G~v~~---------------------------v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g   72 (96)
T 2kvi_A           28 LFRIFSPYGHIMQ---------------------------INIK--------NAFGFIQFDNPQSVRDAIECESQEMNFG   72 (96)
T ss_dssp             HHHHHTTTCCCCE---------------------------EEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            7899999999999                           8773        7899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++++....
T Consensus        73 ~~l~V~~a~~~~~~   86 (96)
T 2kvi_A           73 KKLILEVSSSNARP   86 (96)
T ss_dssp             TTBCEEEEECCCC-
T ss_pred             cEEEEEEcCcCCCC
Confidence            99999999765543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=3.1e-12  Score=83.81  Aligned_cols=60  Identities=17%  Similarity=0.218  Sum_probs=52.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +.|+     ++++|||||+|.++++|+.|+..++  .+.+
T Consensus        34 L~~~F~~~G~V~~---------------------------v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g   79 (100)
T 2d9o_A           34 LLRLLQKYGEVLN---------------------------LVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVD   79 (100)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCC
Confidence            7899999999999                           8886     4689999999999999999999854  4689


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|+++++....
T Consensus        80 ~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           80 NPLKISWLEGQPQD   93 (100)
T ss_dssp             SBCEEECSSCCCCC
T ss_pred             CeEEEEEccCCCCC
Confidence            99999999766543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.36  E-value=2e-12  Score=85.04  Aligned_cols=58  Identities=21%  Similarity=0.322  Sum_probs=52.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce--e
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL--L   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~--l   79 (112)
                      |+++|++||+|..                           +++++      .||+|||+|.+.++|++|+..|+|..  +
T Consensus        38 L~~lF~~fG~V~~---------------------------v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i   84 (100)
T 3r27_A           38 LVEALQEFGPISY---------------------------VVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYI   84 (100)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEE
T ss_pred             HHHHHhccCCEEE---------------------------EEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCcee
Confidence            7899999999999                           88864      46899999999999999999999886  7


Q ss_pred             CCeeEEEEeccCC
Q 033734           80 DGRVIFVDNVRPS   92 (112)
Q Consensus        80 ~g~~i~V~~a~~~   92 (112)
                      .|++|.|.+|+++
T Consensus        85 ~Gr~i~V~~S~~k   97 (100)
T 3r27_A           85 AGHPAFVNYSTSQ   97 (100)
T ss_dssp             TTEEEEEEECSCS
T ss_pred             CCcEEEEEecccc
Confidence            8999999999764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=2.6e-12  Score=81.66  Aligned_cols=61  Identities=23%  Similarity=0.333  Sum_probs=53.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +  +.++.+++   ||||+|.++++|++|+. |||..++|
T Consensus        25 l~~~F~~~G~v~~---------------------------v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g   71 (94)
T 2e5g_A           25 LSEYFLAFGPVAS---------------------------V--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGG   71 (94)
T ss_dssp             HHHHGGGTSCEEE---------------------------E--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------E--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECC
Confidence            7899999999988                           6  66766666   99999999999999999 99999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|+++.++...
T Consensus        72 ~~l~V~~a~~~~~~   85 (94)
T 2e5g_A           72 HRLRVRPREQKEFQ   85 (94)
T ss_dssp             EECCCBCSCCSCCC
T ss_pred             EEEEEEECCcCCCC
Confidence            99999988655443

>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=99.35  E-value=2.7e-12  Score=86.68  Aligned_cols=62  Identities=19%  Similarity=0.307  Sum_probs=54.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCC--cee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG--KLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g--~~l   79 (112)
                      |+++|++||.|.+                           ++|+++      +|||||+|.+.++|++|+..|++  ..+
T Consensus        48 L~~lF~~fG~V~~---------------------------v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l   94 (119)
T 2ad9_A           48 VISLGLPFGKVTN---------------------------LLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVL   94 (119)
T ss_dssp             HHHHHTTTSCCCE---------------------------EEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCB
T ss_pred             HHHHHHhcCCEEE---------------------------EEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            7899999999999                           988876      69999999999999999999884  579


Q ss_pred             CCeeEEEEeccCCCCCC
Q 033734           80 DGRVIFVDNVRPSRRYN   96 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~~   96 (112)
                      .|++|.|++++++....
T Consensus        95 ~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           95 RGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             TTBCCEEEECSSSSCCC
T ss_pred             CCeEEEEEEccCCCCCc
Confidence            99999999998665543

>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=99.35  E-value=3.7e-13  Score=87.81  Aligned_cols=62  Identities=16%  Similarity=0.314  Sum_probs=57.3

Q ss_pred             HHHHhhccCc---ceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQ---VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~---i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|+.||.   |..                           ++|++|+. |+++|||||+|.+.++|++||. +|+..
T Consensus        28 l~~~F~~~g~~~~v~~---------------------------v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~   78 (107)
T 2lmi_A           28 VLNFFSDCRIRNGENG---------------------------IHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMY   78 (107)
T ss_dssp             HHHHTTTSCBTTTTTT---------------------------EECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCC
T ss_pred             HHHHHHhcCCcCCcce---------------------------EEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcce
Confidence            7889999888   888                           99999986 9999999999999999999999 99999


Q ss_pred             eCCeeEEEEeccCC
Q 033734           79 LDGRVIFVDNVRPS   92 (112)
Q Consensus        79 l~g~~i~V~~a~~~   92 (112)
                      ++|+.|.|..+.+.
T Consensus        79 ~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           79 MGQRYVEVYEINNE   92 (107)
T ss_dssp             SSSSCCCCEECCHH
T ss_pred             eCCeEEEEEECCHH
Confidence            99999999998653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.35  E-value=2e-12  Score=82.65  Aligned_cols=61  Identities=20%  Similarity=0.323  Sum_probs=52.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                            .++.+    +++|||||+|.++++|++|+..|||..++|
T Consensus        36 l~~~F~~~G~v~~----------------------------~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   83 (97)
T 2e5j_A           36 LKRALRELGSVPL----------------------------RLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGT   83 (97)
T ss_dssp             HHHHHHHTTCCCS----------------------------EEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSS
T ss_pred             HHHHHHhcCCEEE----------------------------EEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7889999999832                            34433    688999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++++++.+
T Consensus        84 ~~l~V~~a~~~~~   96 (97)
T 2e5j_A           84 DTLRVALARQQRD   96 (97)
T ss_dssp             SCCEEEECCCCCC
T ss_pred             cEEEEEEcCCCCC
Confidence            9999999987643

>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=99.34  E-value=3.1e-12  Score=79.39  Aligned_cols=56  Identities=27%  Similarity=0.474  Sum_probs=51.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhh-CCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM-NGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l-~g~~l~   80 (112)
                      |+++|++||.|..                           ++++++      +|||||+|.+.++|++|+..| +|..++
T Consensus        29 l~~~f~~~G~i~~---------------------------~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~   75 (85)
T 2ytc_A           29 LRNHFYQFGEIRT---------------------------ITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVN   75 (85)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEET
T ss_pred             HHHHHHhCCCEeE---------------------------EEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeEC
Confidence            7899999999999                           888764      689999999999999999999 999999


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      |+.|.|++++
T Consensus        76 g~~l~v~~ak   85 (85)
T 2ytc_A           76 GRRLNVKWGR   85 (85)
T ss_dssp             TEECCEEECC
T ss_pred             CCEEEEEecC
Confidence            9999999874

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.34  E-value=5.7e-12  Score=86.38  Aligned_cols=60  Identities=18%  Similarity=0.337  Sum_probs=54.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccE-EEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGY-GYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~-afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||+|.+                           ++++.+     .+|+ |||+|.+.++|++|+..|||..+.
T Consensus        45 L~~lFs~yG~V~~---------------------------V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~   92 (130)
T 3zzy_A           45 LHQIFSKFGTVLK---------------------------IITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIY   92 (130)
T ss_dssp             HHHHHTTSSCEEE---------------------------EEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEE
T ss_pred             HHHHHhCcCCEEE---------------------------EEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeec
Confidence            7899999999999                           887764     2577 999999999999999999999998


Q ss_pred             C--eeEEEEeccCCC
Q 033734           81 G--RVIFVDNVRPSR   93 (112)
Q Consensus        81 g--~~i~V~~a~~~~   93 (112)
                      |  +.|+|+++++..
T Consensus        93 g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           93 NACCTLRIDFSKLTS  107 (130)
T ss_dssp             TTEEEEEEEECSCSS
T ss_pred             CCCcEEEEEecCCCc
Confidence            8  899999998654

>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=99.34  E-value=2.2e-12  Score=86.34  Aligned_cols=58  Identities=19%  Similarity=0.331  Sum_probs=53.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +.|.++.    ++|++||+|.++++|++|+..|||+.++|
T Consensus        34 l~~~f~kfG~V~~---------------------------v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A           34 VIEECNKHGGVIH---------------------------IYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             HHHHHTTTTCCSE---------------------------EEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhccCCEEE---------------------------EEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            6889999999999                           8886553    58999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|.|.++.
T Consensus        83 R~i~v~~~~   91 (114)
T 3s6e_A           83 KMITAAYVP   91 (114)
T ss_dssp             EECEEEEEC
T ss_pred             EEEEEEEEc
Confidence            999999985

>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=99.34  E-value=5e-12  Score=88.27  Aligned_cols=65  Identities=31%  Similarity=0.581  Sum_probs=58.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+++++.++.++|||||+|.++++|++|+.. ++..++|
T Consensus        30 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g   81 (196)
T 1l3k_A           30 LRSHFEQWGTLTD---------------------------CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDG   81 (196)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECC
Confidence            7899999999999                           99999999999999999999999999999985 8999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|.++.+...
T Consensus        82 ~~l~v~~~~~~~~   94 (196)
T 1l3k_A           82 RVVEPKRAVSRED   94 (196)
T ss_dssp             EECEEEECCC---
T ss_pred             EEeeeecccCccc
Confidence            9999999875543

>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=99.33  E-value=3.9e-12  Score=84.11  Aligned_cols=58  Identities=26%  Similarity=0.357  Sum_probs=50.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.|+.+       |||||+|.++++|++||..|||..++|
T Consensus        33 l~~~F~~~G~v~~---------------------------~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g   78 (115)
T 3beg_B           33 LKDHMREAGDVCY---------------------------ADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRS   78 (115)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCC
T ss_pred             HHHHHHhcCCeEE---------------------------EEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           888766       899999999999999999999999999


Q ss_pred             ee-----EEEEeccCCC
Q 033734           82 RV-----IFVDNVRPSR   93 (112)
Q Consensus        82 ~~-----i~V~~a~~~~   93 (112)
                      +.     |+|..+.+..
T Consensus        79 r~~~~~~i~v~~~~~~~   95 (115)
T 3beg_B           79 HEGETAYIRVKVDGPRS   95 (115)
T ss_dssp             TTSCCCBCEEEECC---
T ss_pred             cEeeeEEEEeccCCCCC
Confidence            98     7777765543

>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=99.32  E-value=4e-13  Score=92.70  Aligned_cols=64  Identities=22%  Similarity=0.208  Sum_probs=57.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++|| |+.                           ++|++|+. ++++|||||+|.++++|++|| .+|+..++|
T Consensus        63 L~~~F~~~G-i~~---------------------------v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~g  112 (139)
T 2hgn_A           63 IYNFFSPLN-PVR---------------------------VHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQH  112 (139)
T ss_dssp             HHHHHCSCC-CSE---------------------------EECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSS
T ss_pred             HHHHHHhcC-CeE---------------------------EEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECC
Confidence            789999999 668                           99999985 999999999999999999999 799999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|..+.+....
T Consensus       113 R~i~V~~a~~~~~~  126 (139)
T 2hgn_A          113 RYIELFLNSTTGAS  126 (139)
T ss_dssp             CCCCCEECCCSCC-
T ss_pred             EEEEEEECCCCCCC
Confidence            99999998765543

>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=99.32  E-value=2.8e-12  Score=85.80  Aligned_cols=61  Identities=15%  Similarity=0.284  Sum_probs=52.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCC--cee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNG--KLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g--~~l   79 (112)
                      |+++|++||.|.+                           ++|++      ++|||||+|.+.++|++|+..|++  ..+
T Consensus        43 L~~lF~~fG~V~~---------------------------v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l   89 (112)
T 1x4f_A           43 VLKLAEPYGKIKN---------------------------YILMR------MKSQAFIEMETREDAMAMVDHCLKKALWF   89 (112)
T ss_dssp             HHTTTTTTSCCSE---------------------------EEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEec------CCCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            7889999999999                           88863      479999999999999999998864  559


Q ss_pred             CCeeEEEEeccCCCCC
Q 033734           80 DGRVIFVDNVRPSRRY   95 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~   95 (112)
                      +|++|.|++++.....
T Consensus        90 ~Gr~l~V~~a~~~~~~  105 (112)
T 1x4f_A           90 QGRCVKVDLSEKYKKL  105 (112)
T ss_dssp             SSSCCEEEEECSCSSS
T ss_pred             CCEEEEEEECcccccc
Confidence            9999999999765443

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.32  E-value=3.6e-12  Score=90.27  Aligned_cols=64  Identities=31%  Similarity=0.501  Sum_probs=57.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|..                           +++++++.+++++|||||+|.++++|++|+..|||..+.|
T Consensus        45 l~~~f~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g   97 (216)
T 2qfj_A           45 IRQAFAPFGPIKS---------------------------IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG   97 (216)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-
T ss_pred             HHHHHHhCCCEEE---------------------------EEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCC
Confidence            7899999999999                           9999999899999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.++...
T Consensus        98 ~~l~v~~~~~~  108 (216)
T 2qfj_A           98 RNIKVGRPSNI  108 (216)
T ss_dssp             CCCEEECCSCC
T ss_pred             eeEEEecCCCc
Confidence            99999887543

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.31  E-value=3.9e-12  Score=94.57  Aligned_cols=63  Identities=25%  Similarity=0.439  Sum_probs=57.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKG-KNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~-t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||.|..                           ++++.+.. |+.++|||||+|.++++|.+|+ .|||..++
T Consensus       228 l~~~F~~~G~v~~---------------------------v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~  279 (292)
T 2ghp_A          228 LRESFEGFGSIEK---------------------------INIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLG  279 (292)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEET
T ss_pred             HHHHHhccCCeeE---------------------------EEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEEC
Confidence            7899999999999                           99999876 5999999999999999999999 99999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|.|.++.++
T Consensus       280 g~~i~V~~a~~k  291 (292)
T 2ghp_A          280 NREISVSLADKK  291 (292)
T ss_dssp             TEEEEEEECCCC
T ss_pred             CcEEEEEEecCC
Confidence            999999999875

>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=99.31  E-value=5.5e-12  Score=86.30  Aligned_cols=61  Identities=30%  Similarity=0.416  Sum_probs=56.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |+++|++||.|..                           +++++++ +|+++|||||+|.++++|++|+..|||..+. 
T Consensus       112 l~~~F~~~G~i~~---------------------------v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~  163 (175)
T 3nmr_A          112 IRVMFSSFGQIEE---------------------------CRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTME  163 (175)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccC
Confidence            7899999999999                           9999997 6999999999999999999999999998876 


Q ss_pred             --CeeEEEEecc
Q 033734           81 --GRVIFVDNVR   90 (112)
Q Consensus        81 --g~~i~V~~a~   90 (112)
                        +++|.|++|.
T Consensus       164 g~~~~l~V~~ad  175 (175)
T 3nmr_A          164 GCSSPMVVKFAD  175 (175)
T ss_dssp             TCSSCCEEEECC
T ss_pred             CCCCCeEEEecC
Confidence              4999999873

>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=99.31  E-value=5e-12  Score=89.80  Aligned_cols=61  Identities=18%  Similarity=0.280  Sum_probs=54.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +.|..+.    ++|||||+|.+.++|++|+..|||..|.|
T Consensus        63 L~~~Fs~fG~V~~---------------------------V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g  111 (164)
T 1sjr_A           63 LHQIFSKFGTVLK---------------------------IITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYN  111 (164)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            7899999999999                           8875442    57999999999999999999999999965


Q ss_pred             --eeEEEEeccCCC
Q 033734           82 --RVIFVDNVRPSR   93 (112)
Q Consensus        82 --~~i~V~~a~~~~   93 (112)
                        +.|+|++++++.
T Consensus       112 ~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A          112 ACCTLRIDFSKLTS  125 (164)
T ss_dssp             SCSCEEEEECSSSS
T ss_pred             CCcEEEEEEecCCc
Confidence              999999998753

>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=99.31  E-value=7.5e-12  Score=92.69  Aligned_cols=65  Identities=23%  Similarity=0.311  Sum_probs=61.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++ +|+++|+|||+|.++++|.+|+..|||..++|
T Consensus       202 l~~~f~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  253 (284)
T 3smz_A          202 LCRALSAVHSPTF---------------------------CQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGG  253 (284)
T ss_dssp             HHHHTCSSSCCSE---------------------------EEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHhhCCCCeEE---------------------------EEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCC
Confidence            7899999999999                           9999997 89999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+...
T Consensus       254 ~~l~v~~a~~~~~  266 (284)
T 3smz_A          254 SHLRVSFCAPGPP  266 (284)
T ss_dssp             EECEEEECCSSSC
T ss_pred             eEEEEEEecCCCc
Confidence            9999999987654

>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=99.30  E-value=4.3e-12  Score=85.22  Aligned_cols=58  Identities=22%  Similarity=0.405  Sum_probs=51.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+++|++||.|.+                           +.|+.      .+|||||+|.++++|++|+..|||+.+  
T Consensus        44 L~~~F~~fG~v~~---------------------------v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           44 LLPVLEKCGLVDA---------------------------LLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             HHHHHHHHSCEEE---------------------------EECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            7899999999988                           77643      379999999999999999999999998  


Q ss_pred             ---CCeeEEEEeccCC
Q 033734           80 ---DGRVIFVDNVRPS   92 (112)
Q Consensus        80 ---~g~~i~V~~a~~~   92 (112)
                         .|++|.|.++...
T Consensus        91 ~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKV  106 (114)
T ss_dssp             TTSCEEECEEEEESCC
T ss_pred             ccCCCcEEEEEecccC
Confidence               6899999998744

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.29  E-value=5.3e-12  Score=80.09  Aligned_cols=60  Identities=25%  Similarity=0.363  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAA-TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||.|..                           + .++.++.++.    |||+|.+.++|++|+..|||..++
T Consensus        32 l~~~F~~~G~v~~---------------------------~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~   80 (96)
T 2e44_A           32 LDSLLVQYGVVES---------------------------CEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLE   80 (96)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCS
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEEC
Confidence            7899999999999                           8 4888875543    999999999999999999999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|.|+++.+.
T Consensus        81 g~~l~V~~a~~~   92 (96)
T 2e44_A           81 NFTLKVAYIPDE   92 (96)
T ss_dssp             SCBCEEEECCCC
T ss_pred             CcEEEEEEcCcc
Confidence            999999999875

>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=99.28  E-value=2.3e-11  Score=90.02  Aligned_cols=66  Identities=23%  Similarity=0.498  Sum_probs=62.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++++.++.+|.++|||||+|.+.++|.+|+..|||..++|
T Consensus       112 l~~~f~~~G~i~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g  164 (284)
T 3smz_A          112 FEELVRPFGSLER---------------------------CFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP  164 (284)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeeE---------------------------EEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|.++.+...
T Consensus       165 ~~i~v~~a~~~~~  177 (284)
T 3smz_A          165 RTLYVHWTDAGQL  177 (284)
T ss_dssp             EECEEEECCGGGC
T ss_pred             cEEEEEECCCCCC
Confidence            9999999976554

>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=99.27  E-value=9.3e-12  Score=89.97  Aligned_cols=59  Identities=15%  Similarity=0.326  Sum_probs=54.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++++++     .+|||||+|.++++|++||..|||..+.|
T Consensus        22 L~~~F~~~G~v~~---------------------------v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g   69 (205)
T 3tyt_A           22 VFNVFCLYGNVEK---------------------------VKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFG   69 (205)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCeEE---------------------------EEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           988765     37999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.+++..
T Consensus        70 ~~l~v~~s~~~   80 (205)
T 3tyt_A           70 QKMNVCVSKQP   80 (205)
T ss_dssp             EECEEEECSCS
T ss_pred             ceEEEEEccCC
Confidence            99999998643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.27  E-value=4e-12  Score=85.92  Aligned_cols=61  Identities=26%  Similarity=0.314  Sum_probs=55.2

Q ss_pred             HHHHhhccCcc----eecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCc
Q 033734            2 LADAFSQFGQV----TEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK   77 (112)
Q Consensus         2 l~~~f~~~G~i----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~   77 (112)
                      |+++|++||.|    ..                           ++|+.|+ +|+++|||||+|.++++|++||.. |+.
T Consensus        40 l~~~F~~~g~v~g~v~~---------------------------v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~   90 (123)
T 2dha_A           40 VVAFFGQHCPITGGKEG---------------------------ILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKD   90 (123)
T ss_dssp             HHHHHHTTSCCTTGGGG---------------------------EEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTE
T ss_pred             HHHHHHhhCCccCCcce---------------------------EEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCC
Confidence            78999999986    57                           8999995 899999999999999999999995 999


Q ss_pred             eeCCeeEEEEeccC
Q 033734           78 LLDGRVIFVDNVRP   91 (112)
Q Consensus        78 ~l~g~~i~V~~a~~   91 (112)
                      .++++.|.|..+.+
T Consensus        91 ~l~gR~i~V~~a~~  104 (123)
T 2dha_A           91 LLGKRYIELFRSTA  104 (123)
T ss_dssp             ESSSCEECCEEECH
T ss_pred             eeCCeEEEEEECCH
Confidence            99999999988754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.27  E-value=1.6e-11  Score=83.32  Aligned_cols=60  Identities=28%  Similarity=0.404  Sum_probs=52.6

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccE-EEEEeCCHHHHHHHHHhhCCcee
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGY-GYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~-afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      .|+++|++||.|.+                           ++|+. +     .|| |||+|.+.++|++|+..|||..|
T Consensus        41 ~L~~~Fs~yG~V~~---------------------------v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i   87 (124)
T 2e5i_A           41 VLYTVCNPVGKVQR---------------------------IVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADI   87 (124)
T ss_dssp             HHHHHHTTTSCEEE---------------------------EEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHhcCCEEE---------------------------EEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEe
Confidence            37899999999999                           88754 2     286 99999999999999999999999


Q ss_pred             CC--eeEEEEeccCCC
Q 033734           80 DG--RVIFVDNVRPSR   93 (112)
Q Consensus        80 ~g--~~i~V~~a~~~~   93 (112)
                      .|  +.|+|.+|++..
T Consensus        88 ~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           88 YAGCCTLKIEYARPTR  103 (124)
T ss_dssp             BTTBSEEEEECCSCSC
T ss_pred             cCCCeEEEEEEecCCc
Confidence            87  689999998664

>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=99.27  E-value=2.6e-11  Score=76.21  Aligned_cols=57  Identities=19%  Similarity=0.293  Sum_probs=51.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++| .|..                           +++.      +++|||||+|.++++|++|+..|||..++|
T Consensus        22 l~~~F~~~-~v~~---------------------------~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   67 (88)
T 1wg1_A           22 VHDLLKDY-DLKY---------------------------CYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG   67 (88)
T ss_dssp             HHHHTCSS-CCCC---------------------------EEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHhhC-CeEE---------------------------EEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            78899999 8888                           8773      578999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++...
T Consensus        68 ~~l~V~~a~~~   78 (88)
T 1wg1_A           68 KDLIVQLQPTD   78 (88)
T ss_dssp             EEEEEEECCCC
T ss_pred             cEEEEEEcCCC
Confidence            99999998653

>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=99.26  E-value=1.4e-11  Score=84.92  Aligned_cols=45  Identities=29%  Similarity=0.526  Sum_probs=42.2

Q ss_pred             CCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCC
Q 033734           48 KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS   92 (112)
Q Consensus        48 ~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~   92 (112)
                      ..++.++|||||+|.++++|.+|+..|||..++|+.|.|+++.++
T Consensus       130 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          130 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            458899999999999999999999999999999999999999765

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.26  E-value=1.4e-11  Score=80.64  Aligned_cols=56  Identities=20%  Similarity=0.237  Sum_probs=50.3

Q ss_pred             HHHHhhcc-CcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQF-GQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~-G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++| |+|.+                           +       ++   |+|||.|.+.++|++|++.|||..+.
T Consensus        30 L~~lF~~yGG~Vl~---------------------------V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~   72 (96)
T 2diu_A           30 LRRLSDNCGGKVLS---------------------------I-------TG---CSAILRFINQDSAERAQKRMENEDVF   72 (96)
T ss_dssp             HHHHHHTTTCCEEE---------------------------C-------CT---TCEEEEESSHHHHHHHHHHHTTCCSS
T ss_pred             HHHHHHHcCCeeEE---------------------------E-------ec---CEEEEEECCHHHHHHHHHHhcCCccC
Confidence            67899999 59988                           4       33   99999999999999999999999999


Q ss_pred             CeeEEEEeccCCCC
Q 033734           81 GRVIFVDNVRPSRR   94 (112)
Q Consensus        81 g~~i~V~~a~~~~~   94 (112)
                      ||+|+|++|+...+
T Consensus        73 gr~i~v~~A~~~sd   86 (96)
T 2diu_A           73 GNRIIVSFTPKNRE   86 (96)
T ss_dssp             SSCCEEESSCCSCC
T ss_pred             CceEEEEecCCCcc
Confidence            99999999986654

>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=99.22  E-value=3.8e-11  Score=86.21  Aligned_cols=61  Identities=18%  Similarity=0.188  Sum_probs=55.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|+++. +++++|||||+|.++++|++|+..+ +..++|
T Consensus       126 L~~~F~~~G~v~~---------------------------v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~G  176 (193)
T 2voo_A          126 IKEWLEDKGQVLN---------------------------IQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKE  176 (193)
T ss_dssp             HHHHHTTSCCEEE---------------------------EEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETT
T ss_pred             HHHHHhcCCCEEE---------------------------EEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECC
Confidence            7899999999999                           9999987 5899999999999999999999865 569999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|.++..
T Consensus       177 r~l~V~~~~~  186 (193)
T 2voo_A          177 TDLLILFKDD  186 (193)
T ss_dssp             EECEEEETTT
T ss_pred             EEEEEEEhHH
Confidence            9999998754

>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=99.22  E-value=3.3e-11  Score=89.11  Aligned_cols=62  Identities=24%  Similarity=0.386  Sum_probs=55.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|++||.|.+                           +++++   +++++|||||+|.+.++|++|+..|||..+.|
T Consensus        30 L~~~F~~~G~i~~---------------------------v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   79 (282)
T 3pgw_A           30 LYAIFSQFGQILD---------------------------ILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   79 (282)
T ss_pred             HHHHHhccCCeEE---------------------------EEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCC
Confidence            4589999999999                           87765   67899999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|++++...
T Consensus        80 ~~l~v~~a~~~~   91 (282)
T 3pgw_A           80 KPMRIQYAKTDS   91 (282)
T ss_pred             cEEEEEEeccCc
Confidence            999999986544

>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=99.21  E-value=3.2e-11  Score=82.42  Aligned_cols=66  Identities=27%  Similarity=0.425  Sum_probs=58.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCC--CcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKN--RSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~--~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||+|..                           +++++++.++  +++|||||+|.++++|++|+..|||..+
T Consensus        20 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~   72 (175)
T 3nmr_A           20 LRELFEQYGAVYE---------------------------INVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKV   72 (175)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEE
Confidence            7899999999999                           9999999877  8999999999999999999999999887


Q ss_pred             C---CeeEEEEeccCCCC
Q 033734           80 D---GRVIFVDNVRPSRR   94 (112)
Q Consensus        80 ~---g~~i~V~~a~~~~~   94 (112)
                      .   ++.+.+..+.+...
T Consensus        73 ~~~~~~~~~~~~~~~~~~   90 (175)
T 3nmr_A           73 LPGMHHPIQMKPADSEKN   90 (175)
T ss_dssp             CTTCSSCCEEEECGGGCC
T ss_pred             ccCCccceEEcccccccc
Confidence            6   67888887765443

>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=99.18  E-value=1.1e-11  Score=84.25  Aligned_cols=60  Identities=25%  Similarity=0.359  Sum_probs=53.7

Q ss_pred             HHHHhhccCcce--ecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQVT--EDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++| .|.  .                           |+|++|+. |+++|||||+|.++++|++||. +++..+
T Consensus        59 L~~~F~~~-~i~~~~---------------------------v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l  108 (126)
T 2hgm_A           59 IVQFFSGL-EIVPNG---------------------------ITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERI  108 (126)
T ss_dssp             HHHHTTTS-CEEEEE---------------------------EECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCB
T ss_pred             HHHHHhcC-CceeeE---------------------------EEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEE
Confidence            78899999 566  7                           89999986 9999999999999999999998 578999


Q ss_pred             CCeeEEEEeccC
Q 033734           80 DGRVIFVDNVRP   91 (112)
Q Consensus        80 ~g~~i~V~~a~~   91 (112)
                      +|+.|.|..+.+
T Consensus       109 ~gR~I~V~~a~~  120 (126)
T 2hgm_A          109 GHRYIEVFKSSQ  120 (126)
T ss_dssp             TTBCCCCEEECH
T ss_pred             CCEEEEEEECCH
Confidence            999999988754

>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=99.18  E-value=2.8e-11  Score=82.51  Aligned_cols=62  Identities=29%  Similarity=0.628  Sum_probs=56.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++++++.+|+++|||||+|.++++|++|+..  +..++|
T Consensus        20 l~~~F~~~G~i~~---------------------------v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g   70 (167)
T 2cjk_A           20 LREYFGKYGTVTD---------------------------LKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDG   70 (167)
T ss_dssp             HHHHHTTTCCEEE---------------------------EECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETT
T ss_pred             HHHHHHhCCCEEE---------------------------EEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCC
Confidence            7899999999999                           99999998999999999999999999999984  578999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.++.+.
T Consensus        71 ~~i~v~~~~~~   81 (167)
T 2cjk_A           71 KVIDPKRAIPR   81 (167)
T ss_dssp             EECCCEECCCH
T ss_pred             eEcccccccch
Confidence            99999887543

>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=99.17  E-value=5.6e-11  Score=75.36  Aligned_cols=57  Identities=28%  Similarity=0.546  Sum_probs=45.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+++|++||+|.+                           ++|+++     ++|||||+|.++++|++    ++|..+  
T Consensus        28 L~~~F~~~G~i~~---------------------------v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~   71 (89)
T 3d2w_A           28 LQQFFCQYGEVVD---------------------------VFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLII   71 (89)
T ss_dssp             HHHHHTTTSCEEE---------------------------EECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEE
T ss_pred             HHHHHhccCCEEE---------------------------EEEeeC-----CCCEEEEEECCHHHHHH----HcCCCccc
Confidence            7899999999999                           888774     78999999999999983    566664  


Q ss_pred             CCeeEEEEeccCCCC
Q 033734           80 DGRVIFVDNVRPSRR   94 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~   94 (112)
                      .|+.|.|.++.++..
T Consensus        72 ~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           72 KGISVHISNAEPKHN   86 (89)
T ss_dssp             TTEEEEEEECC----
T ss_pred             CCEEEEEEEcCCCCc
Confidence            599999999986543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.16  E-value=5.1e-11  Score=89.02  Aligned_cols=59  Identities=24%  Similarity=0.398  Sum_probs=52.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+++|++||+|.+                           ++|+.      ++|||||+|.+.++|+.|+.+|+|..+  
T Consensus       160 L~~~F~~fG~I~~---------------------------v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          160 IRFVFSRLGDIDR---------------------------IRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             HHHHHHccCCEEE---------------------------EEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            7899999999999                           88875      479999999999999999999999999  


Q ss_pred             ----------CCeeEEEEeccCCC
Q 033734           80 ----------DGRVIFVDNVRPSR   93 (112)
Q Consensus        80 ----------~g~~i~V~~a~~~~   93 (112)
                                .|+.|.|++|++..
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC---
T ss_pred             cccccccccCCCCEEEEEEccCCC
Confidence                      89999999997653

>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=99.16  E-value=2.4e-11  Score=76.13  Aligned_cols=63  Identities=25%  Similarity=0.497  Sum_probs=49.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|+.+     ++|||||+|.++++|++|+..  ...+.+
T Consensus        22 l~~~F~~~G~i~~---------------------------v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g   67 (88)
T 1wf0_A           22 LREFFSQYGDVMD---------------------------VFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKG   67 (88)
T ss_dssp             HHHHSTTTSCCCE---------------------------EECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETT
T ss_pred             HHHHHHHcCCeeE---------------------------EEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCC
Confidence            7899999999999                           888654     789999999999999764321  234589


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      +.|.|.++.++....++
T Consensus        68 ~~l~v~~a~~~~~~~~~   84 (88)
T 1wf0_A           68 ISVHISNAEPKHNSNSG   84 (88)
T ss_dssp             EEEEEECCCCCCCCCSC
T ss_pred             EEEEEEecCCCCCCCCC
Confidence            99999999876655443

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.13  E-value=1e-10  Score=72.55  Aligned_cols=40  Identities=20%  Similarity=0.537  Sum_probs=35.9

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEe
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN   88 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~   88 (112)
                      +++.++      +|||||+|.++++|++|+ .|||..++|+.|.|+.
T Consensus        47 ~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           47 VQINQD------KNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             EEECSS------SSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             EEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            777544      799999999999999999 9999999999999873

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.13  E-value=1.3e-10  Score=83.83  Aligned_cols=62  Identities=24%  Similarity=0.414  Sum_probs=56.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCC----CCCcccEEEEEeCCHHHHHHHHHhhCCc
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKG----KNRSKGYGYVTFSTEEEAQKALADMNGK   77 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~----t~~~rG~afV~f~~~~~a~~Ai~~l~g~   77 (112)
                      |.+.|++||.|..                           +.|+++..    +++++|++||+|.+.++|++|+..|||+
T Consensus       146 l~~e~~~~G~v~~---------------------------~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr  198 (222)
T 3dxb_A          146 VTEECGKFGAVNR---------------------------VIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR  198 (222)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             HHHHHHccCCeEE---------------------------EEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCc
Confidence            6788999999999                           88886643    4589999999999999999999999999


Q ss_pred             eeCCeeEEEEecc
Q 033734           78 LLDGRVIFVDNVR   90 (112)
Q Consensus        78 ~l~g~~i~V~~a~   90 (112)
                      .++||.|.+.++.
T Consensus       199 ~~~gr~i~~~~~~  211 (222)
T 3dxb_A          199 WFAGRKVVAEVYD  211 (222)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             eECCeEEEEEEcC
Confidence            9999999999875

>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=1.6e-10  Score=85.40  Aligned_cols=58  Identities=21%  Similarity=0.357  Sum_probs=53.3

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|++||.|.+                           ++++.++     +|||||+|.+.++|.+|+..|||..++
T Consensus       223 ~l~~~F~~~G~i~~---------------------------v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~  270 (282)
T 3pgw_A          223 MLSMLFNQFPGFKE---------------------------VRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKIT  270 (282)
T ss_pred             HHHHHHHhcCCeEE---------------------------EEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeC
Confidence            37899999999999                           8888654     589999999999999999999999999


Q ss_pred             -CeeEEEEecc
Q 033734           81 -GRVIFVDNVR   90 (112)
Q Consensus        81 -g~~i~V~~a~   90 (112)
                       |+.|+|++++
T Consensus       271 ~g~~l~v~~ak  281 (282)
T 3pgw_A          271 QNNAMKISFAK  281 (282)
T ss_pred             CCCEEEEEEec
Confidence             9999999986

>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=99.11  E-value=1.2e-10  Score=86.43  Aligned_cols=66  Identities=15%  Similarity=0.328  Sum_probs=53.3

Q ss_pred             HHHHhhccC-cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFG-QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| .|..                           +.++.++. +.++|||||+|.+.++|.+|+..|||..++
T Consensus       134 l~~~f~~~G~~i~~---------------------------v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~  185 (292)
T 2ghp_A          134 IRDLLQDINVVALS---------------------------IRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIE  185 (292)
T ss_dssp             HHHHHHHTTCCCCE---------------------------EECC--------CCEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             HHHHHHHhCCCeEE---------------------------EEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            789999999 9999                           99998874 889999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCC
Q 033734           81 GRVIFVDNVRPSRRY   95 (112)
Q Consensus        81 g~~i~V~~a~~~~~~   95 (112)
                      |+.|.|.++.+....
T Consensus       186 g~~l~v~~a~~~~~~  200 (292)
T 2ghp_A          186 GYTLVTKVSNPLEKS  200 (292)
T ss_dssp             TEECEEEECCCC---
T ss_pred             CcEEEEEECCCCccc
Confidence            999999999765443

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.11  E-value=1.8e-10  Score=74.68  Aligned_cols=55  Identities=36%  Similarity=0.498  Sum_probs=50.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.+.|++||.|..                           ++++.|+        +||+|.+.++|.+||. |||.+++|
T Consensus        32 L~~~F~~~G~Vi~---------------------------vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A           32 LLQQFASFGEVIL---------------------------IRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             HHHHHHTTCCEEE---------------------------EEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             HHHHHHhCCCeEE---------------------------EEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            6789999999999                           9998875        8999999999999998 99999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|+++++.
T Consensus        76 r~LkV~lkt~d   86 (91)
T 2dnr_A           76 RTITIALKSPS   86 (91)
T ss_dssp             EEEEEEECCCS
T ss_pred             eEEEEEeCCCC
Confidence            99999998764

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.11  E-value=2.2e-10  Score=83.04  Aligned_cols=59  Identities=27%  Similarity=0.438  Sum_probs=54.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +++++++     +|||||+|.++++|++|+..|||..+.|
T Consensus        52 L~~~F~~~G~i~~---------------------------v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g   99 (229)
T 2adc_A           52 LFILFGVYGDVQR---------------------------VKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHG   99 (229)
T ss_dssp             HHHHHHHHTCEEE---------------------------EEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHHhCCCeEE---------------------------EEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            7899999999999                           9998875     7899999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.++++.
T Consensus       100 ~~l~v~~a~~~  110 (229)
T 2adc_A          100 KPIRITLSKHQ  110 (229)
T ss_dssp             SBCEEECCSCC
T ss_pred             eEEEEEEecCc
Confidence            99999998754

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.10  E-value=2.8e-10  Score=84.09  Aligned_cols=64  Identities=36%  Similarity=0.626  Sum_probs=56.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC-CceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN-GKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~-g~~l~   80 (112)
                      |+++|++||.|..                           +.++.|. +|+++|||||+|.+.++|.+|+..|| |..+.
T Consensus       113 l~~~F~~~G~i~~---------------------------v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~  164 (261)
T 3sde_A          113 LEQAFSQFGPVEK---------------------------AVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLL  164 (261)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEES
T ss_pred             HHHHHHhcCCeEE---------------------------EEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEe
Confidence            7899999999999                           9999994 89999999999999999999999995 44554


Q ss_pred             ---CeeEEEEeccCCC
Q 033734           81 ---GRVIFVDNVRPSR   93 (112)
Q Consensus        81 ---g~~i~V~~a~~~~   93 (112)
                         +++|.|+++.+..
T Consensus       165 ~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          165 TTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             SSSCCBCEEEECCCEE
T ss_pred             cCCCceEEEeeccccC
Confidence               8999999987543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.09  E-value=1.2e-10  Score=81.85  Aligned_cols=59  Identities=27%  Similarity=0.438  Sum_probs=54.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           +++++++     +|||||+|.++++|++|+..|||..+.|
T Consensus        21 l~~~F~~~G~i~~---------------------------v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g   68 (198)
T 1qm9_A           21 LFILFGVYGDVQR---------------------------VKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHG   68 (198)
T ss_dssp             HHHHHHTTCCCSE---------------------------EECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSS
T ss_pred             HHHHHHhcCCEEE---------------------------EEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecC
Confidence            7899999999999                           8887774     7899999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.++.+.
T Consensus        69 ~~l~v~~a~~~   79 (198)
T 1qm9_A           69 KPIRITLSKHQ   79 (198)
T ss_dssp             CCCEEEECCCC
T ss_pred             eEEEEEEecCC
Confidence            99999998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.07  E-value=3.1e-10  Score=74.53  Aligned_cols=58  Identities=19%  Similarity=0.339  Sum_probs=45.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCC---CCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGK---NRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t---~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|++||+|..                            .++.++.+   |+++|||||+|.++++|++||..|+  .
T Consensus        25 L~~~F~~~G~i~~----------------------------~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~   74 (114)
T 2dnl_A           25 ITASFRRFGPLVV----------------------------DWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--E   74 (114)
T ss_dssp             HHHHTTTTCCCCE----------------------------ECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--E
T ss_pred             HHHHHHhcCCEEE----------------------------EEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--h
Confidence            7899999999853                            45566656   7999999999999999999999883  3


Q ss_pred             eCCeeEEEEec
Q 033734           79 LDGRVIFVDNV   89 (112)
Q Consensus        79 l~g~~i~V~~a   89 (112)
                      ++|+.+.+..+
T Consensus        75 ~~G~~~~~~~~   85 (114)
T 2dnl_A           75 EDGKLYLCVSS   85 (114)
T ss_dssp             ETTEEEEEECC
T ss_pred             cCCcEEEeccC
Confidence            55555555443

>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=99.03  E-value=3.5e-10  Score=81.62  Aligned_cols=59  Identities=12%  Similarity=0.208  Sum_probs=51.4

Q ss_pred             HHHHhhccCcc--eecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQV--TEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||.|  ..                           ++++.+.  +..+|+|||+|.+.++|.+||..|||..+
T Consensus       140 L~~~F~~~G~v~~~~---------------------------v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~  190 (205)
T 3tyt_A          140 FFEICDELGVKRPTS---------------------------VKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQM  190 (205)
T ss_dssp             HHHHHHHHTCCCCSE---------------------------EEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHhcCCcceEE---------------------------EEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCc
Confidence            78999999999  77                           8887775  56679999999999999999999999999


Q ss_pred             CCe----eEEEEec
Q 033734           80 DGR----VIFVDNV   89 (112)
Q Consensus        80 ~g~----~i~V~~a   89 (112)
                      +|+    ++.|++|
T Consensus       191 ~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          191 KNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCSSSSSCEECEEE
T ss_pred             cCCCCCcceEEEec
Confidence            876    5666664

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.03  E-value=2.3e-10  Score=80.42  Aligned_cols=59  Identities=22%  Similarity=0.273  Sum_probs=53.0

Q ss_pred             HHHHhhccC-cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFG-QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| .|..                           ++++.+     .+|+|||+|.++++|.+|+..|||..++
T Consensus       137 l~~~f~~~G~~v~~---------------------------v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~  184 (198)
T 1qm9_A          137 LKVLFSSNGGVVKG---------------------------FKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLG  184 (198)
T ss_dssp             HHHHHHHTTSCCCE---------------------------EEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCS
T ss_pred             HHHHHHHcCCCceE---------------------------EEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccC
Confidence            789999999 9988                           887554     3799999999999999999999999999


Q ss_pred             -CeeEEEEeccCC
Q 033734           81 -GRVIFVDNVRPS   92 (112)
Q Consensus        81 -g~~i~V~~a~~~   92 (112)
                       |+.|.|+++++.
T Consensus       185 ~g~~l~v~~a~~~  197 (198)
T 1qm9_A          185 ENHHLRVSFSKST  197 (198)
T ss_dssp             SCCSCCEEEECCC
T ss_pred             CCCeEEEEeeccc
Confidence             999999998763

>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=99.02  E-value=1.2e-10  Score=80.23  Aligned_cols=48  Identities=25%  Similarity=0.466  Sum_probs=42.0

Q ss_pred             eeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCC
Q 033734           46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR   94 (112)
Q Consensus        46 ~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~   94 (112)
                      .+..+++++|||||+|.++++|++|+. |||..+.|+.|.|.++.+...
T Consensus        46 ~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~   93 (175)
T 1fje_B           46 VDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDS   93 (175)
T ss_dssp             CEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCSSC
T ss_pred             EECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCccc
Confidence            344578899999999999999999995 999999999999999976543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.99  E-value=3.5e-10  Score=78.93  Aligned_cols=42  Identities=17%  Similarity=0.472  Sum_probs=38.1

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCC
Q 033734           50 KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS   92 (112)
Q Consensus        50 t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~   92 (112)
                      .++++|||||+|.++++|++|+ .|||..++|+.|.|.++.+.
T Consensus        47 ~~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           47 INQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             EETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCC
T ss_pred             ecCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCC
Confidence            3567899999999999999999 89999999999999998654

>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=98.99  E-value=8.2e-10  Score=80.01  Aligned_cols=59  Identities=22%  Similarity=0.273  Sum_probs=53.0

Q ss_pred             HHHHhhccC-cceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFG-QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G-~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| .|..                           ++++.+     .+|+|||+|.+.++|.+|+..|||..++
T Consensus       168 l~~~f~~~G~~i~~---------------------------v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~  215 (229)
T 2adc_A          168 LKVLFSSNGGVVKG---------------------------FKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLG  215 (229)
T ss_dssp             HHHHHHTTSCCEEE---------------------------EEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             HHHHHHHcCCCeeE---------------------------EEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccC
Confidence            789999999 9988                           877543     3689999999999999999999999999


Q ss_pred             -CeeEEEEeccCC
Q 033734           81 -GRVIFVDNVRPS   92 (112)
Q Consensus        81 -g~~i~V~~a~~~   92 (112)
                       |+.|.|+++++.
T Consensus       216 ~g~~l~v~~a~~~  228 (229)
T 2adc_A          216 ENHHLRVSFSKST  228 (229)
T ss_dssp             SSCBCEEEECSSC
T ss_pred             CCCeEEEEEecCC
Confidence             999999999763

>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=98.94  E-value=2.4e-09  Score=79.08  Aligned_cols=58  Identities=21%  Similarity=0.471  Sum_probs=52.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+.+      .+|||||+|.++++|++|+..+||..+.|
T Consensus        39 l~~~F~~~G~i~~---------------------------v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g   85 (261)
T 3sde_A           39 FKRLFERYGEPSE---------------------------VFINR------DRGFGFIRLESRTLAEIAKAELDGTILKS   85 (261)
T ss_dssp             HHHHTGGGCCCSE---------------------------EEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhcCCEEE---------------------------EEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECC
Confidence            7899999999999                           88753      46999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|.++.+.
T Consensus        86 ~~l~v~~a~~~   96 (261)
T 3sde_A           86 RPLRIRFATHG   96 (261)
T ss_dssp             EECEEEECCCS
T ss_pred             ceeEeeecccC
Confidence            99999998753

>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=98.90  E-value=2e-09  Score=70.14  Aligned_cols=53  Identities=21%  Similarity=0.375  Sum_probs=49.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.+.|++||.|..                           ++++.|+        +||+|.+.++|.+||. |||.+++|
T Consensus        41 L~~~F~~~G~Vil---------------------------vr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~G   84 (95)
T 1ufw_A           41 LMQTLGSYGTIVL---------------------------VRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             HHHHHHHHSCCSE---------------------------EEEETTE--------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             HHHHHHHCCCEEE---------------------------EEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCC
Confidence            6789999999999                           9998885        9999999999999999 99999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      |.|+|++-.
T Consensus        85 r~L~V~~k~   93 (95)
T 1ufw_A           85 RAVKISGPS   93 (95)
T ss_dssp             EEEEEECCC
T ss_pred             eEEEEeccC
Confidence            999998754

>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=98.83  E-value=1e-08  Score=69.92  Aligned_cols=42  Identities=17%  Similarity=0.500  Sum_probs=37.5

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCC
Q 033734           51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR   93 (112)
Q Consensus        51 ~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~   93 (112)
                      ++++|||||+|.++++|++|+ .+||..++|+.|.|.++.+..
T Consensus        48 ~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~   89 (172)
T 2g4b_A           48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQ   89 (172)
T ss_dssp             ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCC
T ss_pred             cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccC
Confidence            456899999999999999999 899999999999999876543

>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=98.79  E-value=8.6e-09  Score=80.48  Aligned_cols=56  Identities=25%  Similarity=0.475  Sum_probs=46.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |+++|++||+|..                           +.+..      +||||||+|.+.++|++|+..|||..+. 
T Consensus        37 L~~~F~~~G~V~~---------------------------v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           37 LLPVLEKCGLVDA---------------------------LLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             HHHHHHhcCCeEE---------------------------EEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            7899999999988                           66532      5799999999999999999999999983 


Q ss_pred             --Ce--eEEEEecc
Q 033734           81 --GR--VIFVDNVR   90 (112)
Q Consensus        81 --g~--~i~V~~a~   90 (112)
                        |+  .+.+.++.
T Consensus        84 ~~g~~~~ly~~~~~   97 (345)
T 3tht_A           84 DLGQKITLYLNFVE   97 (345)
T ss_dssp             TTSCEEECEEEECS
T ss_pred             ccCCceEEEEEEee
Confidence              44  56777763

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.20  E-value=1.8e-06  Score=58.28  Aligned_cols=56  Identities=20%  Similarity=0.242  Sum_probs=48.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCC-HHHHHHHHHhhC--Cce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFST-EEEAQKALADMN--GKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~-~~~a~~Ai~~l~--g~~   78 (112)
                      |+++|++||+|..                           |.++++..      .|||.|.+ +++|..|+..+|  +..
T Consensus        36 Lke~F~~~G~V~~---------------------------Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~   82 (121)
T 1owx_A           36 LHILFSNHGEIKW---------------------------IDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQ   82 (121)
T ss_dssp             HHHHTCSSCCEEE---------------------------EECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBC
T ss_pred             HHHHHHhcCCEEE---------------------------EEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcE
Confidence            7899999999999                           98888764      49999999 899999999995  677


Q ss_pred             eCCeeEEEEecc
Q 033734           79 LDGRVIFVDNVR   90 (112)
Q Consensus        79 l~g~~i~V~~a~   90 (112)
                      |.|..+.+++..
T Consensus        83 i~g~~~~~evL~   94 (121)
T 1owx_A           83 LRNKEVTWEVLE   94 (121)
T ss_dssp             TTSSSEEEEECC
T ss_pred             EeCcEEEEEECC
Confidence            889988887754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.36  E-value=0.0006  Score=45.52  Aligned_cols=42  Identities=24%  Similarity=0.333  Sum_probs=36.8

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEec
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV   89 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a   89 (112)
                      +.+..|-      |-|+|+|.+...|-+|.-+|||.+++|+.|+|--.
T Consensus        56 I~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gTv   97 (117)
T 2l9w_A           56 ILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGTI   97 (117)
T ss_dssp             EEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEECH
T ss_pred             EEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEEecCH
Confidence            7777774      57999999999999999999999999999998643

>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=97.13  E-value=0.00054  Score=46.19  Aligned_cols=35  Identities=14%  Similarity=0.145  Sum_probs=29.8

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      ++|+++.  .+++|||||+|.++++|++|+..+++..
T Consensus         3 ~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~   37 (158)
T 2kn4_A            3 YKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDN   37 (158)
T ss_dssp             EEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             EEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccC
Confidence            5777885  4799999999999999999999887643

>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=0.00057  Score=45.96  Aligned_cols=41  Identities=20%  Similarity=0.167  Sum_probs=37.6

Q ss_pred             CCCcccEEEEEeCCHHHHHHHHHhh-CCceeCCeeEEEEeccC
Q 033734           50 KNRSKGYGYVTFSTEEEAQKALADM-NGKLLDGRVIFVDNVRP   91 (112)
Q Consensus        50 t~~~rG~afV~f~~~~~a~~Ai~~l-~g~~l~g~~i~V~~a~~   91 (112)
                      ..+.+|+++++|.+.++|++|+..+ ||..++| .+.++.+..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            4678999999999999999999999 9999999 999998764

>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=96.69  E-value=0.011  Score=38.79  Aligned_cols=37  Identities=14%  Similarity=0.047  Sum_probs=33.9

Q ss_pred             EEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCC
Q 033734           56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS   92 (112)
Q Consensus        56 ~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~   92 (112)
                      -..|.|.++++|.+|-..||+..++|++++|-++.+.
T Consensus        48 Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~   84 (104)
T 1wey_A           48 RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             EEEEEeCChHHHHHHHHHhccceecCceeEEEecCCC
Confidence            4579999999999999999999999999999999844

>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=96.43  E-value=0.017  Score=38.71  Aligned_cols=55  Identities=18%  Similarity=0.380  Sum_probs=43.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      +.+.|++||.|.+                           ...  .    ....+-.|.|.+..+|++||. .||..+++
T Consensus        40 VL~~F~~~G~Iv~---------------------------~~~--~----~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g   85 (119)
T 1wwh_A           40 ILLQFAQYGNILK---------------------------HVM--S----NTGNWMHIRYQSKLQARKALS-KDGRIFGE   85 (119)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEE--C----SSSSEEEEEESSHHHHHHHHT-TTTCEETT
T ss_pred             HHHHHHhhCcEEE---------------------------ecc--C----CCCCeEEEEeCCHHHHHHHHH-hCCeEecC
Confidence            5688999999988                           443  1    123588999999999999998 79999985


Q ss_pred             -eeEEEEecc
Q 033734           82 -RVIFVDNVR   90 (112)
Q Consensus        82 -~~i~V~~a~   90 (112)
                       -.|-|..+.
T Consensus        86 ~~mIGV~p~~   95 (119)
T 1wwh_A           86 SIMIGVKPCI   95 (119)
T ss_dssp             TEECEEEECC
T ss_pred             CEEEEEEECC
Confidence             677887753

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.37  E-value=0.0033  Score=42.86  Aligned_cols=36  Identities=22%  Similarity=0.330  Sum_probs=32.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEecc
Q 033734           54 KGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVR   90 (112)
Q Consensus        54 rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~   90 (112)
                      ..+-.|+|.++.+|++||. .||..++|..|.|...+
T Consensus        62 ~NWikItYds~~~A~rAL~-~NG~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           62 NSWTKITYDNPASAVDALL-ENGAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TTEEEEEBSSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             CcEEEEEcCCHHHHHHHHH-hCCeEeCcEEEEEEECC
Confidence            4688999999999999998 89999999988998875

>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=92.87  E-value=0.19  Score=32.58  Aligned_cols=38  Identities=32%  Similarity=0.484  Sum_probs=31.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhh
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM   74 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l   74 (112)
                      |.++|++||.| .                           ++.+-|-       .|||.|.+++.|..|+..+
T Consensus        32 I~~lFs~fggv-~---------------------------I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           32 LYQLFSAFGNI-Q---------------------------ISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             HHHHHTTTCSC-C---------------------------CEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             HHHHhhccCCE-E---------------------------EEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            67899999855 3                           5666663       7999999999999999966

>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=90.66  E-value=0.2  Score=32.52  Aligned_cols=27  Identities=22%  Similarity=0.311  Sum_probs=22.7

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN   75 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~   75 (112)
                      ++.+-|-       .|||.|.+++.|..|+..+.
T Consensus        34 I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A           34 ISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            5666663       89999999999999999764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=83.38  E-value=0.8  Score=36.85  Aligned_cols=39  Identities=21%  Similarity=0.260  Sum_probs=28.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHH
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALA   72 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~   72 (112)
                      |.++|++||+|..                           +.+..++  |   -|+.|+|.+.+++++++.
T Consensus        69 l~~y~~~~g~i~~---------------------------~~~~~~~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           69 FLKYLSQFGPINN---------------------------HFFYESF--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHHGGGSCCCC---------------------------EEEECSS--S---EEEEEECC---CCHHHHS
T ss_pred             HHHHHHhcCCcce---------------------------EEEEccC--C---eEEEEEeCCHHHHHHHHh
Confidence            6789999999988                           5554432  2   599999999999997765

---

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	112
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-09
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	6e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-08
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-08
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	9e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	1e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-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:) 4e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-05
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.001

>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 = 54.2 bits (130), Expect = 1e-11
 Identities = 11/50 (22%), Positives = 18/50 (36%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRY 95
          +        G   V+F   EEA   +  ++G+   GR I       +  Y
Sbjct: 49 LLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 98

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.0 bits (124), Expect = 8e-11
 Identities = 11/58 (18%), Positives = 23/58 (39%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
          +  F      +  +  +    K    G   V F + +EA  A+ D+N + +  R + +
Sbjct: 26 ILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 83

>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 = 51.9 bits (124), Expect = 1e-10
 Identities = 9/59 (15%), Positives = 22/59 (37%)

Query: 46  MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQ 104
                  ++G  YV +    +A+ A   ++G  +  R + V     +R +       ++
Sbjct: 38  RVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKE 96

>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 = 50.4 bits (120), Expect = 3e-10
 Identities = 15/66 (22%), Positives = 26/66 (39%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          +   L S   L A  ++ D     SKGY +  +       +A+A +NG  L  + + V  
Sbjct: 18 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 77

Query: 89 VRPSRR 94
               +
Sbjct: 78 ASVGAK 83

>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 = 49.9 bits (119), Expect = 5e-10
 Identities = 20/88 (22%), Positives = 35/88 (39%), Gaps = 15/88 (17%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
            TE+ +Y  F                        +DK K  + G+ +V + +  +A+ A
Sbjct: 18 YTTEEQIYELFSKSGDIKKIIM------------GLDKMKKTACGFCFVEYYSRADAENA 65

Query: 71 LADMNGKLLDGRVIFVD---NVRPSRRY 95
          +  +NG  LD R+I  D     +  R+Y
Sbjct: 66 MRYINGTRLDDRIIRTDWDAGFKEGRQY 93

>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 = 48.6 bits (115), Expect = 2e-09
 Identities = 18/72 (25%), Positives = 32/72 (44%)

Query: 29  LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
           L     +   L      +D    + KG+ +VTF   E A KA A+++G++  GR++ V  
Sbjct: 25  LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP 84

Query: 89  VRPSRRYNTDAP 100
               +  +   P
Sbjct: 85  STIKKEASQSGP 96

>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 = 47.7 bits (113), Expect = 3e-09
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          +D    + +G+ +V F   E+A  A+ +MN   L GR I V+  +P R
Sbjct: 39 LDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR 86

>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 = 47.7 bits (113), Expect = 4e-09
 Identities = 19/94 (20%), Positives = 31/94 (32%), Gaps = 24/94 (25%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   FS+ G +    +                               G   S G+G+V 
Sbjct: 14 TLKGVFSKVGAIKSCTISKKKNKA------------------------GVLLSMGFGFVE 49

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          +   E+AQKAL  + G  +DG  + V     + +
Sbjct: 50 YKKPEQAQKALKQLQGHTVDGHKLEVRISERATK 83

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 4e-09
 Identities = 9/40 (22%), Positives = 23/40 (57%)

Query: 55 GYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          G+ +V +  E  A+ A+A  +G+++ G+V+ ++     + 
Sbjct: 51 GFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKV 90

>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 = 47.8 bits (113), Expect = 4e-09
 Identities = 12/51 (23%), Positives = 21/51 (41%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
            I  K +     + +V F    +A+ A+   +G   DG  + V+  R  R
Sbjct: 42 RDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR 92

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 4e-09
 Identities = 22/65 (33%), Positives = 34/65 (52%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          L         +    ++ D+   RS+G+G+VTF   ++A+ A+  MNGK +DGR I VD 
Sbjct: 22 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ 81

Query: 89 VRPSR 93
             S 
Sbjct: 82 AGKSS 86

>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 = 49.2 bits (116), Expect = 5e-09
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 29  LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
           L  +      +    I+ D+G  + +G+ +VTF   +   K +       ++G    V  
Sbjct: 114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK 172

Query: 89  VRP 91
              
Sbjct: 173 ALS 175

>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 = 47.7 bits (113), Expect = 5e-09
 Identities = 11/48 (22%), Positives = 21/48 (43%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          +D  +    G  +V F++  + QKA+  + G+    RV+      P  
Sbjct: 50 VDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS 97

>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 = 46.8 bits (111), Expect = 6e-09
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            +  D    RS GY YV F    +A++AL  MN  ++ G+ +    +  S+R
Sbjct: 30 IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV---RIMWSQR 79

>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 = 46.1 bits (109), Expect = 2e-08
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 2/46 (4%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           D     SKG+G+V F+  E   K ++  +   +DGR         
Sbjct: 42 KDLKTGHSKGFGFVRFTEYETQVKVMSQRHM--IDGRWCDCKLPNS 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-08
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 13/81 (16%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          + TE+ +  Y++                      + D    RS+G+G+VTFS+  E   A
Sbjct: 31 ETTEESLRNYYEQWGKLTDCVV------------MRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 71 LADMNGKLLDGRVIFVDNVRP 91
          +A      +DGRV+       
Sbjct: 79 MA-ARPHSIDGRVVEPKRAVA 98

>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-08
 Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 2/57 (3%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK--LLDGRVIFVDNVRPSRRYNTD 98
                K +++G+ +V + +   A  A   +      L G  I VD   P    + D
Sbjct: 35 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDED 91

>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 = 45.5 bits (107), Expect = 3e-08
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS 92
          YG+V +   ++A+KA+  +NG  L  + I V   RPS
Sbjct: 46 YGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS 82

>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 = 45.0 bits (106), Expect = 3e-08
 Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 13/77 (16%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          Q T++ +  YF                       + D    RS+G+G+VTF  +    K 
Sbjct: 11 QTTQEGLREYFGQFGEVKECLV------------MRDPLTKRSRGFGFVTFMDQAGVDKV 58

Query: 71 LADMNGKLLDGRVIFVD 87
          LA  +   LD + I   
Sbjct: 59 LA-QSRHELDSKTIDPK 74

>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 = 45.4 bits (107), Expect = 3e-08
 Identities = 16/44 (36%), Positives = 26/44 (59%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           + + Y +V FS  E+A +A+  +NGK+LDG  I V   +P  +
Sbjct: 41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 84

>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 = 45.3 bits (107), Expect = 3e-08
 Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 12/78 (15%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          Q  +  +   F +                         G    +G+G+V F T+++A+KA
Sbjct: 19 QANQREIRELFSTFG-----------ELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 71 LADM-NGKLLDGRVIFVD 87
             + +   L GR + ++
Sbjct: 68 FNALCHSTHLYGRRLVLE 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 = 45.4 bits (107), Expect = 3e-08
 Identities = 16/47 (34%), Positives = 27/47 (57%)

Query: 50 KNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYN 96
          +  SKG+G+VTF    +A +A   ++G +++GR I V+N       N
Sbjct: 47 ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 45.5 bits (107), Expect = 4e-08
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 46  MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNT 97
           +DK   + KG   V++     A+ A+   +GK   G  + V   R     N+
Sbjct: 50  LDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 101

>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 = 45.0 bits (106), Expect = 4e-08
 Identities = 16/60 (26%), Positives = 28/60 (46%)

Query: 34 ISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          + + F  A  I +     +SKG  Y+ F +E +A+K L +  G  +DGR + +       
Sbjct: 33 LKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 92

>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 = 45.1 bits (106), Expect = 6e-08
 Identities = 13/40 (32%), Positives = 22/40 (55%)

Query: 55 GYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
          GYG+  +  +E A  A+ ++NG+   GR + VDN    + 
Sbjct: 51 GYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKN 90

>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 = 44.3 bits (104), Expect = 8e-08
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 12/82 (14%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
             E  +   F+        Y               DK   +SKG+ +++F   E+A +A
Sbjct: 19 DTRETDLQELFRPFGSISRIYL------------AKDKTTGQSKGFAFISFHRREDAARA 66

Query: 71 LADMNGKLLDGRVIFVDNVRPS 92
          +A ++G   D  ++ V+  +PS
Sbjct: 67 IAGVSGFGYDHLILNVEWAKPS 88

>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 = 43.8 bits (103), Expect = 8e-08
 Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 13/76 (17%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
            T+  +  YF                        +D    RS+G+G+V F   E   K 
Sbjct: 10 DTTKKDLKDYFSKFGEVVDCTL------------KLDPITGRSRGFGFVLFKESESVDKV 57

Query: 71 LADMNGKLLDGRVIFV 86
          + D     L+G+VI  
Sbjct: 58 M-DQKEHKLNGKVIDP 72

>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 = 43.8 bits (103), Expect = 9e-08
 Identities = 14/43 (32%), Positives = 20/43 (46%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          +      RS G   V F  + +A KA+   NG  LDGR + + 
Sbjct: 32 VHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 74

>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 = 43.6 bits (102), Expect = 1e-07
 Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 12/83 (14%)

Query: 9  FGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQ 68
             + E+L+   F+                         K  + +    ++ F  ++ A+
Sbjct: 14 TELLDENLLRESFEGFGSIEKINI-----------PAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 69 KALADMNGKLLDGRVIFVDNVRP 91
          +AL  MN  LL  R I V     
Sbjct: 63 RALQ-MNRSLLGNREISVSLADK 84

>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 = 43.5 bits (102), Expect = 1e-07
 Identities = 16/41 (39%), Positives = 24/41 (58%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFV 86
           D+   RS+G+ +V F   ++A++A    NG  LDGR I V
Sbjct: 43 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

>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 = 44.0 bits (103), Expect = 1e-07
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          L  +      +  A +I D+   +S+GYG+VT +    A++A  D N   +DGR   V+ 
Sbjct: 27 LRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-IDGRKANVNL 85

Query: 89 VRPSRR 94
               +
Sbjct: 86 AYLGAK 91

>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 = 43.5 bits (102), Expect = 2e-07
 Identities = 8/41 (19%), Positives = 14/41 (34%)

Query: 47 DKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
               + +G  +V F     A  AL  M G     + + + 
Sbjct: 39 VSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 79

>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 = 43.5 bits (102), Expect = 2e-07
 Identities = 17/66 (25%), Positives = 30/66 (45%)

Query: 29  LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
           L    +    + +A + +DK  N SK +G+V++     AQ A+  MNG  +  + + V  
Sbjct: 35  LLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 94

Query: 89  VRPSRR 94
            R    
Sbjct: 95  KRSKND 100

>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 = 43.2 bits (101), Expect = 2e-07
 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 12/77 (15%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          +  ED +   F         +              +D+    SKGY  V + T ++A  A
Sbjct: 18 EAQEDEIQEKFCDYGEIKNIHL------------NLDRRTGFSKGYALVEYETHKQALAA 65

Query: 71 LADMNGKLLDGRVIFVD 87
             +NG  + G+ I VD
Sbjct: 66 KEALNGAEIMGQTIQVD 82

>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 = 42.8 bits (100), Expect = 2e-07
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 11/81 (13%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          ++ E L+Y  F +  +                 I+ D     SKGY ++ F++ + +  A
Sbjct: 9  EIDEKLLYDTFSAFGVILQTPK-----------IMRDPDTGNSKGYAFINFASFDASDAA 57

Query: 71 LADMNGKLLDGRVIFVDNVRP 91
          +  MNG+ L  R I V     
Sbjct: 58 IEAMNGQYLCNRPITVSYAFK 78

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 3e-07
 Identities = 15/49 (30%), Positives = 26/49 (53%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           D+   + +GYG+V F +EE+A  A+  M+   L G+ I V+      +
Sbjct: 43 KDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 43.1 bits (101), Expect = 3e-07
 Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 13/83 (15%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          ++    +  +F            + D       II D+   RSKG  YV F   +    A
Sbjct: 29 RIRPRDLEDFFS-------AVGKVRD-----VRIISDRNSRRSKGIAYVEFCEIQSVPLA 76

Query: 71 LADMNGKLLDGRVIFVDNVRPSR 93
          +  + G+ L G  I V   +  +
Sbjct: 77 IG-LTGQRLLGVPIIVQASQAEK 98

>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 = 42.7 bits (100), Expect = 3e-07
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 27/91 (29%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   F   G +                               I+ D     S GY +V 
Sbjct: 18 ELYALFRAIGPINT---------------------------CRIMRDYKTGYSYGYAFVD 50

Query: 61 FSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          F++E ++Q+A+  +NG  +  + + V   RP
Sbjct: 51 FTSEMDSQRAIKVLNGITVRNKRLKVSYARP 81

>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 = 42.7 bits (100), Expect = 3e-07
 Identities = 20/51 (39%), Positives = 31/51 (60%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
            +   +N SKGYG+V F T+E A++A+  MNG LL+ R +FV   +  + 
Sbjct: 38 CKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE 88

>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 = 42.3 bits (99), Expect = 4e-07
 Identities = 13/48 (27%), Positives = 21/48 (43%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
            M      +  Y +V F    +A  ALA MNG+ + G+ + V+    
Sbjct: 38 CKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT 85

>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 = 42.4 bits (99), Expect = 4e-07
 Identities = 10/83 (12%), Positives = 32/83 (38%), Gaps = 8/83 (9%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
           +TE+ +  +F +          +          ++    N+ K + ++ F + +E  +A
Sbjct: 12 GITEEAMMDFFNA-------QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 64

Query: 71 LADMNGKLLDGRVIFVDNVRPSR 93
          +   +G +  G+ + +      +
Sbjct: 65 M-AFDGIIFQGQSLKIRRPHDYQ 86

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.5 bits (99), Expect = 5e-07
 Identities = 7/56 (12%), Positives = 16/56 (28%)

Query: 39 LFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
                 +     +  G G V +  +E+ + AL  ++             +R    
Sbjct: 35 HMREAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE 90

>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 = 41.9 bits (98), Expect = 5e-07
 Identities = 7/32 (21%), Positives = 16/32 (50%)

Query: 56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
          +G++   T   A+ A  +++   L G+ + V 
Sbjct: 46 FGFIRLETRTLAEIAKVELDNMPLRGKQLRVR 77

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.9 bits (98), Expect = 6e-07
 Identities = 13/89 (14%), Positives = 31/89 (34%), Gaps = 29/89 (32%)

Query: 1  MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVT 60
           L   F ++G + +  +     +                              +G  +V 
Sbjct: 22 QLDTIFGKYGSIVQKNILRDKLTGR---------------------------PRGVAFVR 54

Query: 61 FSTEEEAQKALADMNGKLLDG--RVIFVD 87
          ++  EEAQ+A++ +N  + +G  + + V 
Sbjct: 55 YNKREEAQEAISALNNVIPEGGSQPLSVR 83

>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 = 41.6 bits (97), Expect = 7e-07
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 13/77 (16%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
          + T++ +  +F+                      + D    RS+G+G+VT++T EE   A
Sbjct: 17 ETTDESLRSHFEQWGTLTDCVV------------MRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 71 LADMNGKLLDGRVIFVD 87
          + +     +DGRV+   
Sbjct: 65 M-NARPHKVDGRVVEPK 80

>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 = 41.6 bits (97), Expect = 7e-07
 Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 43 TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNT 97
           ++        + + +VTF+ ++ AQ         ++ G  + + N  P    N+
Sbjct: 31 DVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDLIIKGISVHISNAEPKHNSNS 83

>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 = 41.5 bits (97), Expect = 8e-07
 Identities = 12/47 (25%), Positives = 25/47 (53%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          I+D   +  +   +VT+   E A +A+A++NG  ++   + V+  R 
Sbjct: 30 IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 76

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (97), Expect = 9e-07
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 1/60 (1%)

Query: 46  MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQS 105
           +     +  G   V F  E++A+K+   ++ K L+GR  FV  V        +     Q 
Sbjct: 42  LVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQG 100

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (97), Expect = 1e-06
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 29  LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
           +  F      +  +  I      ++ G G+V F  E + + AL   + + +  R I V  
Sbjct: 35  VIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP 93

Query: 89  VRPSRRYNTDAPLARQSAQS 108
           +   +       + R+  QS
Sbjct: 94  ITK-KGMLEKIDMIRKRLQS 112

>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 = 41.3 bits (96), Expect = 1e-06
 Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 6/69 (8%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN------GKLLDGR 82
          L   L     L    +++      SKG  +  F T+E AQK LA  +      G  LDGR
Sbjct: 25 LGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR 84

Query: 83 VIFVDNVRP 91
           + VD    
Sbjct: 85 QLKVDLAVT 93

>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 = 40.7 bits (95), Expect = 1e-06
 Identities = 8/49 (16%), Positives = 26/49 (53%), Gaps = 3/49 (6%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
          I+    + +  + ++ + ++ +A+KAL+  +G++    ++    V+P  
Sbjct: 30 ILKHVMSNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMI--GVKPCI 75

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 3e-06
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
          L         + +   I+DK  N+ KGYG+V F +   AQKA+  +    +  ++ 
Sbjct: 15 LVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 70

>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 = 40.3 bits (94), Expect = 3e-06
 Identities = 15/42 (35%), Positives = 22/42 (52%)

Query: 52 RSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
            KGY +V FST E A  A+  +NG  ++G V+     + S 
Sbjct: 52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 93

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 3e-06
 Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 13/76 (17%)

Query: 11 QVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKA 70
             E+ +  YF                        MD   N+ +G+ ++TF  EE  +K 
Sbjct: 10 DTPEEKIREYFGGFGEVESIEL------------PMDNKTNKRRGFCFITFKEEEPVKKI 57

Query: 71 LADMNGKLLDGRVIFV 86
          + +     +      +
Sbjct: 58 M-EKKYHNVGLSKCEI 72

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 3e-06
 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 45 IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKL-LDGRVIFVDNVRPSRR 94
           +        GY +V +  +  A +A+  ++GK+ L G+++ VD     + 
Sbjct: 28 PLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 78

>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 = 40.0 bits (93), Expect = 4e-06
 Identities = 14/43 (32%), Positives = 24/43 (55%)

Query: 45  IMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           + D   +   G  YV F  EE+A+KA+ D+N +  +G+ I  +
Sbjct: 59  VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>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 = 4e-06
 Identities = 9/48 (18%), Positives = 17/48 (35%)

Query: 44 IIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
           I+      S+G G+    + E+ +  +   NGK +           P
Sbjct: 49 RILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 39.6 bits (92), Expect = 4e-06
 Identities = 11/37 (29%), Positives = 21/37 (56%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGR 82
          +D+    S+G G++ F    EA++A+  +NG+   G 
Sbjct: 40 VDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 76

>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 = 38.9 bits (90), Expect = 7e-06
 Identities = 11/42 (26%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           DK  NR +G+G+VTF +E+  +K    ++   ++ +++   
Sbjct: 33 FDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECK 73

>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 = 38.5 bits (89), Expect = 8e-06
 Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
           D+G  + +G+ +VTF   +   K +       ++G    V 
Sbjct: 36 TDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR 76

>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 = 39.0 bits (90), Expect = 1e-05
 Identities = 7/59 (11%), Positives = 17/59 (28%), Gaps = 1/59 (1%)

Query: 51  NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTDAPLARQSAQSP 109
            +S     + FS    A  A   ++     G+ + +   +      +         +S 
Sbjct: 43  FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQT-LHIGSSHLAPPNPDKSG 100

>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 = 38.2 bits (88), Expect = 1e-05
 Identities = 9/46 (19%), Positives = 22/46 (47%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
               N S+ + Y+  +++E+A+  +  +NG  ++G  +      P
Sbjct: 35 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP 80

>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 = 38.6 bits (89), Expect = 2e-05
 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 5/59 (8%)

Query: 56  YGYVTFSTEEEAQKALADMNGKLLDGRVIFVD-----NVRPSRRYNTDAPLARQSAQSP 109
              V  +   +AQ A++ +NG  L G+ I +      NV+  R    D  L +    SP
Sbjct: 42  NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 100

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-05
 Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 1/66 (1%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          +  F    +              R KG+GY  F   +    AL+ +N + L  + I VD 
Sbjct: 32 IKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV 90

Query: 89 VRPSRR 94
             ++ 
Sbjct: 91 ADQAQD 96

>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 = 38.7 bits (89), Expect = 3e-05
 Identities = 11/39 (28%), Positives = 20/39 (51%)

Query: 56  YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRR 94
           YG+V F +   AQ+A+A +NG  +  + + V       +
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 38.1 bits (88), Expect = 3e-05
 Identities = 5/45 (11%), Positives = 18/45 (40%), Gaps = 2/45 (4%)

Query: 51 NRSKGYGYVTFSTEEEAQKALADMNGKLL--DGRVIFVDNVRPSR 93
            ++    + ++    AQ A   ++G+ +      + +D  + + 
Sbjct: 42 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 86

>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 = 37.8 bits (87), Expect = 3e-05
 Identities = 10/42 (23%), Positives = 18/42 (42%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVD 87
               +R+K   +VT    E+AQ A+   +     G+ + V 
Sbjct: 32 KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ 73

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 3e-05
 Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          +  F      +     +    + RS G  +V F+++E A+KAL   + + +  R I +  
Sbjct: 32 IVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFK 90

Query: 89 VRPS 92
             +
Sbjct: 91 SSRA 94

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.2 bits (85), Expect = 4e-05
 Identities = 6/38 (15%), Positives = 12/38 (31%)

Query: 56 YGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSR 93
           G V F  +E+   A+  ++             +R   
Sbjct: 37 TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV 74

>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 = 37.5 bits (86), Expect = 5e-05
 Identities = 14/65 (21%), Positives = 27/65 (41%)

Query: 29 LHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDN 88
          L              I       R +G  ++TF  +E A +AL  +NG  L G+++ ++ 
Sbjct: 35 LVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF 94

Query: 89 VRPSR 93
           +  +
Sbjct: 95 GKNKK 99

>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 = 36.7 bits (84), Expect = 7e-05
 Identities = 11/39 (28%), Positives = 19/39 (48%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVI 84
             G        YVT+   E+A +A+  +N  ++DGR +
Sbjct: 48 SYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 86

>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 = 36.5 bits (83), Expect = 8e-05
 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 46 MDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRP 91
          +D     ++ +GYV F + E+ +KAL ++ G  + G  I ++  + 
Sbjct: 46 VDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKG 90

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 1e-04
 Identities = 11/65 (16%), Positives = 20/65 (30%), Gaps = 1/65 (1%)

Query: 30 HYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNV 89
            +            I      R  G   V F+T E+A  A+A  +   +  R + +   
Sbjct: 31 DIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN 89

Query: 90 RPSRR 94
            +  
Sbjct: 90 STAGT 94

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.0 bits (80), Expect = 3e-04
 Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 2/41 (4%)

Query: 56 YGYVTFSTEEEAQKALADMNGKLLDG--RVIFVDNVRPSRR 94
          + Y+ + + + AQ A A M G  L G  R + VD  +    
Sbjct: 55 FAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS 95

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.5 bits (76), Expect = 0.001
 Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 56 YGYVTFSTEEEAQKALADMNGK-LLDGR 82
          Y +  + T EE+++A   +NGK ++D  
Sbjct: 58 YSFARYRTTEESKRAYVTLNGKEVVDDL 85

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	112
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.7
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.69
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.69
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.69
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.69
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.68
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.68
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.66
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.66
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.65
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.65
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.63
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.62
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.62
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.61
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.61
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.6
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.59
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.59
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.59
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.58
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.58
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.58
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.58
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.57
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.56
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.55
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.55
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.53
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.53
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.52
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.52
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.51
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.48
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.48
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.48
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.48
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.47
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.47
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.46
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.45
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.45
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.45
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.44
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.43
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.41
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.41
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.41
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.41
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.41
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.4
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.4
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.39
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.38
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.38
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.38
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.37
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.37
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.36
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.33
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.33
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.33
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.32
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.26
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.22
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.2
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.2
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.17
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.17
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.15
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.09
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.07
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.9
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.89
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.84
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.36
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.18

>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=99.70  E-value=2.3e-17  Score=102.08  Aligned_cols=63  Identities=29%  Similarity=0.509  Sum_probs=61.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++++|+.+++++|||||+|.++++|++|+..|||..++|
T Consensus        19 l~~~F~~~G~v~~---------------------------~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g   71 (82)
T d1b7fa1          19 LYALFRAIGPINT---------------------------CRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN   71 (82)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHHhCCcce---------------------------eeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|+|++|+|
T Consensus        72 ~~l~v~~a~p   81 (82)
T d1b7fa1          72 KRLKVSYARP   81 (82)
T ss_dssp             EECEEEECCC
T ss_pred             EEEEEEEcCC
Confidence            9999999976

>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=99.69  E-value=2.6e-17  Score=103.74  Aligned_cols=66  Identities=35%  Similarity=0.588  Sum_probs=62.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++++|+.+++++|||||+|.++++|++|+..|||..++|
T Consensus        22 l~~~F~~~G~i~~---------------------------v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g   74 (89)
T d2cqba1          22 LHAAFIPFGDITD---------------------------IQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG   74 (89)
T ss_dssp             HHHHHTTTSCCCC---------------------------EECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHhhCCeEEe---------------------------cccccccccccccceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++|++.+.
T Consensus        75 ~~l~v~~a~p~~~   87 (89)
T d2cqba1          75 RTIRVNLAKPMRI   87 (89)
T ss_dssp             EEEEEEECCCCCC
T ss_pred             EEEEEEEeCCCCC
Confidence            9999999987544

>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=99.69  E-value=5.2e-17  Score=104.06  Aligned_cols=67  Identities=30%  Similarity=0.526  Sum_probs=63.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+++++|||||+|.+.++|+.|+..|||..++|
T Consensus        25 l~~~F~~~g~v~~---------------------------v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (99)
T d1whwa_          25 LEKLFSAYGPLSE---------------------------LHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG   77 (99)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS
T ss_pred             HHHHHHhcCCcee---------------------------eeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|++++++...
T Consensus        78 r~i~V~~a~~~~~~   91 (99)
T d1whwa_          78 RMLHVLPSTIKKEA   91 (99)
T ss_dssp             CEEEEEECCCCSTT
T ss_pred             EEEEEEECCCCCcc
Confidence            99999999876544

>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=99.69  E-value=3.9e-17  Score=103.12  Aligned_cols=65  Identities=29%  Similarity=0.569  Sum_probs=62.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|+.|+.++.++|||||+|.+.++|+.|+..|||..++|
T Consensus        25 l~~~f~~~G~v~~---------------------------v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g   77 (90)
T d2cq0a1          25 LQELFRPFGSISR---------------------------IYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH   77 (90)
T ss_dssp             HHTTSTTTCCEEE---------------------------EEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             HHHHHHHhccccc---------------------------ccccccccccccccceeEEECCHHHHHHHHHHhCCCEECC
Confidence            7889999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|++|+++.
T Consensus        78 ~~i~v~~akp~~   89 (90)
T d2cq0a1          78 LILNVEWAKPST   89 (90)
T ss_dssp             EECEEEESSCCC
T ss_pred             EEEEEEeeeCCC
Confidence            999999998764

>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=99.69  E-value=6e-17  Score=100.06  Aligned_cols=65  Identities=31%  Similarity=0.571  Sum_probs=61.7

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|++||+|.+                           +++++|..+++++|||||+|.++++|++|+..|||..++
T Consensus        18 ~l~~~f~~~G~v~~---------------------------v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~   70 (82)
T d1fxla1          18 EFRSLFGSIGEIES---------------------------CKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ   70 (82)
T ss_dssp             HHHHHHHTTSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             HHHHHHHHhCCccc---------------------------ccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEEC
Confidence            37899999999999                           999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|+|++|+|.
T Consensus        71 g~~l~v~~AkPs   82 (82)
T d1fxla1          71 TKTIKVSYARPS   82 (82)
T ss_dssp             TEECEEEECCCC
T ss_pred             CEEEEEEEeeCc
Confidence            999999999863

>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=99.69  E-value=4.6e-17  Score=102.47  Aligned_cols=64  Identities=27%  Similarity=0.469  Sum_probs=61.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++++|+.+|+++|||||+|.+.++|+.|+..|||..++|
T Consensus        24 l~~~F~~~G~i~~---------------------------v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g   76 (88)
T d1rk8a_          24 IQEKFCDYGEIKN---------------------------IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG   76 (88)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHHcCCccc---------------------------ccccccccccccccceeEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|++|.++
T Consensus        77 ~~l~V~~a~~k   87 (88)
T d1rk8a_          77 QTIQVDWCFVK   87 (88)
T ss_dssp             EECEEEESEEC
T ss_pred             EEEEEEEecCC
Confidence            99999999764

>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=99.68  E-value=4.7e-17  Score=101.96  Aligned_cols=66  Identities=20%  Similarity=0.456  Sum_probs=62.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.||+++|||||+|.++++|+.|+..|||..++|
T Consensus        18 l~~~F~~~G~v~~---------------------------v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g   70 (85)
T d2u2fa_          18 VKELLTSFGPLKA---------------------------FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD   70 (85)
T ss_dssp             HHHHHTSSSCEEE---------------------------EEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSS
T ss_pred             HHHHHHhcCccce---------------------------EEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      ++|.|++|.+..+
T Consensus        71 ~~l~V~~A~~~~~   83 (85)
T d2u2fa_          71 KKLLVQRASVGAK   83 (85)
T ss_dssp             SCCEEEECCCCCC
T ss_pred             EEEEEEECCCCCC
Confidence            9999999976543

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=6.8e-17  Score=100.27  Aligned_cols=67  Identities=31%  Similarity=0.521  Sum_probs=61.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAA-TIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||.|.+                           + ++++|+.+++++|||||+|.++++|+.|+..|||..++
T Consensus        15 l~~~F~~~G~i~~---------------------------~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~   67 (83)
T d1x5ta1          15 LYDTFSAFGVILQ---------------------------TPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC   67 (83)
T ss_dssp             HHHHHHTTSCBSS---------------------------CCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET
T ss_pred             HHHHHHHhCceee---------------------------eEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEEC
Confidence            7899999999976                           4 78899999999999999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCC
Q 033734           81 GRVIFVDNVRPSRRY   95 (112)
Q Consensus        81 g~~i~V~~a~~~~~~   95 (112)
                      |++|+|++|.++..+
T Consensus        68 gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          68 NRPITVSYAFKKDSK   82 (83)
T ss_dssp             TEECEEEESCCCCCC
T ss_pred             CEEEEEEEecCCCcC
Confidence            999999999876544

>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=99.68  E-value=8.6e-17  Score=99.49  Aligned_cols=62  Identities=29%  Similarity=0.454  Sum_probs=60.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+|+++|||||+|.++++|+.|+..|||..++|
T Consensus        17 l~~~F~~~G~i~~---------------------------v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~g   69 (80)
T d1cvja1          17 LYEKFSPAGPILS---------------------------IRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG   69 (80)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETT
T ss_pred             HHHHHHHhCCEeE---------------------------EEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      ++|+|++|+
T Consensus        70 r~i~v~~a~   78 (80)
T d1cvja1          70 KPVRIMWSQ   78 (80)
T ss_dssp             EECEEEECC
T ss_pred             EEEEEEEeC
Confidence            999999985

>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=99.68  E-value=1.6e-16  Score=100.99  Aligned_cols=64  Identities=27%  Similarity=0.427  Sum_probs=61.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++++++.++.++|||||+|.+.++|+.|+..|||..++|
T Consensus        24 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   76 (93)
T d1h2vz_          24 IYELFSKSGDIKK---------------------------IIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD   76 (93)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT
T ss_pred             HHHHHHHHCCcce---------------------------eccccccccccccceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|+++.+.
T Consensus        77 r~i~V~~a~~~   87 (93)
T d1h2vz_          77 RIIRTDWDAGF   87 (93)
T ss_dssp             EECEEEEESCC
T ss_pred             EEEEEEEcCCC
Confidence            99999998654

>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=99.67  E-value=5.6e-17  Score=103.12  Aligned_cols=66  Identities=30%  Similarity=0.454  Sum_probs=62.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|++|+.++.++|||||+|.+.++|++|+..|||..++|
T Consensus        26 l~~~F~~~G~v~~---------------------------v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   78 (93)
T d1x5ua1          26 LWELFLQAGPVVN---------------------------THMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG   78 (93)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS
T ss_pred             HHHHHHHhCCccc---------------------------cceeecccccccccceEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|+|++|++..+
T Consensus        79 ~~l~V~~A~~~~~   91 (93)
T d1x5ua1          79 KPIRVNKASAHNK   91 (93)
T ss_dssp             CBCEEEETTTTSC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987654

>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=99.66  E-value=1.8e-16  Score=102.33  Aligned_cols=67  Identities=31%  Similarity=0.476  Sum_probs=63.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.++.++.++|||||+|.++++|+.||..|||..++|
T Consensus        35 l~~~F~~~G~i~~---------------------------~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   87 (102)
T d2cpza1          35 LLQMFMPFGNVVS---------------------------AKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   87 (102)
T ss_dssp             HHHHHGGGSCCSE---------------------------EEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHhhccccc---------------------------cceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|++++++..+
T Consensus        88 ~~i~V~~a~~k~~~  101 (102)
T d2cpza1          88 KRLKVQLKRSKNDS  101 (102)
T ss_dssp             EECEEECCCCSCCC
T ss_pred             EEEEEEEeCCCCCC
Confidence            99999999876543

>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=99.66  E-value=1.8e-16  Score=106.80  Aligned_cols=67  Identities=27%  Similarity=0.526  Sum_probs=63.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|.+                           ++|++|+.+++++|||||+|.+.++|+.||..|||..++|
T Consensus        59 l~~~F~~~G~i~~---------------------------v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~g  111 (139)
T d1u6fa1          59 LRQLFERYGPIES---------------------------VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN  111 (139)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS
T ss_pred             HHHHHHhhccccc---------------------------cccccccccccccceeeEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|+++++...+
T Consensus       112 r~l~V~~a~~~~~~  125 (139)
T d1u6fa1         112 KRLKVALAASGHQR  125 (139)
T ss_dssp             CEEEEEESSCCCCC
T ss_pred             EEEEEEEcCCCCCC
Confidence            99999999765544

>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=99.65  E-value=2.5e-17  Score=106.33  Aligned_cols=66  Identities=32%  Similarity=0.661  Sum_probs=62.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++++.+|+++|||||+|.+.++|+.|+..|||..++|
T Consensus        25 l~~~f~~~G~i~~---------------------------v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g   77 (104)
T d1p1ta_          25 LKDIFSEVGPVVS---------------------------FRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG   77 (104)
T ss_dssp             HHHHHHTTSCCSE---------------------------EEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS
T ss_pred             HHHhhhccccccc---------------------------cccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.+...
T Consensus        78 ~~i~V~~a~~~~~   90 (104)
T d1p1ta_          78 RALRVDNAASEKN   90 (104)
T ss_dssp             SCBEEEETTCTTH
T ss_pred             EEEEEEECCCCCC
Confidence            9999999876543

>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=99.65  E-value=2.7e-16  Score=96.85  Aligned_cols=62  Identities=32%  Similarity=0.546  Sum_probs=58.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|+.++ +++++|||||+|.++++|+.|+..|||..++|
T Consensus        17 l~~~F~~~G~v~~---------------------------~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g   68 (78)
T d1no8a_          17 IQELFAEFGTLKK---------------------------AAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDG   68 (78)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHHhCCCeE---------------------------EEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9999997 89999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      ++|+|+++.+
T Consensus        69 ~~l~V~~a~S   78 (78)
T d1no8a_          69 RPMNIQLVTS   78 (78)
T ss_dssp             EECEEEEECC
T ss_pred             EEEEEEEeeC
Confidence            9999999863

>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=99.64  E-value=4.3e-16  Score=96.92  Aligned_cols=64  Identities=34%  Similarity=0.553  Sum_probs=58.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHHhhCCce
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKN---RSKGYGYVTFSTEEEAQKALADMNGKL   78 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~---~~rG~afV~f~~~~~a~~Ai~~l~g~~   78 (112)
                      |+++|++||+|..                           ++|++++.++   .++|||||+|.++++|+.|+..|||..
T Consensus        15 l~~~F~~~G~v~~---------------------------v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~   67 (85)
T d2cpfa1          15 LKGVFSKVGAIKS---------------------------CTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHT   67 (85)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCE
T ss_pred             HHHHHHHhCCccc---------------------------cceecccccccccccceEEEEEECCHHHHHHHHHHhCCCE
Confidence            7899999999999                           9999987665   468999999999999999999999999


Q ss_pred             eCCeeEEEEeccCC
Q 033734           79 LDGRVIFVDNVRPS   92 (112)
Q Consensus        79 l~g~~i~V~~a~~~   92 (112)
                      ++|++|.|+++.+.
T Consensus        68 ~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          68 VDGHKLEVRISERA   81 (85)
T ss_dssp             ETTEECEEECSSCS
T ss_pred             ECCEEEEEEECCCC
Confidence            99999999998643

>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=99.63  E-value=5e-16  Score=96.85  Aligned_cols=61  Identities=28%  Similarity=0.551  Sum_probs=58.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++++|+.+++++|||||+|.++++|+.|+..|||..+.|
T Consensus        23 l~~~F~~~G~i~~---------------------------~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   75 (85)
T d1b7fa2          23 LDTIFGKYGSIVQ---------------------------KNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG   75 (85)
T ss_dssp             HHHHHTSSSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             HHHHHHhhCCEee---------------------------eeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            7899999999999                           9999999999999999999999999999999999999976


Q ss_pred             --eeEEEEec
Q 033734           82 --RVIFVDNV   89 (112)
Q Consensus        82 --~~i~V~~a   89 (112)
                        ++|.|++|
T Consensus        76 ~~~~l~V~~A   85 (85)
T d1b7fa2          76 GSQPLSVRLA   85 (85)
T ss_dssp             CSSCCEEEEC
T ss_pred             CCeEEEEEEC
Confidence              88999986

>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=99.63  E-value=5.7e-16  Score=96.80  Aligned_cols=61  Identities=31%  Similarity=0.573  Sum_probs=57.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++++|+.+|+++|||||+|.++++|+.|+..|||..++|
T Consensus        23 L~~~F~~~G~v~~---------------------------v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G   75 (85)
T d1fxla2          23 LEQLFSQYGRIIT---------------------------SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG   75 (85)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             HHHHHHHhCCccc---------------------------cccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           9999999999999999999999999999999999999997


Q ss_pred             --eeEEEEec
Q 033734           82 --RVIFVDNV   89 (112)
Q Consensus        82 --~~i~V~~a   89 (112)
                        ++|.|++|
T Consensus        76 ~~~~i~V~~A   85 (85)
T d1fxla2          76 ATEPITVKFA   85 (85)
T ss_dssp             CSSCCEEEEC
T ss_pred             CCEEEEEEeC
Confidence              55888875

>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=99.62  E-value=4.5e-16  Score=96.07  Aligned_cols=63  Identities=17%  Similarity=0.367  Sum_probs=53.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.+..+|+++|||||+|.++++|++|+..|||..++|
T Consensus        18 l~~~f~~~G~v~~---------------------------~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g   70 (81)
T d2ghpa1          18 IRDLLQDINVVAL---------------------------SIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG   70 (81)
T ss_dssp             HHHHHHHTTCCCC---------------------------EEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHHhCcEEe---------------------------eeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECC
Confidence            7889999999998                           8888888899999999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      ++|.|++++|
T Consensus        71 ~~i~V~~a~P   80 (81)
T d2ghpa1          71 YTLVTKVSNP   80 (81)
T ss_dssp             EECEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999986

>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=99.62  E-value=5.1e-16  Score=97.54  Aligned_cols=66  Identities=41%  Similarity=0.760  Sum_probs=62.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.++.+..++.++|||||+|.++++|+.|+..|||..++|
T Consensus        22 l~~~F~~~G~i~~---------------------------~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g   74 (90)
T d1x5sa1          22 LEQVFSKYGQISE---------------------------VVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG   74 (90)
T ss_dssp             HHHHHHHHSCCCE---------------------------EEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS
T ss_pred             HHHhhhccccccc---------------------------eeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++|.++..
T Consensus        75 ~~l~V~~a~~~~~   87 (90)
T d1x5sa1          75 RQIRVDQAGKSSD   87 (90)
T ss_dssp             CCCEEEEEECCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999976544

>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=99.62  E-value=1.3e-15  Score=95.11  Aligned_cols=62  Identities=32%  Similarity=0.597  Sum_probs=58.6

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|++||+|..                           ++|++|+.+|+++|||||+|.++++|++|+. ++++.++
T Consensus        22 ~l~~~F~~~G~i~~---------------------------v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~   73 (84)
T d1l3ka1          22 SLRSHFEQWGTLTD---------------------------CVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVD   73 (84)
T ss_dssp             HHHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEET
T ss_pred             HHHHHHHhhccccc---------------------------eeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEEC
Confidence            37899999999999                           9999999999999999999999999999998 6899999


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      |+.|.|+.|.
T Consensus        74 Gr~i~V~~A~   83 (84)
T d1l3ka1          74 GRVVEPKRAV   83 (84)
T ss_dssp             TEECEEEECC
T ss_pred             CEEEEEEeee
Confidence            9999999885

>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=99.62  E-value=2.5e-16  Score=97.15  Aligned_cols=60  Identities=35%  Similarity=0.561  Sum_probs=57.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+++++|||||+|.++++|++|+. ++++.++|
T Consensus        17 l~~~F~~~G~i~~---------------------------v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~G   68 (77)
T d1uawa_          17 LREYFGQFGEVKE---------------------------CLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDS   68 (77)
T ss_dssp             HHHHHTTTSCCCC---------------------------EEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSS
T ss_pred             HHHHHHHhCCcce---------------------------eeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECC
Confidence            7899999999999                           9999999999999999999999999999998 79999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|+.|
T Consensus        69 r~i~V~~A   76 (77)
T d1uawa_          69 KTIDPKVA   76 (77)
T ss_dssp             CCCEEEEC
T ss_pred             eEEEEEEC
Confidence            99999876

>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=99.62  E-value=9.8e-16  Score=95.00  Aligned_cols=58  Identities=36%  Similarity=0.697  Sum_probs=56.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+++++|||||+|.+.++|+.|+..|||..++|
T Consensus        26 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   78 (83)
T d2cqca1          26 LREVFSKYGPIAD---------------------------VSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG   78 (83)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHHhCCCcc---------------------------ccccccccccccccceEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeEEE
Q 033734           82 RVIFV   86 (112)
Q Consensus        82 ~~i~V   86 (112)
                      +.|+|
T Consensus        79 r~i~V   83 (83)
T d2cqca1          79 RRIRV   83 (83)
T ss_dssp             EEEEE
T ss_pred             EEeEC
Confidence            99987

>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=99.61  E-value=9.3e-16  Score=99.44  Aligned_cols=66  Identities=30%  Similarity=0.573  Sum_probs=61.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +.|++|+.++.++|||||+|.+.++|++|+. ++|..++|
T Consensus        37 L~~~F~~~G~i~~---------------------------~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G   88 (103)
T d1x4ba1          37 LRNYYEQWGKLTD---------------------------CVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDG   88 (103)
T ss_dssp             HHHHHTSSCCCSE---------------------------EEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETT
T ss_pred             HHHHHHhhCcccc---------------------------eeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECC
Confidence            7899999999999                           9999999999999999999999999999996 89999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|++|.++..+
T Consensus        89 ~~i~V~~a~~ke~~  102 (103)
T d1x4ba1          89 RVVEPKRAVAREES  102 (103)
T ss_dssp             EEEEEECCSSCCCC
T ss_pred             EEEEEEECcccCCC
Confidence            99999999876654

>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=99.61  E-value=1.3e-15  Score=96.50  Aligned_cols=64  Identities=28%  Similarity=0.467  Sum_probs=58.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+|+++|||||+|.++++|++||..  .+.++|
T Consensus        25 l~~~F~~~G~i~~---------------------------v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~G   75 (90)
T d2cqga1          25 LKEYFSTFGEVLM---------------------------VQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDG   75 (90)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETT
T ss_pred             HHHHHHhhcccce---------------------------eeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCC
Confidence            7899999999999                           99999999999999999999999999999985  458999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.++..
T Consensus        76 r~i~v~~a~~k~~   88 (90)
T d2cqga1          76 RWCDCKLPNSKQS   88 (90)
T ss_dssp             EEEEEECCCTTCC
T ss_pred             EEeEEEeCCCCCC
Confidence            9999999977543

>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=99.61  E-value=7.9e-16  Score=97.87  Aligned_cols=65  Identities=23%  Similarity=0.490  Sum_probs=59.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHhh-CCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKG-KNRSKGYGYVTFSTEEEAQKALADM-NGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~-t~~~rG~afV~f~~~~~a~~Ai~~l-~g~~l   79 (112)
                      |+++|++||+|..                           ++|+++.. +|+++|||||+|.++++|.+|+..| ||..+
T Consensus        25 l~~~F~~~G~i~~---------------------------v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~   77 (94)
T d2cpha1          25 IRELFSTFGELKT---------------------------VRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL   77 (94)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS
T ss_pred             HHHHHHHhCCceE---------------------------EEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEE
Confidence            7899999999999                           99988854 7899999999999999999999998 89999


Q ss_pred             CCeeEEEEeccCCC
Q 033734           80 DGRVIFVDNVRPSR   93 (112)
Q Consensus        80 ~g~~i~V~~a~~~~   93 (112)
                      +|++|.|++|.+..
T Consensus        78 ~Gr~l~V~~A~~~~   91 (94)
T d2cpha1          78 YGRRLVLEWADSEV   91 (94)
T ss_dssp             SSCBCEEEECCCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999997654

>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=99.60  E-value=1.7e-15  Score=97.78  Aligned_cols=63  Identities=35%  Similarity=0.605  Sum_probs=59.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+++++|||||+|.++++|++||+.+|+ .++|
T Consensus        27 l~~~F~~~G~i~~---------------------------v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~G   78 (103)
T d2cqda1          27 LRKYFEGFGDIEE---------------------------AVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG   78 (103)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT
T ss_pred             HHHHHhhcccccc---------------------------eeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCC
Confidence            7899999999999                           99999999999999999999999999999998875 7999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++...
T Consensus        79 r~l~V~~a~~~   89 (103)
T d2cqda1          79 RKANVNLAYLG   89 (103)
T ss_dssp             EECEEEESTTT
T ss_pred             EEEEEEEcCCC
Confidence            99999998754

>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=99.59  E-value=2.3e-15  Score=95.98  Aligned_cols=75  Identities=27%  Similarity=0.300  Sum_probs=62.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|....                   ......+.+.+|+.+++++|||||+|.++++|.+|+..|||..++|
T Consensus        25 l~~~F~~~G~i~~~~-------------------~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1          25 LADFFKQCGVVKMNK-------------------RTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             HHHHHTTTSCBCBCS-------------------SSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHHHCceEEEee-------------------ecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            789999999986511                   1111227788899999999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|++++++.+.
T Consensus        86 r~i~V~~a~~~~p~   99 (101)
T d2cpea1          86 SKLKVSLARKKPPM   99 (101)
T ss_dssp             EECEEECSSCCCCS
T ss_pred             EEEEEEEcCCCCCC
Confidence            99999999875543

>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=99.59  E-value=1.3e-15  Score=95.34  Aligned_cols=63  Identities=27%  Similarity=0.444  Sum_probs=55.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEee-CCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMD-KGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d-~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||.|..                           ++|+++ +.+++++|||||+|.+.++|++|+. |||..++
T Consensus        22 l~~~F~~~G~i~~---------------------------v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~   73 (86)
T d2ghpa3          22 LRESFEGFGSIEK---------------------------INIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLG   73 (86)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEET
T ss_pred             HHHHHHhhhhccc---------------------------eeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEEC
Confidence            7889999999999                           888764 5688999999999999999999995 9999999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|.|++|.++
T Consensus        74 gr~l~V~~a~~k   85 (86)
T d2ghpa3          74 NREISVSLADKK   85 (86)
T ss_dssp             TEEEEEEECCCC
T ss_pred             CEEEEEEEcCCC
Confidence            999999999764

>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=99.59  E-value=8.6e-16  Score=93.99  Aligned_cols=60  Identities=35%  Similarity=0.627  Sum_probs=56.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++|++|+.+++++|||||+|.++++|++|+. +++..++|
T Consensus        16 l~~~F~~~G~i~~---------------------------~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~G   67 (75)
T d1hd0a_          16 LKDYFSKFGEVVD---------------------------CTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNG   67 (75)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTT
T ss_pred             HHHHHHhhccccc---------------------------cccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECC
Confidence            7899999999999                           9999999999999999999999999999997 79999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|+.|
T Consensus        68 r~i~V~rA   75 (75)
T d1hd0a_          68 KVIDPKRA   75 (75)
T ss_dssp             BCCEECCC
T ss_pred             CEEEeeEC
Confidence            99999754

>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=99.58  E-value=9.2e-16  Score=99.05  Aligned_cols=63  Identities=35%  Similarity=0.548  Sum_probs=59.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|.+                           ++|++|+.+|+++|||||+|.++++|++|+. |||..++|
T Consensus        35 l~~~F~~~G~V~~---------------------------v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G   86 (101)
T d2cq4a1          35 LEDFFSAVGKVRD---------------------------VRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLG   86 (101)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETT
T ss_pred             HHHHHcCCCeEEE---------------------------EEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECC
Confidence            7899999999999                           9999999999999999999999999999995 99999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|.|+++.+.
T Consensus        87 ~~l~V~~a~~~   97 (101)
T d2cq4a1          87 VPIIVQASQAE   97 (101)
T ss_dssp             EEEEEEEHHHH
T ss_pred             EEEEEEECCCC
Confidence            99999998643

>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=99.58  E-value=3.6e-15  Score=95.68  Aligned_cols=61  Identities=21%  Similarity=0.562  Sum_probs=54.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|        ++|||||+|.+.++|++||..|||..++|
T Consensus        33 L~~~F~~~G~i~~---------------------------~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (98)
T d1wf2a_          33 VEAIFSKYGKIVG---------------------------CSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAG   77 (98)
T ss_dssp             HHHSSTTSSCEEE---------------------------EEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETT
T ss_pred             HHHHHhhcCCEEE---------------------------EEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           877        47899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNT   97 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~   97 (112)
                      +.|+|+++++.....+
T Consensus        78 ~~l~V~~a~~~~~~~~   93 (98)
T d1wf2a_          78 QVLDINLAAEPKVNRS   93 (98)
T ss_dssp             EECEEEETTSCCCCSS
T ss_pred             EEEEEEECCCCCCCCC
Confidence            9999999976544333

>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=99.58  E-value=1.4e-15  Score=95.59  Aligned_cols=64  Identities=42%  Similarity=0.811  Sum_probs=58.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++|+.++  +.++|||||+|.++++|++|+..|||..++|
T Consensus        25 l~~~F~~~G~v~~---------------------------~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   75 (89)
T d1cvja2          25 LYDTFSAFGNILS---------------------------CKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLND   75 (89)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETT
T ss_pred             HHHHHHhcCCceE---------------------------EEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999986  4478999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++++++..
T Consensus        76 ~~i~V~~a~~~~~   88 (89)
T d1cvja2          76 RKVFVGRFKSRKE   88 (89)
T ss_dssp             EEEEEEECCCTTT
T ss_pred             EEEEEEECCCCCC
Confidence            9999999987653

>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=99.58  E-value=7.7e-15  Score=92.90  Aligned_cols=64  Identities=34%  Similarity=0.677  Sum_probs=58.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           ++++.++  +.++|||||+|.++++|++|+..|||..++|
T Consensus        28 L~~~F~~~G~v~~---------------------------v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g   78 (93)
T d2cq3a1          28 LRQMFGQFGKILD---------------------------VEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEG   78 (93)
T ss_dssp             HHHHGGGTSCEEE---------------------------EEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhhcceeee---------------------------ccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           9999986  3478999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++|+++..
T Consensus        79 ~~l~V~~A~~r~~   91 (93)
T d2cq3a1          79 RKIEVNNATARVM   91 (93)
T ss_dssp             EECEEEECCSSCC
T ss_pred             EEEEEEecCcCCC
Confidence            9999999987543

>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=99.57  E-value=7.8e-15  Score=92.29  Aligned_cols=63  Identities=27%  Similarity=0.456  Sum_probs=57.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||+|.+                           ++++.|+.+  .+|||||+|.+.++|+.|+..|||..+.|
T Consensus        25 l~~~F~~~G~i~~---------------------------v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g   75 (90)
T d2cqia1          25 ILQLFSQIGPCKS---------------------------CKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILG   75 (90)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhcCCcee---------------------------eeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECC
Confidence            7899999999999                           999999754  47999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|+|++|++..
T Consensus        76 ~~i~v~~a~~~~   87 (90)
T d2cqia1          76 KEVKVNWATTPS   87 (90)
T ss_dssp             EEEEEEECCCTT
T ss_pred             EEEEEEEcCCCC
Confidence            999999997543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=3.2e-15  Score=97.05  Aligned_cols=60  Identities=27%  Similarity=0.483  Sum_probs=56.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|+++. +++++|+|||+|.+.++|++|+..|||+.++|
T Consensus        44 l~e~f~k~G~I~~---------------------------v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~g   95 (104)
T d1jmta_          44 FTEMEEKYGEVEE---------------------------MNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG   95 (104)
T ss_dssp             HHHHHHHTCCEEE---------------------------EEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHhccCCCEEE---------------------------EEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECC
Confidence            6788999999999                           9998775 89999999999999999999999999999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      ++|.|+++
T Consensus        96 r~i~v~~s  103 (104)
T d1jmta_          96 QPIHAELS  103 (104)
T ss_dssp             EECCEEEC
T ss_pred             EEEEEEEC
Confidence            99999875

>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=99.55  E-value=1.1e-15  Score=93.98  Aligned_cols=60  Identities=22%  Similarity=0.396  Sum_probs=56.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++|++|+.+++++|||||+|.+.++|++||. .+++.++|
T Consensus        16 l~~~F~~~G~I~~---------------------------v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g   67 (75)
T d1x0fa1          16 IREYFGGFGEVES---------------------------IELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGL   67 (75)
T ss_dssp             HHHHHHHHSCEEE---------------------------EECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTT
T ss_pred             HHHHHHHhCCccc---------------------------ccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECC
Confidence            7899999999999                           9999999999999999999999999999997 57889999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|+.|
T Consensus        68 ~~i~vk~A   75 (75)
T d1x0fa1          68 SKCEIKVA   75 (75)
T ss_dssp             BCCEEECC
T ss_pred             EEeEEEEC
Confidence            99999875

>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=99.55  E-value=1.2e-14  Score=88.91  Aligned_cols=60  Identities=25%  Similarity=0.537  Sum_probs=57.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.|+.+++++|||||+|.+++++++|+. +||..++|
T Consensus        19 l~~~F~~~G~i~~---------------------------~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~G   70 (79)
T d1l3ka2          19 LRDYFEQYGKIEV---------------------------IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNG   70 (79)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETT
T ss_pred             HHHHHHHhccccc---------------------------cccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECC
Confidence            7899999999999                           9999999999999999999999999999996 89999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|+.|
T Consensus        71 r~i~V~~A   78 (79)
T d1l3ka2          71 HNCEVRKA   78 (79)
T ss_dssp             EECEEEEC
T ss_pred             EEEEEEEC
Confidence            99999876

>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=99.53  E-value=2.2e-15  Score=96.33  Aligned_cols=67  Identities=24%  Similarity=0.402  Sum_probs=61.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.++.+..+|+++|||||+|.++++|+.|+..|||..+.|
T Consensus        35 l~~~f~~~G~v~~---------------------------~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g   87 (102)
T d2cpxa1          35 LVSLFARFQEKKG---------------------------PPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG   87 (102)
T ss_dssp             HHHHTHHHHHSSS---------------------------SCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             HHHHHhhccceee---------------------------EEeecccccccccccceEEeccHHHHHHHHHHhCCCEECC
Confidence            7899999999998                           7888887889999999999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|++++++..+
T Consensus        88 ~~l~V~~ak~k~~r  101 (102)
T d2cpxa1          88 KILVIEFGKNKKQR  101 (102)
T ss_dssp             CBCEEEECCCCSCC
T ss_pred             EEEEEEeCCCcccC
Confidence            99999999876543

>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=99.53  E-value=5.8e-15  Score=89.39  Aligned_cols=60  Identities=28%  Similarity=0.607  Sum_probs=57.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+++++.+++++|||||+|.++++|++|++ +||+.++|
T Consensus        16 l~~~F~~~G~i~~---------------------------~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~g   67 (75)
T d2msta_          16 VKHYFEQFGKVDD---------------------------AMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINN   67 (75)
T ss_dssp             HHHHHHTTSCCSE---------------------------ECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTT
T ss_pred             HHHHHHHhCCcce---------------------------eeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECC
Confidence            7899999999999                           9999999999999999999999999999997 99999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|+|+.|
T Consensus        68 r~i~V~~A   75 (75)
T d2msta_          68 KMVECKKA   75 (75)
T ss_dssp             BCCEEEEC
T ss_pred             eEEEEEEC
Confidence            99999875

>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=99.52  E-value=1.4e-14  Score=91.20  Aligned_cols=58  Identities=26%  Similarity=0.457  Sum_probs=52.9

Q ss_pred             HHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCc---ccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            3 ADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRS---KGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         3 ~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~---rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      +++|++||+|..                           +.+++|+.++.+   +|||||+|.++++|++|+..|||..+
T Consensus        29 ~e~F~~~G~I~~---------------------------v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~   81 (89)
T d2cpia1          29 PEYFGKFGKIHK---------------------------VVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   81 (89)
T ss_dssp             TTTTTTTSCEEE---------------------------EEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             HHHhcccCCceE---------------------------EEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEE
Confidence            567999999999                           999999877654   49999999999999999999999999


Q ss_pred             CCeeEEEE
Q 033734           80 DGRVIFVD   87 (112)
Q Consensus        80 ~g~~i~V~   87 (112)
                      +|+.|+|+
T Consensus        82 ~gr~lkvS   89 (89)
T d2cpia1          82 DGRTLKAS   89 (89)
T ss_dssp             TTEEEEEE
T ss_pred             CCEEEEEC
Confidence            99999985

>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=99.52  E-value=2.5e-14  Score=90.43  Aligned_cols=65  Identities=34%  Similarity=0.540  Sum_probs=59.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC------
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN------   75 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~------   75 (112)
                      |+++|++||+|..                           +.++.++.++.++|||||+|.++++|..|+..|+      
T Consensus        25 l~~~f~~~G~v~~---------------------------~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~   77 (98)
T d1x4ha1          25 LGEVLQQFGDLKY---------------------------VRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGG   77 (98)
T ss_dssp             HHHHHHTTSCEEE---------------------------EECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTC
T ss_pred             HHHHHhcccccee---------------------------eeeccccccccccceEEEEEcCHHHHHHHHHHcccccccC
Confidence            7899999999999                           9999999999999999999999999999999886      


Q ss_pred             CceeCCeeEEEEeccCCC
Q 033734           76 GKLLDGRVIFVDNVRPSR   93 (112)
Q Consensus        76 g~~l~g~~i~V~~a~~~~   93 (112)
                      |..++|+.|+|+++.++.
T Consensus        78 g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          78 GLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             CEESSSCEEEEECCCCCC
T ss_pred             CcEECCEEEEEEECCCCC
Confidence            677899999999998654

>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=99.51  E-value=2.2e-14  Score=91.54  Aligned_cols=60  Identities=35%  Similarity=0.626  Sum_probs=54.9

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|++||+|.+                           ++++.|      +|||||+|.++++|+.|+..|||..++
T Consensus        34 ~L~~~F~~fG~i~~---------------------------v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~   80 (96)
T d1x4ga1          34 LMRQTFSPFGQIME---------------------------IRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIE   80 (96)
T ss_dssp             HHHHHHHHHSCEEE---------------------------EEEETT------TTEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             HHHHHHHHhCCceE---------------------------EEEEec------ceEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            37899999999999                           988866      689999999999999999999999999


Q ss_pred             CeeEEEEeccCCC
Q 033734           81 GRVIFVDNVRPSR   93 (112)
Q Consensus        81 g~~i~V~~a~~~~   93 (112)
                      |+.|+|+++++++
T Consensus        81 g~~l~v~~ak~~p   93 (96)
T d1x4ga1          81 GHVVKCYWGKESP   93 (96)
T ss_dssp             TEECEEECCCCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999987643

>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=99.48  E-value=5e-14  Score=90.70  Aligned_cols=59  Identities=27%  Similarity=0.438  Sum_probs=54.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|.+                           ++|++++     +|||||+|.++++|++|+..|||..++|
T Consensus        20 L~~~F~~fG~I~~---------------------------v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g   67 (109)
T d2adca1          20 LFILFGVYGDVQR---------------------------VKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHG   67 (109)
T ss_dssp             HHHHHHHHTCEEE---------------------------EEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHhhccccce---------------------------EEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           9998774     7899999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|++++..
T Consensus        68 ~~l~v~~s~~~   78 (109)
T d2adca1          68 KPIRITLSKHQ   78 (109)
T ss_dssp             SBCEEECCSCC
T ss_pred             EEEEEEECCCC
Confidence            99999998644

>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=99.48  E-value=6.2e-14  Score=91.14  Aligned_cols=60  Identities=18%  Similarity=0.330  Sum_probs=54.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           |++..+   +.++|||||+|.+.++|..|+..|||..++|
T Consensus        24 l~~~F~~~G~v~~---------------------------i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~g   73 (114)
T d2f9da1          24 MYDIFGKYGPIRQ---------------------------IRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCN   73 (114)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhhcCCeEe---------------------------eccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           888654   5678999999999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      ++|.|.++.+
T Consensus        74 r~l~V~~a~~   83 (114)
T d2f9da1          74 RYLVVLYYNA   83 (114)
T ss_dssp             EECEEEECCH
T ss_pred             EEEEEEEcCC
Confidence            9999999854

>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=99.48  E-value=6e-14  Score=89.96  Aligned_cols=68  Identities=21%  Similarity=0.396  Sum_probs=57.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeC-CCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK-GKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~-~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++|| +++                           ++++.+. .+++++|||||+|.++++|++|+ .||+..++
T Consensus        32 l~~~f~~~g-~~~---------------------------~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~   82 (104)
T d1wi8a_          32 IKEFFRGLN-ISA---------------------------VRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG   82 (104)
T ss_dssp             HHHHTTTSC-EEE---------------------------EECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET
T ss_pred             HHHHHHHhc-ccc---------------------------ceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEEC
Confidence            789999999 667                           6776665 47889999999999999998777 59999999


Q ss_pred             CeeEEEEeccCCCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~~~   98 (112)
                      |+.|+|++|.+......+
T Consensus        83 gr~l~V~~a~~~~~~~~~  100 (104)
T d1wi8a_          83 NKRIRVDVADQAQDKDSG  100 (104)
T ss_dssp             TEECEEEECCCCCCCCCC
T ss_pred             CEEEEEEECCCCCCCCCC
Confidence            999999999876655443

>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=99.48  E-value=4.3e-14  Score=86.93  Aligned_cols=58  Identities=28%  Similarity=0.499  Sum_probs=53.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++.+      .+|||||+|.+.++|..|+..|||..++|
T Consensus        20 L~~~F~~~G~I~~---------------------------v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g   66 (79)
T d2bz2a1          20 LRGAFSPFGNIID---------------------------LSMDP------PRNCAFVTYEKMESADQAVAELNGTQVES   66 (79)
T ss_dssp             HHHHHSTTCCCSC---------------------------EEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHhccCccce---------------------------eeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECC
Confidence            7899999999999                           88754      35899999999999999999999999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|+++++.
T Consensus        67 ~~l~V~~a~~~   77 (79)
T d2bz2a1          67 VQLKVNIARKQ   77 (79)
T ss_dssp             CBCEEEECCSS
T ss_pred             EEEEEEEecCC
Confidence            99999999754

>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=99.47  E-value=9e-14  Score=88.08  Aligned_cols=62  Identities=21%  Similarity=0.411  Sum_probs=55.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|..                           +.+..+   +.++|||||+|.++++|+.||..|||..++|
T Consensus        31 l~~~F~~~G~v~~---------------------------~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g   80 (95)
T d1x4aa1          31 IEDVFYKYGAIRD---------------------------IDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG   80 (95)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             HHHHHhcCCceEE---------------------------EEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999988                           776443   4578999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|+|+++++.+
T Consensus        81 ~~l~V~~a~~~r   92 (95)
T d1x4aa1          81 YRLRVEFPRSGR   92 (95)
T ss_dssp             EECEEECCCCCC
T ss_pred             EEEEEEeccCCC
Confidence            999999998653

>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=99.47  E-value=7.9e-15  Score=92.80  Aligned_cols=62  Identities=23%  Similarity=0.371  Sum_probs=56.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.|..                           ++|+.+ .+|+++|||||+|.+.++|++|++ |||..++|
T Consensus        30 l~~~F~~~G~i~~---------------------------~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g   80 (91)
T d1fjeb1          30 LKVAISELFAKND---------------------------LAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG   80 (91)
T ss_dssp             HHHHHHHHHHHHT---------------------------CCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETT
T ss_pred             HHHHHhcCCcEEE---------------------------eeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECC
Confidence            7899999999988                           777655 489999999999999999999996 99999999


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.|+|++|+++
T Consensus        81 ~~i~V~~ak~k   91 (91)
T d1fjeb1          81 NEIKLEKPKGR   91 (91)
T ss_dssp             EEEEEECCCCS
T ss_pred             EEEEEEecCCC
Confidence            99999998753

>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=99.46  E-value=1.1e-14  Score=87.73  Aligned_cols=56  Identities=29%  Similarity=0.589  Sum_probs=53.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++.+++.++.++|+|||+|.++++|++|+..|||..++|
T Consensus        15 l~~~F~~~G~v~~---------------------------~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~G   67 (72)
T d1x4ea1          15 LVKLCQPYGKIVS---------------------------TKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA   67 (72)
T ss_dssp             HHTTSTTTSCEEE---------------------------EEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCE
T ss_pred             HHHHHhhhccccc---------------------------cccccccccccccceeEEEECCHHHHHHHHHHhCCCEECC
Confidence            7889999999999                           9999999999999999999999999999999999999999


Q ss_pred             eeE
Q 033734           82 RVI   84 (112)
Q Consensus        82 ~~i   84 (112)
                      +.+
T Consensus        68 r~~   70 (72)
T d1x4ea1          68 QMA   70 (72)
T ss_dssp             ESC
T ss_pred             EEC
Confidence            875

>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=99.46  E-value=1.6e-13  Score=88.80  Aligned_cols=61  Identities=13%  Similarity=0.045  Sum_probs=54.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+.+|++||.|++                           +++.+      ++|||||+|.++++|++|+..|||..++|
T Consensus        27 l~~lF~~~G~i~~---------------------------~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g   73 (104)
T d1weya_          27 FESLFRTYDKDTT---------------------------FQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLG   73 (104)
T ss_dssp             HHHHHHTTCSSCE---------------------------EEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETT
T ss_pred             HHHHhcccccceE---------------------------EEEec------CCCEEEEEECCHHHHHHHHHHhcccccCC
Confidence            6789999999999                           87753      56899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|+|.++++....
T Consensus        74 ~~l~v~~a~~~~~~   87 (104)
T d1weya_          74 KEMKLYFAQTLHIG   87 (104)
T ss_dssp             EECEEECCCCSSCC
T ss_pred             CEeEEeecccCCCC
Confidence            99999999765543

>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=99.45  E-value=6.5e-14  Score=86.98  Aligned_cols=61  Identities=20%  Similarity=0.294  Sum_probs=53.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.+..                           ..++.+..+++++|+|||+|.++++|++|+..|||..++|
T Consensus        26 i~~~F~~~~~~~~---------------------------~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~g   78 (86)
T d2cqpa1          26 ILDFFYGYQVIPG---------------------------SVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS   78 (86)
T ss_dssp             HHHHTTTSCCCTT---------------------------TCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT
T ss_pred             HHHHHhhccccee---------------------------EEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECC
Confidence            7889999999876                           4444455689999999999999999999999999999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      ++|+|+++
T Consensus        79 r~i~v~l~   86 (86)
T d2cqpa1          79 RKVKLVLG   86 (86)
T ss_dssp             EECEEEES
T ss_pred             EEEEEEEC
Confidence            99999875

>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=99.45  E-value=2.6e-14  Score=91.62  Aligned_cols=63  Identities=24%  Similarity=0.472  Sum_probs=57.0

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|++||+|..                           +.+..+. +++++|||||+|.++++|++|+..|||..+.
T Consensus        34 ~L~~~F~~~G~i~~---------------------------~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~   85 (101)
T d1x5oa1          34 ELENMLKPFGQVIS---------------------------TRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIK   85 (101)
T ss_dssp             HHHHTTTTTSCEEE---------------------------EEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCC
T ss_pred             HHHHHHhhcccccc---------------------------eeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEEC
Confidence            37899999999999                           8888885 8899999999999999999999999999999


Q ss_pred             CeeEEEEeccC
Q 033734           81 GRVIFVDNVRP   91 (112)
Q Consensus        81 g~~i~V~~a~~   91 (112)
                      |+++.|..+.|
T Consensus        86 gr~~~v~~~~P   96 (101)
T d1x5oa1          86 TPPGVSAPTEP   96 (101)
T ss_dssp             CCTTSCCCSSC
T ss_pred             CcCCccCCCCC
Confidence            99988866654

>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=99.45  E-value=1.5e-13  Score=85.69  Aligned_cols=60  Identities=18%  Similarity=0.200  Sum_probs=55.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||+|..                           ++|..+. +++++|||||+|.++++|++|+. ++|..++|
T Consensus        23 l~~~F~~~G~v~~---------------------------v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g   73 (85)
T d1zh5a2          23 IKEWLEDKGQVLN---------------------------IQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKE   73 (85)
T ss_dssp             HHHHHTTSCCEEE---------------------------EEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETT
T ss_pred             HHHHHHHhccccc---------------------------ceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECC
Confidence            7899999999999                           9988886 89999999999999999999996 79999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      ++|.|.+..
T Consensus        74 ~~l~v~~~~   82 (85)
T d1zh5a2          74 TDLLILFKD   82 (85)
T ss_dssp             EECEEEEGG
T ss_pred             EEEEEEEcC
Confidence            999998864

>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=99.44  E-value=1.6e-13  Score=88.18  Aligned_cols=69  Identities=22%  Similarity=0.257  Sum_probs=60.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.+|.+..                           ..++.+..+++++|||||+|.++++|++|+. +|+..|+|
T Consensus        32 I~~~F~~~g~v~~---------------------------~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~g   83 (104)
T d1wg5a_          32 IVQFFSGLEIVPN---------------------------GMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGH   83 (104)
T ss_dssp             HHHHTTTCCEEEE---------------------------EEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSS
T ss_pred             HHHHHHhcCCceE---------------------------EEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcc
Confidence            7899999999887                           6677777799999999999999999999996 99999999


Q ss_pred             eeEEEEeccCCCCCCCC
Q 033734           82 RVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        82 ~~i~V~~a~~~~~~~~~   98 (112)
                      |.|.|..+.+.+....+
T Consensus        84 R~i~V~~~~~~~~~~sg  100 (104)
T d1wg5a_          84 RYIEIFKSSRAEVRTSG  100 (104)
T ss_dssp             SCCEEEEECTTTSCCSS
T ss_pred             eEEEEEECCHHHhccCC
Confidence            99999999876554443

>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=99.43  E-value=3.8e-14  Score=88.61  Aligned_cols=60  Identities=22%  Similarity=0.256  Sum_probs=52.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           ++++.|       |||||+|.+.++|++||..|||..++|
T Consensus        17 l~~~F~~~G~v~~---------------------------~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g   62 (87)
T d3begb1          17 LKDHMREAGDVCY---------------------------ADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRS   62 (87)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCC
T ss_pred             HHHHHhhhccccc---------------------------cccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           887544       899999999999999999999999999


Q ss_pred             eeEEEEeccCCCCC
Q 033734           82 RVIFVDNVRPSRRY   95 (112)
Q Consensus        82 ~~i~V~~a~~~~~~   95 (112)
                      +.|.|.+++.....
T Consensus        63 ~~i~v~~~~~~~~~   76 (87)
T d3begb1          63 HEGETAYIRVKVDG   76 (87)
T ss_dssp             TTSCCCBCEEEECC
T ss_pred             cEeEEeEEecCcCC
Confidence            99999887654433

>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=99.41  E-value=1.7e-13  Score=87.83  Aligned_cols=55  Identities=20%  Similarity=0.193  Sum_probs=47.7

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCCCCCC
Q 033734           42 ATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        42 ~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~~~~~   98 (112)
                      +.++.+. ++..+|||||+|.++++|++|+. +|+..|+||.|+|.++.+......+
T Consensus        44 v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~~~~   98 (102)
T d1weza_          44 VHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGSG   98 (102)
T ss_dssp             EEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCCCCC
T ss_pred             eeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCCCCC
Confidence            7778876 68999999999999999999986 8999999999999998876554443

>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=99.41  E-value=2.7e-13  Score=84.96  Aligned_cols=47  Identities=21%  Similarity=0.273  Sum_probs=40.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCCCCCCC
Q 033734           51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPSRRYNT   97 (112)
Q Consensus        51 ~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~~~~~~   97 (112)
                      ++.+|||||+|.++++|++|+..|||..++|++|.|+++++......
T Consensus        37 ~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~~~~   83 (88)
T d1wg1a_          37 DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCS   83 (88)
T ss_dssp             EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCSC
T ss_pred             eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCCCC
Confidence            45689999999999999999999999999999999999976544333

>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=99.41  E-value=2.4e-13  Score=86.14  Aligned_cols=67  Identities=18%  Similarity=0.311  Sum_probs=57.3

Q ss_pred             HHHHhhccCc-ceecceeeeccCCCCCcccccccccccceEEEEEeeC-CCCCcccEEEEEeCCHHHHHHHHHhhCCce-
Q 033734            2 LADAFSQFGQ-VTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDK-GKNRSKGYGYVTFSTEEEAQKALADMNGKL-   78 (112)
Q Consensus         2 l~~~f~~~G~-i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~-~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~-   78 (112)
                      |+++|+.||+ |..                           +.++.|. .+++++|||||+|.++++|..|+..|++.. 
T Consensus        18 l~~~f~~~g~~i~~---------------------------v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~   70 (96)
T d2disa1          18 ILEEIAKVTEGVLD---------------------------VIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRI   70 (96)
T ss_dssp             HHHHHHHHSTTEEE---------------------------EECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCS
T ss_pred             HHHHHHHhCCcceE---------------------------EEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCe
Confidence            7899999996 777                           8888885 468999999999999999999999997554 


Q ss_pred             -eCCeeEEEEeccCCCCC
Q 033734           79 -LDGRVIFVDNVRPSRRY   95 (112)
Q Consensus        79 -l~g~~i~V~~a~~~~~~   95 (112)
                       ++|+.|.|++|++....
T Consensus        71 ~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          71 QLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             CBTTBCCEEEESCSSCST
T ss_pred             EECCEEEEEEEcCCCCCC
Confidence             57999999999875443

>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=99.41  E-value=2.9e-13  Score=85.84  Aligned_cols=61  Identities=25%  Similarity=0.433  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           ++.     +++++|||||+|.+.++|++|+..|||..++|
T Consensus        33 l~~~F~~~g~v~~---------------------------~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g   80 (96)
T d1fjca_          33 LKEVFEDALEIRL---------------------------VSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             HHHHHCSEEEECC---------------------------EEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             HHHHHHhccccee---------------------------eee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            7889999998766                           532     67899999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|+++.++..
T Consensus        81 r~i~V~~a~~k~~   93 (96)
T d1fjca_          81 RSVSLYYTGEKGG   93 (96)
T ss_dssp             EEEEEEECSSSCC
T ss_pred             EEEEEEEeCCCCC
Confidence            9999999987654

>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=99.41  E-value=4.1e-13  Score=83.35  Aligned_cols=60  Identities=28%  Similarity=0.543  Sum_probs=52.8

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+      ++++|||||+|.++++|..|+..|||..++|
T Consensus        25 l~~~F~~~g~i~~---------------------------~~~------~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g   71 (86)
T d2cpda1          25 IEKEFNNIKPGAV---------------------------ERV------KKIRDYAFVHFSNREDAVEAMKALNGKVLDG   71 (86)
T ss_dssp             HHHHHHTTSTTCE---------------------------EEE------EECSSEEEEEESSHHHHHHHHHHHSSEEETT
T ss_pred             HHHhhcccceeee---------------------------EEE------ccccEEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            7889999999877                           554      3457899999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++++|..+
T Consensus        72 ~~i~V~~akP~~~   84 (86)
T d2cpda1          72 SPIEVTLAKPVDK   84 (86)
T ss_dssp             EEEEEECCCCCCC
T ss_pred             EEEEEEeccCCCC
Confidence            9999999986544

>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=99.40  E-value=2.6e-13  Score=84.68  Aligned_cols=59  Identities=25%  Similarity=0.436  Sum_probs=54.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|.+                           +++.++      +|||||+|.+.++|+.|+..|||..++|
T Consensus        25 l~~~F~~~G~i~~---------------------------i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g   71 (86)
T d2cpja1          25 MRKLFEKYGKAGE---------------------------VFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRG   71 (86)
T ss_dssp             HHHHTSTTCCCSE---------------------------EEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTT
T ss_pred             HHHHHHHhCCceE---------------------------eeeecc------cceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            7899999999999                           888755      5899999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|+|++|.+..
T Consensus        72 ~~l~V~~A~~~~   83 (86)
T d2cpja1          72 KQLRVRFACHSA   83 (86)
T ss_dssp             BCCEEEESSCCS
T ss_pred             EEEEEEECCCcC
Confidence            999999997653

>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=99.40  E-value=3.2e-13  Score=83.17  Aligned_cols=62  Identities=21%  Similarity=0.396  Sum_probs=53.3

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCc-ee
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGK-LL   79 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~-~l   79 (112)
                      .|+++|++||.|..                           +++..      ++|||||+|.++++|+.|+..|||. .+
T Consensus        17 ~L~~~F~~~G~i~~---------------------------~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~   63 (80)
T d2cqha1          17 DLRQLFGDRKLPLA---------------------------GQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVEL   63 (80)
T ss_dssp             HHHHHHHHTTCCCS---------------------------SCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEE
T ss_pred             HHHHHHHHhCcEEE---------------------------eEEec------ccceEEEEECCHHHHHHHHHHhCCCeEE
Confidence            37899999999987                           55544      4689999999999999999999996 69


Q ss_pred             CCeeEEEEeccCCCCC
Q 033734           80 DGRVIFVDNVRPSRRY   95 (112)
Q Consensus        80 ~g~~i~V~~a~~~~~~   95 (112)
                      +|++|.|+++.++..+
T Consensus        64 ~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1          64 HGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             TTEECEEEECCCCCCC
T ss_pred             CCEEEEEEEcCCcCcC
Confidence            9999999999876543

>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=99.39  E-value=1.9e-13  Score=85.95  Aligned_cols=62  Identities=23%  Similarity=0.387  Sum_probs=54.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.++|++||+|..                           +++..   +++++|||||+|.+.++|..|+..+||..++|
T Consensus        24 l~~~f~~~G~i~~---------------------------i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g   73 (91)
T d1nu4a_          24 LHAIFSRFGQILD---------------------------ILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   73 (91)
T ss_dssp             HHHHHGGGSCEEE---------------------------EECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             HHHHhcccccccc---------------------------eEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECC
Confidence            3567999999988                           76533   56789999999999999999999999999999


Q ss_pred             eeEEEEeccCCC
Q 033734           82 RVIFVDNVRPSR   93 (112)
Q Consensus        82 ~~i~V~~a~~~~   93 (112)
                      +.|.|++|++..
T Consensus        74 ~~l~v~~ak~~~   85 (91)
T d1nu4a_          74 KPMRIQYAKTDS   85 (91)
T ss_dssp             EECEEEECSSCC
T ss_pred             EEEEEEEeCCCc
Confidence            999999997643

>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=99.38  E-value=5.8e-13  Score=85.72  Aligned_cols=60  Identities=17%  Similarity=0.217  Sum_probs=53.3

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|++||+|.+                           +.|.      ..+|||||+|.++++|++|+..|||..+.
T Consensus        26 ~L~~~F~~fG~I~~---------------------------v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~   72 (111)
T d1whxa_          26 EIQETFSRFGSLGR---------------------------VLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFH   72 (111)
T ss_dssp             HHHHHHHTTSCEEE---------------------------EECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSS
T ss_pred             HHHhhhhccCCccE---------------------------EEee------ccCceEEEEEcCHHHHHHHHHHHcCCccC
Confidence            38899999999998                           7662      35799999999999999999999999999


Q ss_pred             CeeEEEEeccCCC
Q 033734           81 GRVIFVDNVRPSR   93 (112)
Q Consensus        81 g~~i~V~~a~~~~   93 (112)
                      |+.|.|+++....
T Consensus        73 gr~l~v~~a~~~~   85 (111)
T d1whxa_          73 HVPLYLEWAPIGV   85 (111)
T ss_dssp             SSBCEEEEEETTT
T ss_pred             CCeEEEEECCCCc
Confidence            9999999986543

>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=99.38  E-value=1.1e-12  Score=79.91  Aligned_cols=58  Identities=14%  Similarity=0.259  Sum_probs=52.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||+|..                           ++++.++.  ..+|||||+|.++++|++|+. +|++.++|
T Consensus        17 l~~~F~~~G~I~~---------------------------v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g   66 (75)
T d2ghpa2          17 VYKYFKHCGPIIH---------------------------VDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQ   66 (75)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETT
T ss_pred             HHHHHhcCCceEE---------------------------EEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECC
Confidence            7899999999999                           99999874  345799999999999999996 89999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      ++|.|+.+
T Consensus        67 ~~i~V~~~   74 (75)
T d2ghpa2          67 NEIIVSHL   74 (75)
T ss_dssp             EECEEEEC
T ss_pred             EEEEEEEC
Confidence            99999865

>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=99.38  E-value=2.6e-13  Score=84.91  Aligned_cols=64  Identities=25%  Similarity=0.480  Sum_probs=53.9

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|++||.|.+                           +++.     ..++|||||+|.++++|++|+.  +++.++
T Consensus        21 ~L~~~F~~~G~v~~---------------------------v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~   66 (88)
T d1wf0a_          21 ELREFFSQYGDVMD---------------------------VFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIK   66 (88)
T ss_dssp             HHHHHSTTTSCCCE---------------------------EECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEET
T ss_pred             HHHHHHHHcCCceE---------------------------EEEe-----eccCceEEEEECCHHHHHHHHh--CCCEEC
Confidence            38899999999998                           7653     4578999999999999999985  788999


Q ss_pred             CeeEEEEeccCCCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~~~   98 (112)
                      |+.|.|++++++.....+
T Consensus        67 g~~l~v~~a~~k~~~~~~   84 (88)
T d1wf0a_          67 GISVHISNAEPKHNSNSG   84 (88)
T ss_dssp             TEEEEEECCCCCCCCCSC
T ss_pred             CEEeEEEeCCCCCCCCCC
Confidence            999999999876655443

>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=99.37  E-value=3.5e-13  Score=86.15  Aligned_cols=64  Identities=19%  Similarity=0.242  Sum_probs=55.8

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      .|+++|++||+|..                           +.|.+       +|||||+|.++++|++||+.|||..++
T Consensus        31 ~L~~~F~~~G~v~~---------------------------~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~   76 (98)
T d1wg4a_          31 DLKDHMREAGDVCY---------------------------ADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFR   76 (98)
T ss_dssp             HHHHHHTTSSCEEE---------------------------EEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEE
T ss_pred             HHHHHHHhhccccc---------------------------ccccc-------cceEEEEECCHHHHHHHHHHhCCCEeC
Confidence            37899999999999                           87743       489999999999999999999999999


Q ss_pred             CeeEEEEeccCCCCCCCC
Q 033734           81 GRVIFVDNVRPSRRYNTD   98 (112)
Q Consensus        81 g~~i~V~~a~~~~~~~~~   98 (112)
                      |+.|.|.+++..+.+..+
T Consensus        77 g~~i~v~~~~~~~~~~~~   94 (98)
T d1wg4a_          77 SHEGETSYIRVYPERSSG   94 (98)
T ss_dssp             CTTSCEEEEEEECCCSSC
T ss_pred             CeEEEEEEEecCCCCCCC
Confidence            999999999876655443

>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=99.37  E-value=1e-12  Score=84.80  Aligned_cols=61  Identities=18%  Similarity=0.281  Sum_probs=54.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee--
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL--   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l--   79 (112)
                      |+++|++||.|.+                           +.++.++    .+|+|||+|.++++|+.|+..|||..+  
T Consensus        24 L~~~F~~~G~i~~---------------------------~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~   72 (108)
T d2adba1          24 LHQIFSKFGTVLK---------------------------IITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYN   72 (108)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSST
T ss_pred             HHHHHccCCcEEE---------------------------EEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEecc
Confidence            7899999999999                           9888775    579999999999999999999999998  


Q ss_pred             CCeeEEEEeccCCC
Q 033734           80 DGRVIFVDNVRPSR   93 (112)
Q Consensus        80 ~g~~i~V~~a~~~~   93 (112)
                      .++.|+|.++++..
T Consensus        73 ~~~~l~v~~s~~~~   86 (108)
T d2adba1          73 ACCTLRIDFSKLTS   86 (108)
T ss_dssp             TCCCCEEEECSSCS
T ss_pred             CCcEEEEEecCCcc
Confidence            47889999887644

>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=99.36  E-value=9.8e-13  Score=81.91  Aligned_cols=60  Identities=22%  Similarity=0.313  Sum_probs=51.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee-C
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL-D   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l-~   80 (112)
                      |+++|++||.|.+                           +.+..+    +.+|||||+|.++++|.+|+..|||..+ +
T Consensus        27 l~~~F~~~G~v~~---------------------------~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~   75 (88)
T d2adca2          27 LKVLFSSNGGVVK---------------------------GFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGE   75 (88)
T ss_dssp             HHHHHHTTSCCEE---------------------------EEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             HHHHhhccCCEEE---------------------------EEEeee----cccceeEEEECCHHHHHHHHHhccCCEecC
Confidence            7899999999988                           655443    4578999999999999999999999998 5


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |+.|+|++++++
T Consensus        76 g~~l~v~~sk~~   87 (88)
T d2adca2          76 NHHLRVSFSKST   87 (88)
T ss_dssp             SCBCEEEECSSC
T ss_pred             CCEEEEEeCCCC
Confidence            899999999753

>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=99.34  E-value=1.5e-12  Score=89.43  Aligned_cols=64  Identities=23%  Similarity=0.488  Sum_probs=59.6

Q ss_pred             CHHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC
Q 033734            1 MLADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD   80 (112)
Q Consensus         1 ~l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~   80 (112)
                      +|+++|+.||.|..                           +.++.|..+++++|||||+|.++++|++|+. +++..++
T Consensus       113 ~L~~~f~~~G~v~~---------------------------~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~  164 (183)
T d1u1qa_         113 HLRDYFEQYGKIEV---------------------------IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVN  164 (183)
T ss_dssp             HHHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEET
T ss_pred             HHhhhhccCCceee---------------------------eeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeEC
Confidence            37899999999999                           9999999999999999999999999999997 7899999


Q ss_pred             CeeEEEEeccCC
Q 033734           81 GRVIFVDNVRPS   92 (112)
Q Consensus        81 g~~i~V~~a~~~   92 (112)
                      |++|.|++|.++
T Consensus       165 G~~i~V~~A~~k  176 (183)
T d1u1qa_         165 GHNCEVRKALSK  176 (183)
T ss_dssp             TEEEEEEECCCH
T ss_pred             CEEEEEEecCCc
Confidence            999999998764

>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=99.33  E-value=2.7e-12  Score=82.10  Aligned_cols=62  Identities=24%  Similarity=0.402  Sum_probs=55.0

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+..|++||.|..                           +.+..+    ..+|++||+|.++++|++|+..|||+.++|
T Consensus        36 v~~~~~~~G~V~~---------------------------v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1          36 LRVECSKFGQIRK---------------------------LLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             HHHHGGGTSCCSE---------------------------EEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             HHHHhcCcccEEE---------------------------EeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            5788999999998                           776544    467999999999999999999999999999


Q ss_pred             eeEEEEeccCCCC
Q 033734           82 RVIFVDNVRPSRR   94 (112)
Q Consensus        82 ~~i~V~~a~~~~~   94 (112)
                      +.|.|++..+...
T Consensus        85 r~i~v~~~~g~~~   97 (99)
T d2dita1          85 RQITAQAWDGTTD   97 (99)
T ss_dssp             EECEEEECCSCCC
T ss_pred             EEEEEEEeCCcCC
Confidence            9999999887654

>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=99.33  E-value=8.4e-13  Score=84.42  Aligned_cols=61  Identities=23%  Similarity=0.341  Sum_probs=54.4

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.+..                           +.++.+..+|+++|+|||+|.++++|++|+. +||..|+|
T Consensus        25 l~~~F~~~g~i~~---------------------------~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~g   76 (103)
T d2cpya1          25 VLQFLEGIPVDEN---------------------------AVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNG   76 (103)
T ss_dssp             HHHHTTTSCCCST---------------------------TEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETT
T ss_pred             HhhhhcccceEEE---------------------------EEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECC
Confidence            7889999998877                           5556666699999999999999999999996 99999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|.|..+.
T Consensus        77 r~i~V~~~~   85 (103)
T d2cpya1          77 REAFVHVVT   85 (103)
T ss_dssp             EEEEEEEEC
T ss_pred             cEEEEEECC
Confidence            999999875

>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=99.33  E-value=1.2e-12  Score=80.92  Aligned_cols=57  Identities=19%  Similarity=0.341  Sum_probs=51.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeC-
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLD-   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~-   80 (112)
                      |+++|++||+|.+                           ++++++     .+|||||+|.+.++|+.|+..|||..+. 
T Consensus        25 l~~~f~~~G~i~~---------------------------v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~   72 (83)
T d2b0ga1          25 LSMLFNQFPGFKE---------------------------VRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITP   72 (83)
T ss_dssp             HHHHHTTSTTEEE---------------------------EEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSST
T ss_pred             HHhhhccCccEEE---------------------------eeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCC
Confidence            7899999999999                           888654     3689999999999999999999999985 


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      |+.|+|++|+
T Consensus        73 ~~~i~v~~ak   82 (83)
T d2b0ga1          73 THAMKITFAK   82 (83)
T ss_dssp             TCBCEEEECC
T ss_pred             CcEEEEEEec
Confidence            6899999986

>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=99.32  E-value=2.9e-12  Score=78.02  Aligned_cols=42  Identities=24%  Similarity=0.325  Sum_probs=38.9

Q ss_pred             CCcccEEEEEeCCHHHHHHHHHhhCCceeCCeeEEEEeccCC
Q 033734           51 NRSKGYGYVTFSTEEEAQKALADMNGKLLDGRVIFVDNVRPS   92 (112)
Q Consensus        51 ~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g~~i~V~~a~~~   92 (112)
                      ++++|||||+|.+.++|++|+..|||..+.|++|.|++++..
T Consensus        30 ~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          30 DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            457899999999999999999999999999999999999654

>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=99.26  E-value=6.6e-12  Score=79.59  Aligned_cols=59  Identities=29%  Similarity=0.506  Sum_probs=52.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||+|..                           +++.++      ++||||+|.+.++|+.|+..||+..++|
T Consensus        34 l~~~f~~~G~i~~---------------------------~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g   80 (97)
T d1whya_          34 LAREFDRFGSIRT---------------------------IDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGG   80 (97)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             HHHHHHhhcccce---------------------------Eeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCC
Confidence            7899999999999                           887654      5799999999999999999999999986


Q ss_pred             --eeEEEEeccCCC
Q 033734           82 --RVIFVDNVRPSR   93 (112)
Q Consensus        82 --~~i~V~~a~~~~   93 (112)
                        ++|+|+++++.+
T Consensus        81 ~~~~l~v~~ak~~~   94 (97)
T d1whya_          81 PDRRLRVDFAKSGP   94 (97)
T ss_dssp             SSCBCEEEECCCCC
T ss_pred             CceEEEEEeCCCCC
Confidence              589999998643

>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=99.22  E-value=1.2e-11  Score=79.54  Aligned_cols=62  Identities=23%  Similarity=0.335  Sum_probs=55.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCC--CcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKN--RSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~--~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+..|++||.|.+                           +.|++++.+.  ...|++||+|.++++|.+|+..|||+.+
T Consensus        31 i~~e~~k~G~v~~---------------------------v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_          31 VRDECSKYGLVKS---------------------------IEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             HHHHHTTTSCEEE---------------------------EECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             HHHHhcccCceEE---------------------------EEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            6788999999999                           9888876543  4569999999999999999999999999


Q ss_pred             CCeeEEEEecc
Q 033734           80 DGRVIFVDNVR   90 (112)
Q Consensus        80 ~g~~i~V~~a~   90 (112)
                      +||.|.|.+..
T Consensus        84 ~gR~v~v~f~~   94 (104)
T d1o0pa_          84 ANRVVVTKYCD   94 (104)
T ss_dssp             SSSCCEEEEEC
T ss_pred             CCeEEEEEEcC
Confidence            99999999875

>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=99.20  E-value=2.1e-11  Score=76.35  Aligned_cols=58  Identities=21%  Similarity=0.291  Sum_probs=51.1

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhh--CCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM--NGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l--~g~~l   79 (112)
                      |.++|++||.|..                           +.++.++      ++|||+|.+.++|.+|+..+  ++..+
T Consensus        26 L~~lF~~fG~I~~---------------------------i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~   72 (89)
T d1x4da1          26 LLQLVEPFGVISN---------------------------HLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALV   72 (89)
T ss_dssp             HHTTTGGGSCEEE---------------------------EEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             HHHHHHhhCCeEE---------------------------EEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCcc
Confidence            7889999999999                           8886553      68999999999999999966  67789


Q ss_pred             CCeeEEEEeccCC
Q 033734           80 DGRVIFVDNVRPS   92 (112)
Q Consensus        80 ~g~~i~V~~a~~~   92 (112)
                      .|++|.|++|++.
T Consensus        73 ~gr~l~V~~s~~~   85 (89)
T d1x4da1          73 FGKPVRVHLSQKY   85 (89)
T ss_dssp             TTEECEEEEECCC
T ss_pred             CCceEEEEECCCc
Confidence            9999999999753

>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=99.20  E-value=4.2e-12  Score=82.52  Aligned_cols=62  Identities=23%  Similarity=0.398  Sum_probs=54.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.+..                           +.++.+..+|.++|+|||+|.+.++|++|+. +||..|+|
T Consensus        35 i~~~F~~~g~~~~---------------------------~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~g   86 (112)
T d1wela1          35 VIDFFKKLDIVED---------------------------SIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN   86 (112)
T ss_dssp             HHHHSCSSCBCTT---------------------------TCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT
T ss_pred             HhhHHhhcccccc---------------------------ceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCC
Confidence            6789999998877                           5566666799999999999999999999996 99999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      +.|.|..+.+
T Consensus        87 R~i~V~~~~~   96 (112)
T d1wela1          87 RFIQVHPITK   96 (112)
T ss_dssp             SCBEEEEECH
T ss_pred             EEEEEEEcCh
Confidence            9999988753

>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=2.1e-11  Score=77.66  Aligned_cols=58  Identities=16%  Similarity=0.261  Sum_probs=51.2

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHH--hhCCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALA--DMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~--~l~g~~l   79 (112)
                      |.++|++||.|.+                           +.++++      +|+|||+|.++++|..|+.  .+++..+
T Consensus        36 l~~~F~~fG~V~~---------------------------v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~   82 (99)
T d1x4fa1          36 VLKLAEPYGKIKN---------------------------YILMRM------KSQAFIEMETREDAMAMVDHCLKKALWF   82 (99)
T ss_dssp             HHTTTTTTSCCSE---------------------------EEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             HHhhhccccceeE---------------------------EEEeec------CCcEEEEecchHHHHHHHHHHhcCCceE
Confidence            7889999999999                           887654      5899999999999999997  5778889


Q ss_pred             CCeeEEEEeccCC
Q 033734           80 DGRVIFVDNVRPS   92 (112)
Q Consensus        80 ~g~~i~V~~a~~~   92 (112)
                      +|+.|.|++|+..
T Consensus        83 ~gr~l~V~~s~~~   95 (99)
T d1x4fa1          83 QGRCVKVDLSEKY   95 (99)
T ss_dssp             SSSCCEEEEECSC
T ss_pred             CCEEEEEEEcCCc
Confidence            9999999999654

>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=99.17  E-value=8.4e-11  Score=75.19  Aligned_cols=59  Identities=19%  Similarity=0.325  Sum_probs=50.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhC--Ccee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMN--GKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~--g~~l   79 (112)
                      |+.+|++||.|..                           +++.+      .+|+|||+|.++++|++|+..|+  +..+
T Consensus        32 l~~~F~~fG~I~~---------------------------~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~   78 (104)
T d1wexa_          32 LVEALEKFGTICY---------------------------VMMMP------FKRQALVEFENIDSAKECVTFAADVPVYI   78 (104)
T ss_dssp             HHHHHTTTSCEEE---------------------------EEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBS
T ss_pred             HHHhhhhcccceE---------------------------EEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEE
Confidence            7899999999999                           87754      46899999999999999999885  4567


Q ss_pred             CCeeEEEEeccCCC
Q 033734           80 DGRVIFVDNVRPSR   93 (112)
Q Consensus        80 ~g~~i~V~~a~~~~   93 (112)
                      .|++|+|++++..+
T Consensus        79 ~g~~l~v~~s~~~~   92 (104)
T d1wexa_          79 AGQQAFFNYSTSKR   92 (104)
T ss_dssp             SSSBCEEEECSSSS
T ss_pred             eeEEEEEEEcCCCc
Confidence            89999999997543

>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=99.15  E-value=8e-11  Score=73.04  Aligned_cols=58  Identities=19%  Similarity=0.256  Sum_probs=50.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhh--CCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADM--NGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l--~g~~l   79 (112)
                      |+++|++||.|..                           +++..+      +|+|||+|.++++|++|+..+  ++..+
T Consensus        25 L~~~f~~~G~i~~---------------------------v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~   71 (88)
T d2cq1a1          25 VIALGLPFGKVTN---------------------------ILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHL   71 (88)
T ss_dssp             HHHTTTTTSCEEE---------------------------EEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             HHHHHhccccccc---------------------------cccccc------ceEEEEEeCCHHHHHHHHHHHccCCCcc
Confidence            7899999999999                           877644      479999999999999999865  56789


Q ss_pred             CCeeEEEEeccCC
Q 033734           80 DGRVIFVDNVRPS   92 (112)
Q Consensus        80 ~g~~i~V~~a~~~   92 (112)
                      .|++|+|++++.+
T Consensus        72 ~g~~l~v~~sk~~   84 (88)
T d2cq1a1          72 RNQPIYIQYSNHK   84 (88)
T ss_dssp             TTEECEEEECSCS
T ss_pred             CCCEEEEEECCCC
Confidence            9999999999754

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.09  E-value=1.8e-12  Score=81.00  Aligned_cols=66  Identities=15%  Similarity=0.328  Sum_probs=51.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|+.||.+....+.                      ....+.+..+++++|||||+|.++++|++|+. |||..++|
T Consensus        18 l~~~F~~~g~~~~~~~~----------------------~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~G   74 (90)
T d1u2fa_          18 MMDFFNAQMRLGGLTQA----------------------PGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQG   74 (90)
T ss_dssp             HHHHHHHHHTTTTSCCS----------------------SSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSS
T ss_pred             HHHHHHhhCcEEEEEEe----------------------ccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECC
Confidence            78999999998761110                      01223455678899999999999999999995 99999999


Q ss_pred             eeEEEEecc
Q 033734           82 RVIFVDNVR   90 (112)
Q Consensus        82 ~~i~V~~a~   90 (112)
                      +.|+|+.++
T Consensus        75 r~l~V~r~k   83 (90)
T d1u2fa_          75 QSLKIRRPH   83 (90)
T ss_dssp             SCCCCBCTT
T ss_pred             EEEEECCCC
Confidence            999997443

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.07  E-value=1.7e-10  Score=71.36  Aligned_cols=56  Identities=18%  Similarity=0.385  Sum_probs=47.3

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      +.++|++||+|.+                           +++      ++.+|||||+|.++++|++|+. +||..++|
T Consensus        20 il~~F~~~G~I~~---------------------------~~~------~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g   65 (81)
T d1wwha1          20 ILLQFAQYGNILK---------------------------HVM------SNTGNWMHIRYQSKLQARKALS-KDGRIFGE   65 (81)
T ss_dssp             HHHHHHTTSCEEE---------------------------EEE------CSSSSEEEEEESSHHHHHHHHT-TTTCEETT
T ss_pred             HHHHHHhhhhhhe---------------------------EEe------cCCCCEEEEEEcccHHHHHHHh-cCCCeECC
Confidence            4568999999999                           765      3457999999999999999996 99999999


Q ss_pred             e-eEEEEeccC
Q 033734           82 R-VIFVDNVRP   91 (112)
Q Consensus        82 ~-~i~V~~a~~   91 (112)
                      + .|.|..+..
T Consensus        66 ~~~vgV~~~~~   76 (81)
T d1wwha1          66 SIMIGVKPCID   76 (81)
T ss_dssp             TEECEEEECCC
T ss_pred             cEEEEEEeCCC
Confidence            7 467887764

>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=98.90  E-value=9.7e-10  Score=70.14  Aligned_cols=45  Identities=27%  Similarity=0.469  Sum_probs=40.6

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCcee
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLL   79 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l   79 (112)
                      |+++|++||.|..                           ++++.+      +|||||+|.+.++|.+|+..|||..+
T Consensus        37 L~~~F~~~G~i~~---------------------------i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          37 LLPVLEKCGLVDA---------------------------LLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             HHHHHHHHSCEEE---------------------------EECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             HHHHHHhhCcccE---------------------------EeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            7899999999998                           776544      57999999999999999999999987

>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=98.89  E-value=5.6e-09  Score=71.08  Aligned_cols=63  Identities=32%  Similarity=0.596  Sum_probs=56.5

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |+++|++||.|..                           +.+++++.++.++|||||+|.++++|+.|+. +++..+++
T Consensus        23 L~~~F~~~G~v~~---------------------------~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~   74 (183)
T d1u1qa_          23 LRSHFEQWGTLTD---------------------------CVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDG   74 (183)
T ss_dssp             HHHHHGGGSCEEE---------------------------EEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETT
T ss_pred             HHHHHHHcCCEEE---------------------------EEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccc
Confidence            7899999999999                           9999999999999999999999999999998 56778899


Q ss_pred             eeEEEEeccCC
Q 033734           82 RVIFVDNVRPS   92 (112)
Q Consensus        82 ~~i~V~~a~~~   92 (112)
                      +.+.+....+.
T Consensus        75 ~~~~~~~~~~~   85 (183)
T d1u1qa_          75 RVVEPKRAVSR   85 (183)
T ss_dssp             EECEEEECCCT
T ss_pred             cchhhhhhhhc
Confidence            88888776543

>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=98.84  E-value=8e-10  Score=71.67  Aligned_cols=56  Identities=23%  Similarity=0.169  Sum_probs=47.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCH-HHHHHHHHhhCCceeC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTE-EEAQKALADMNGKLLD   80 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~-~~a~~Ai~~l~g~~l~   80 (112)
                      |+++|++||+|..                           +.|+++      +|||||.|.++ ++|.+|+..+++..+.
T Consensus        28 Lk~~F~~fG~V~~---------------------------v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~   74 (113)
T d1owxa_          28 LHILFSNHGEIKW---------------------------IDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQ   74 (113)
T ss_dssp             HHHHTCSSCCEEE---------------------------EECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBC
T ss_pred             HHHHHHhcCChhe---------------------------EEEecC------CceEEEEecCcHHHHHHHHHHhcCCcee
Confidence            7899999999999                           888643      68999999985 6899999999999988


Q ss_pred             CeeEEEEecc
Q 033734           81 GRVIFVDNVR   90 (112)
Q Consensus        81 g~~i~V~~a~   90 (112)
                      ++.+.|.++.
T Consensus        75 ~~~~~v~~~~   84 (113)
T d1owxa_          75 LRNKEVTWEV   84 (113)
T ss_dssp             TTSSSEEEEE
T ss_pred             cCceEEEEee
Confidence            7777776654

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.00043  Score=41.15  Aligned_cols=60  Identities=17%  Similarity=0.229  Sum_probs=48.9

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |...|.++|+|..                           +.+..-.   ...=.|-|...+..+|+.|+..||.+++++
T Consensus        13 L~~~f~~h~~V~s---------------------------v~l~~~~---dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~   62 (73)
T d2dgxa1          13 LQEAFARHGKVKS---------------------------VELSPHT---DYQLKAVVQMENLQDAIGAVNSLHRYKIGS   62 (73)
T ss_dssp             HHHHHHHHSCEEE---------------------------EEECSCC---STTCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             HHHHHHhheeEEE---------------------------EEEEecc---CCcEEEEEEcCCHHHHHHHHHHHHHHhcCC
Confidence            6788999999988                           5443321   122368899999999999999999999999


Q ss_pred             eeEEEEeccC
Q 033734           82 RVIFVDNVRP   91 (112)
Q Consensus        82 ~~i~V~~a~~   91 (112)
                      ++|.|.+++.
T Consensus        63 KRI~Vs~~~~   72 (73)
T d2dgxa1          63 KKILVSLATG   72 (73)
T ss_dssp             EEEEEEECCC
T ss_pred             eEEEEEEecC
Confidence            9999999864

>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=97.18  E-value=0.00047  Score=42.92  Aligned_cols=52  Identities=21%  Similarity=0.384  Sum_probs=45.7

Q ss_pred             HHHHhhccCcceecceeeeccCCCCCcccccccccccceEEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHhhCCceeCC
Q 033734            2 LADAFSQFGQVTEDLVYFYFKSQPLFPLHYFLISDSFLFAATIIMDKGKNRSKGYGYVTFSTEEEAQKALADMNGKLLDG   81 (112)
Q Consensus         2 l~~~f~~~G~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~d~~t~~~rG~afV~f~~~~~a~~Ai~~l~g~~l~g   81 (112)
                      |.+.|..||+|.-                           +|.+.|.        ..|+|.+-.+|-+|+. ++|.++.|
T Consensus        41 Llq~l~~~GeViL---------------------------vRFv~d~--------mwVTF~dG~SAL~al~-l~g~~v~G   84 (95)
T d1ufwa_          41 LMQTLGSYGTIVL---------------------------VRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKG   84 (95)
T ss_dssp             HHHHHHHHSCCSE---------------------------EEEETTE--------EEEECSCSHHHHHHHH-GGGSEETT
T ss_pred             HHHHHhhCCeEEE---------------------------EEEeCCe--------EEEEECCcHHHHHHhc-cCCeEEcc
Confidence            5678999999988                           8887774        6999999999999998 99999999


Q ss_pred             eeEEEEec
Q 033734           82 RVIFVDNV   89 (112)
Q Consensus        82 ~~i~V~~a   89 (112)
                      +.|.|..-
T Consensus        85 ~~l~It~~   92 (95)
T d1ufwa_          85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecC
Confidence            99998653