Citrus Sinensis ID: 032111

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------
Protein Sequence
MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGGGNDGSYGGNRGGYRVNYRGGDDGF
Secondary Structure (PSIPRED)
ccccccccccEEEccccccccccccccccccccccEEEEcccccccHHHHHHHHHccccEEEEEEccccccccccccEEEEEccHHHHHHHHHHcccccccccEEEEEccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHcccEEEEcccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHccHcccEEccEEEEEEEccccccccccccccccccccccccccEEEEEccccccc
Coil and Loop (DISEMBL)
mafcgklgmlvrqngqapkaSLINAVRFMSQSQTKLFVgglswgtddsSLKEAFSnfgditeakviteresgksrgfgfvtydsnesassaqsamdgqelngrnirvsfandrpprsdggygggndgsyggnrggyrvnyrggddgf
Flexible Loop (DISEMBL)
MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFsnfgditeakviteresgksrgFGFVTYDSNESASSAQSAMDGQELNGRNIRvsfandrpprsdggygggndgsyggnrggyrvnyrggddgf
Low Complexity Region (SEG)
MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPrsdggygggndgsyggnrggyrvnyrggddgF
Disordered region (IsUnstruct)
***CGKLGMLVR*******ASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVI***********GFV*******************************************************************
Disordered Region (DISOPRED)
****GKLG***************************LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR*****************************************
Disordered Region (DISEMBL)
MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDS*************QELNGRNIRVSFANDRPPRSDGGYGGGNDGSYGGNRGGYRVNYRGGDDGF
Disordered Region (DISPRO)
*AFCGKLGMLVRQNGQ***************SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND*****************GGNRGGYRVNYRGG****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGGGNDGSYGGNRGGYRVNYRGGDDGF
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	147	2.2.26 [Sep-21-2011]
Q9SVM8	158	Glycine-rich RNA-binding	yes	no	0.775	0.721	0.585	5e-35
Q9LIS2	136	Glycine-rich RNA-binding	no	no	0.775	0.838	0.552	1e-31
P39697	212	40S ribosomal protein S19	no	no	0.755	0.523	0.543	2e-27
Q9FNR1	309	Glycine-rich RNA-binding	no	no	0.755	0.359	0.471	3e-25
Q9C909	289	Glycine-rich RNA-binding	no	no	0.741	0.377	0.482	2e-23
Q43472	161	Glycine-rich RNA-binding	N/A	no	0.598	0.546	0.544	2e-21
Q03878	157	Glycine-rich RNA-binding	N/A	no	0.557	0.522	0.548	2e-20
Q9ZUU4	289	Ribonucleoprotein At2g372	no	no	0.551	0.280	0.536	4e-20
Q08937	291	29 kDa ribonucleoprotein	N/A	no	0.564	0.285	0.517	2e-19
Q04836	329	31 kDa ribonucleoprotein,	no	no	0.721	0.322	0.422	3e-19

>sp|Q9SVM8|RBG2_ARATH Glycine-rich RNA-binding protein 2, mitochondrial OS=Arabidopsis thaliana GN=RBG2 PE=1 SV=1

 Score =  146 bits (368), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 72/123 (58%), Positives = 97/123 (78%), Gaps = 9/123 (7%)

Query: 1   MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KLG L+RQN    G  P  S++ ++R MS   TKLF+GGLSWGTDD+SL++AF++
Sbjct: 1   MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMS---TKLFIGGLSWGTDDASLRDAFAH 57

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP-- 114
           FGD+ +AKVI +RE+G+SRGFGFV ++   +A++A S MDG+ELNGR+IRV+ ANDRP  
Sbjct: 58  FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSA 117

Query: 115 PRS 117
           PR+
Sbjct: 118 PRA 120

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

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

 Score =  135 bits (339), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 68/123 (55%), Positives = 93/123 (75%), Gaps = 9/123 (7%)

Query: 1   MAFCGKLGMLVRQ----NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KL  ++RQ    +   P  S++ ++R+MS   +KLFVGGLSWGTDDSSLK+AF++
Sbjct: 1   MAFCNKLSGILRQGVSQSSNGPVTSMLGSLRYMS---SKLFVGGLSWGTDDSSLKQAFTS 57

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR--P 114
           FG++TEA VI +RE+G+SRGFGFV++   +SA++A   MDG+ELNGR IRV+ A +R   
Sbjct: 58  FGEVTEATVIADRETGRSRGFGFVSFSCEDSANNAIKEMDGKELNGRQIRVNLATERSSA 117

Query: 115 PRS 117
           PRS
Sbjct: 118 PRS 120

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

Arabidopsis thaliana (taxid: 3702)

>sp|P39697|RT19_ARATH 40S ribosomal protein S19, mitochondrial OS=Arabidopsis thaliana GN=RPS19 PE=1 SV=2

 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 62/114 (54%), Positives = 86/114 (75%), Gaps = 3/114 (2%)

Query: 1   MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDI 60
           MAFC KLG   +Q    P +S++ ++R+MS   TKL++GGLS GTD+ SLK+AFS+F  +
Sbjct: 1   MAFCTKLGGHWKQGVNVPVSSMLGSLRYMS---TKLYIGGLSPGTDEHSLKDAFSSFNGV 57

Query: 61  TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
           TEA+V+T + +G+SRG+GFV + S +SA+SA SAM+GQELNG NI V+ A D P
Sbjct: 58  TEARVMTNKVTGRSRGYGFVNFISEDSANSAISAMNGQELNGFNISVNVAKDWP 111

The RNA-binding domain found in RPS19 may functionally replaces the missing mitochondrial RPS13.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FNR1|RBG3_ARATH Glycine-rich RNA-binding protein 3, mitochondrial OS=Arabidopsis thaliana GN=RBG3 PE=2 SV=1

 Score =  114 bits (284), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 57/121 (47%), Positives = 87/121 (71%), Gaps = 10/121 (8%)

Query: 1   MAFCGKLGMLVRQ------NGQAP--KASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKE 52
           MAF  K G +++Q      N Q      SL  A+R MS S  KLF+GG+++  D+ SL+E
Sbjct: 1   MAFLSKFGNILKQTTNKQLNAQVSLSSPSLFQAIRCMSSS--KLFIGGMAYSMDEDSLRE 58

Query: 53  AFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND 112
           AF+ +G++ + +VI +RE+G+SRGFGFVT+ S+E+ASSA  A+DG++L+GR ++V++AND
Sbjct: 59  AFTKYGEVVDTRVILDRETGRSRGFGFVTFTSSEAASSAIQALDGRDLHGRVVKVNYAND 118

Query: 113 R 113
           R
Sbjct: 119 R 119

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C909|RBG5_ARATH Glycine-rich RNA-binding protein 5, mitochondrial OS=Arabidopsis thaliana GN=RBG5 PE=2 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/114 (48%), Positives = 81/114 (71%), Gaps = 5/114 (4%)

Query: 1   MAFCGKLGMLVRQNGQAPKAS--LINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFG 58
           MAF  K+G L  Q      AS  ++ ++R MS S  K+FVGG+S+ TD+  L+EAFS +G
Sbjct: 1   MAFLSKVGRLFSQTSSHVTASSSMLQSIRCMSSS--KIFVGGISYSTDEFGLREAFSKYG 58

Query: 59  DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND 112
           ++ +AK+I +RE+G+SRGF FVT+ S E AS+A   +DGQ+L+GR IRV++A +
Sbjct: 59  EVVDAKIIVDRETGRSRGFAFVTFTSTEEASNAMQ-LDGQDLHGRRIRVNYATE 111

Possibly has a role in RNA transcription or processing during stress (By similarity). Binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. Displays strong affinity to poly(U) sequence.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  100 bits (250), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 49/90 (54%), Positives = 68/90 (75%), Gaps = 2/90 (2%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M+  + + FVGGL W TDD SL+ AFS +GD+ ++K+IT+RE+G+SRGFGFVT+ S+E+ 
Sbjct: 1   MADVEYRCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAM 60

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPRSD 118
             A  AM+GQ+L+GRNI V+ A  R  RSD
Sbjct: 61  RQAIEAMNGQDLDGRNITVNEAQSR--RSD 88

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

Hordeum vulgare (taxid: 4513)

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

 Score = 98.2 bits (243), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 45/82 (54%), Positives = 64/82 (78%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M++ + + FVGGL+W T+D SL++AFS FGDIT++K+I +RE+G+SRGFGFVT+   +S 
Sbjct: 1   MAEVEYRCFVGGLAWATNDESLEQAFSQFGDITDSKIINDRETGRSRGFGFVTFKDEKSM 60

Query: 89  SSAQSAMDGQELNGRNIRVSFA 110
             A   M+GQEL+GRNI V+ A
Sbjct: 61  RDAIEGMNGQELDGRNITVNEA 82

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

Daucus carota (taxid: 4039)

>sp|Q9ZUU4|ROC1_ARATH Ribonucleoprotein At2g37220, chloroplastic OS=Arabidopsis thaliana GN=At2g37220 PE=1 SV=1

 Score = 97.1 bits (240), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 44/82 (53%), Positives = 62/82 (75%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +++VG LSWG DD +L+  FS  G + EA+VI +R+SG+S+GFGFVTYDS++   +A  +
Sbjct: 205 RVYVGNLSWGVDDMALESLFSEQGKVVEARVIYDRDSGRSKGFGFVTYDSSQEVQNAIKS 264

Query: 95  MDGQELNGRNIRVSFANDRPPR 116
           +DG +L+GR IRVS A  RPPR
Sbjct: 265 LDGADLDGRQIRVSEAEARPPR 286

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q08937|ROC2_NICSY 29 kDa ribonucleoprotein B, chloroplastic OS=Nicotiana sylvestris PE=2 SV=1

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/85 (51%), Positives = 65/85 (76%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S  +++VG LSWG DD +LKE FS  G++ +AKV+ +R+SG+SRGFGFVTY S++  + A
Sbjct: 205 SSNRVYVGNLSWGVDDLALKELFSEQGNVVDAKVVYDRDSGRSRGFGFVTYSSSKEVNDA 264

Query: 92  QSAMDGQELNGRNIRVSFANDRPPR 116
             +++G +L+GR+IRVS A +RP R
Sbjct: 265 IDSLNGVDLDGRSIRVSAAEERPRR 289

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

Nicotiana sylvestris (taxid: 4096)

>sp|Q04836|ROC3_ARATH 31 kDa ribonucleoprotein, chloroplastic OS=Arabidopsis thaliana GN=RBP31 PE=1 SV=1

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/109 (42%), Positives = 67/109 (61%)

Query: 8   GMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVIT 67
           G L+  N  AP+ S       + +   +++VG L W  D+  L++ FS  G + EA+V+ 
Sbjct: 218 GRLLTVNKAAPRGSRPERAPRVYEPAFRVYVGNLPWDVDNGRLEQLFSEHGKVVEARVVY 277

Query: 68  ERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPR 116
           +RE+G+SRGFGFVT    +  + A SA+DGQ L GR IRV+ A +RPPR
Sbjct: 278 DRETGRSRGFGFVTMSDVDELNEAISALDGQNLEGRAIRVNVAEERPPR 326

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

Arabidopsis thaliana (taxid: 3702)

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	147
224128992	131	predicted protein [Populus trichocarpa]	0.843	0.946	0.613	7e-36
255563618	134	glycine-rich RNA-binding protein, putati	0.850	0.932	0.607	8e-36
1778374	146	glycine-rich RNA-binding protein PsGRBP	0.775	0.780	0.622	2e-35
351723185	143	uncharacterized protein LOC100499841 [Gl	0.761	0.783	0.627	4e-34
351725255	138	uncharacterized protein LOC100527220 [Gl	0.761	0.811	0.627	5e-34
118487563	133	unknown [Populus trichocarpa]	0.850	0.939	0.585	2e-33
76160980	150	RNA binding protein-like protein [Solanu	0.782	0.766	0.563	2e-33
2826811	150	AtGRP2 [Arabidopsis thaliana]	0.775	0.76	0.585	3e-33
30682622	153	glycine-rich RNA-binding protein 2 [Arab	0.775	0.745	0.585	4e-33
15236359	158	glycine-rich RNA-binding protein 2 [Arab	0.775	0.721	0.585	4e-33

>gi|224128992|ref|XP_002328863.1| predicted protein [Populus trichocarpa] gi|118482403|gb|ABK93124.1| unknown [Populus trichocarpa] gi|222839293|gb|EEE77630.1| predicted protein [Populus trichocarpa]

 Score =  155 bits (391), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 81/132 (61%), Positives = 100/132 (75%), Gaps = 8/132 (6%)

Query: 1   MAFCGKLGMLVRQ----NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAF  K G LVRQ    NGQ P AS++N++R MS S  KLF+GGL+W TDD SLK+AFS 
Sbjct: 1   MAFFNKFGSLVRQSVSQNGQVPMASMLNSIRCMSSS--KLFIGGLAWSTDDQSLKDAFSG 58

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR--P 114
           FG++TEA+VIT+R++G+SRGFGFV+Y+S ESAS A SAMDGQEL GRNIRV +A D+  P
Sbjct: 59  FGEVTEARVITDRDTGRSRGFGFVSYESTESASEALSAMDGQELGGRNIRVGYATDKRQP 118

Query: 115 PRSDGGYGGGND 126
              +  YGG  D
Sbjct: 119 QPYNSNYGGNPD 130

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563618|ref|XP_002522811.1| glycine-rich RNA-binding protein, putative [Ricinus communis] gi|223538049|gb|EEF39662.1| glycine-rich RNA-binding protein, putative [Ricinus communis]

 Score =  154 bits (390), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 82/135 (60%), Positives = 104/135 (77%), Gaps = 10/135 (7%)

Query: 1   MAFCGKLGMLVRQ----NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC K+G LVRQ    NG+ P +S++N++R MS S  KLF+GGLS+GT+D SLK+AFS 
Sbjct: 1   MAFCNKIGSLVRQSVAQNGKVPVSSMLNSIRCMSSS--KLFIGGLSYGTNDDSLKDAFSG 58

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPR 116
           FGD+  A+VIT+R++G+SRGFGFV + S +SASSA SAMDGQEL+GRNIRVS+A +R PR
Sbjct: 59  FGDVVTARVITDRDTGRSRGFGFVDFSSVDSASSALSAMDGQELHGRNIRVSYATERAPR 118

Query: 117 SDG----GYGGGNDG 127
             G      G GNDG
Sbjct: 119 PGGPRSFNNGFGNDG 133

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|1778374|gb|AAB71417.1| glycine-rich RNA-binding protein PsGRBP [Pisum sativum] gi|206586422|gb|ACI15745.1| glycine-rich RNA-binding protein [Pisum sativum]

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 76/122 (62%), Positives = 100/122 (81%), Gaps = 8/122 (6%)

Query: 1   MAFCGKLGMLVRQ----NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KLG L+RQ    +  AP +S++N +R MS S  KLF+GGLS+G DD SLK+AF++
Sbjct: 1   MAFCNKLGNLLRQGATQSSHAPVSSMLNYLRHMSSS--KLFIGGLSYGVDDQSLKDAFAS 58

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP-- 114
           +G++ EA+VIT+R++G+SRGFGFV + S+ESA+SA SAMDGQ+LNGRNIRVS+ANDRP  
Sbjct: 59  YGEVVEARVITDRDTGRSRGFGFVNFTSDESATSALSAMDGQDLNGRNIRVSYANDRPSA 118

Query: 115 PR 116
           PR
Sbjct: 119 PR 120

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351723185|ref|NP_001236758.1| uncharacterized protein LOC100499841 [Glycine max] gi|255627057|gb|ACU13873.1| unknown [Glycine max]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 74/118 (62%), Positives = 97/118 (82%), Gaps = 6/118 (5%)

Query: 1   MAFCGKLGMLVRQ----NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC K+G ++RQ    +  AP AS++N +R MS S  KLF+GGLS+G DD SLK+AFS 
Sbjct: 1   MAFCNKVGNVLRQGAARSTHAPVASMLNYIRCMSSS--KLFIGGLSYGVDDQSLKDAFSG 58

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
           FGD+ +AKVIT+R+SG+SRGFGFV + ++ESASSA SAMDG++LNGR+IRVS+AND+P
Sbjct: 59  FGDVVDAKVITDRDSGRSRGFGFVNFSNDESASSALSAMDGKDLNGRSIRVSYANDKP 116

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725255|ref|NP_001236574.1| uncharacterized protein LOC100527220 [Glycine max] gi|255631812|gb|ACU16273.1| unknown [Glycine max]

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 74/118 (62%), Positives = 98/118 (83%), Gaps = 6/118 (5%)

Query: 1   MAFCGKLGMLVRQ----NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC K+G ++RQ    + QAP +S++N +R MS S  KLF+GGLS+G DD SLK+AFS 
Sbjct: 1   MAFCNKVGNVLRQGAARSTQAPVSSMLNYIRCMSSS--KLFIGGLSYGVDDQSLKDAFSG 58

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
           FGD+ +AKVIT+R+SG+SRGFGFV + ++ESASSA SAMDG++L+GR+IRVS+ANDRP
Sbjct: 59  FGDVVDAKVITDRDSGRSRGFGFVNFSNDESASSALSAMDGKDLDGRSIRVSYANDRP 116

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487563|gb|ABK95608.1| unknown [Populus trichocarpa]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 79/135 (58%), Positives = 98/135 (72%), Gaps = 10/135 (7%)

Query: 1   MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAF  KLG L RQ+    GQ P  S++N++R MS S  KLF+GGL W TDD +LK+AFS 
Sbjct: 1   MAFFNKLGSLARQSISQKGQVPMVSMVNSIRCMSSS--KLFIGGLPWSTDDQTLKDAFSG 58

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND-RPP 115
           FG++TEA+VI +RE+G+SRGFGFV YDS E+AS A SAMDGQ L GR +RVSFA + RPP
Sbjct: 59  FGEVTEARVIMDRETGRSRGFGFVHYDSVENASEALSAMDGQNLGGRTVRVSFAEERRPP 118

Query: 116 RSDGGYGGGNDGSYG 130
           +S   Y   + GS G
Sbjct: 119 QS---YNDNHQGSRG 130

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|76160980|gb|ABA40453.1| RNA binding protein-like protein [Solanum tuberosum] gi|76160996|gb|ABA40461.1| RNA binding protein-like protein [Solanum tuberosum]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 71/126 (56%), Positives = 94/126 (74%), Gaps = 11/126 (8%)

Query: 1   MAFCGKLGMLVRQN--------GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKE 52
           MAFC KLG L+RQ+          +P  +++NA+R MS   ++LFVGGLSWGTDD SLKE
Sbjct: 1   MAFCNKLGGLLRQSISTGNAASANSPTPAMLNAIRCMS---SRLFVGGLSWGTDDQSLKE 57

Query: 53  AFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND 112
           AF++FGD+ +AKVI +R+SG+SRGFGFV +   + A  A +AMDGQ+L+GRNIRV+ A +
Sbjct: 58  AFTSFGDVVDAKVIIDRDSGRSRGFGFVNFSDEDCAKEAMNAMDGQQLHGRNIRVNLAQE 117

Query: 113 RPPRSD 118
           R PRSD
Sbjct: 118 RAPRSD 123

Source: Solanum tuberosum

Species: Solanum tuberosum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2826811|emb|CAA05727.1| AtGRP2 [Arabidopsis thaliana]

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 72/123 (58%), Positives = 97/123 (78%), Gaps = 9/123 (7%)

Query: 1   MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KLG L+RQN    G  P  S++ ++R MS   TKLF+GGLSWGTDD+SL++AF++
Sbjct: 1   MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMS---TKLFIGGLSWGTDDASLRDAFAH 57

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP-- 114
           FGD+ +AKVI +RE+G+SRGFGFV ++   +A++A S MDG+ELNGR+IRV+ ANDRP  
Sbjct: 58  FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSA 117

Query: 115 PRS 117
           PR+
Sbjct: 118 PRA 120

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30682622|ref|NP_849377.1| glycine-rich RNA-binding protein 2 [Arabidopsis thaliana] gi|332657934|gb|AEE83334.1| glycine-rich RNA-binding protein 2 [Arabidopsis thaliana]

 Score =  146 bits (368), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 72/123 (58%), Positives = 97/123 (78%), Gaps = 9/123 (7%)

Query: 1   MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KLG L+RQN    G  P  S++ ++R MS   TKLF+GGLSWGTDD+SL++AF++
Sbjct: 1   MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMS---TKLFIGGLSWGTDDASLRDAFAH 57

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP-- 114
           FGD+ +AKVI +RE+G+SRGFGFV ++   +A++A S MDG+ELNGR+IRV+ ANDRP  
Sbjct: 58  FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSA 117

Query: 115 PRS 117
           PR+
Sbjct: 118 PRA 120

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15236359|ref|NP_193121.1| glycine-rich RNA-binding protein 2 [Arabidopsis thaliana] gi|25090505|sp|Q9SVM8.1|GRP2_ARATH RecName: Full=Glycine-rich RNA-binding protein 2, mitochondrial; Short=AtGRP2; Flags: Precursor gi|4455314|emb|CAB36849.1| glycine-rich RNA-binding protein AtGRP2-like [Arabidopsis thaliana] gi|7268089|emb|CAB78427.1| glycine-rich RNA-binding protein AtGRP2-like [Arabidopsis thaliana] gi|18252853|gb|AAL62353.1| glycine-rich RNA-binding protein AtGRP2 - like [Arabidopsis thaliana] gi|21553749|gb|AAM62842.1| glycine-rich RNA-binding protein AtGRP2-like [Arabidopsis thaliana] gi|25084267|gb|AAN72208.1| glycine-rich RNA-binding protein AtGRP2 - like [Arabidopsis thaliana] gi|332657933|gb|AEE83333.1| glycine-rich RNA-binding protein 2 [Arabidopsis thaliana]

 Score =  146 bits (368), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 72/123 (58%), Positives = 97/123 (78%), Gaps = 9/123 (7%)

Query: 1   MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KLG L+RQN    G  P  S++ ++R MS   TKLF+GGLSWGTDD+SL++AF++
Sbjct: 1   MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMS---TKLFIGGLSWGTDDASLRDAFAH 57

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP-- 114
           FGD+ +AKVI +RE+G+SRGFGFV ++   +A++A S MDG+ELNGR+IRV+ ANDRP  
Sbjct: 58  FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSA 117

Query: 115 PRS 117
           PR+
Sbjct: 118 PRA 120

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	147
TAIR|locus:2119495	158	GR-RBP2 "AT4G13850" [Arabidops	0.755	0.702	0.593	5.2e-33
TAIR|locus:2076096	136	GRP4 "glycine-rich RNA-binding	0.748	0.808	0.572	2.3e-30
TAIR|locus:2171539	212	RPS19 "ribosomal protein S19"	0.755	0.523	0.543	5.7e-27
TAIR|locus:2159401	309	GR-RBP3 "glycine-rich RNA-bind	0.755	0.359	0.471	9.7e-25
TAIR|locus:2019622	289	GR-RBP5 "AT1G74230" [Arabidops	0.748	0.380	0.478	1.6e-24
UNIPROTKB|Q43472	161	blt801 "Glycine-rich RNA-bindi	0.578	0.527	0.541	1.9e-21
TAIR|locus:2049721	289	AT2G37220 [Arabidopsis thalian	0.571	0.290	0.523	2.7e-20
TAIR|locus:2077427	143	AT3G08000 [Arabidopsis thalian	0.714	0.734	0.442	2.7e-20
TAIR|locus:2122009	329	RBP31 "AT4G24770" [Arabidopsis	0.734	0.328	0.416	6.5e-19
TAIR|locus:2136298	169	CCR1 "cold, circadian rhythm,	0.578	0.502	0.482	1.7e-18

TAIR|locus:2119495 GR-RBP2 "AT4G13850" [Arabidopsis thaliana (taxid:3702)]

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 70/118 (59%), Positives = 94/118 (79%)

Query:     1 MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
             MAFC KLG L+RQN    G  P  S++ ++R MS   TKLF+GGLSWGTDD+SL++AF++
Sbjct:     1 MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMS---TKLFIGGLSWGTDDASLRDAFAH 57

Query:    57 FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
             FGD+ +AKVI +RE+G+SRGFGFV ++   +A++A S MDG+ELNGR+IRV+ ANDRP
Sbjct:    58 FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRP 115

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

GO:0005739 "mitochondrion" evidence=ISM;IDA

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

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

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

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

GO:0005524 "ATP binding" evidence=IDA

GO:0001072 "RNA binding transcription antitermination factor activity" evidence=IDA

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

GO:0009631 "cold acclimation" evidence=IMP

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

GO:0009845 "seed germination" evidence=IMP

GO:0031564 "transcription antitermination" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

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

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 67/117 (57%), Positives = 91/117 (77%)

Query:     1 MAFCGKL-GML---VRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
             MAFC KL G+L   V Q+   P  S++ ++R+MS   +KLFVGGLSWGTDDSSLK+AF++
Sbjct:     1 MAFCNKLSGILRQGVSQSSNGPVTSMLGSLRYMS---SKLFVGGLSWGTDDSSLKQAFTS 57

Query:    57 FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR 113
             FG++TEA VI +RE+G+SRGFGFV++   +SA++A   MDG+ELNGR IRV+ A +R
Sbjct:    58 FGEVTEATVIADRETGRSRGFGFVSFSCEDSANNAIKEMDGKELNGRQIRVNLATER 114

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:2171539 RPS19 "ribosomal protein S19" [Arabidopsis thaliana (taxid:3702)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 62/114 (54%), Positives = 86/114 (75%)

Query:     1 MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDI 60
             MAFC KLG   +Q    P +S++ ++R+MS   TKL++GGLS GTD+ SLK+AFS+F  +
Sbjct:     1 MAFCTKLGGHWKQGVNVPVSSMLGSLRYMS---TKLYIGGLSPGTDEHSLKDAFSSFNGV 57

Query:    61 TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
             TEA+V+T + +G+SRG+GFV + S +SA+SA SAM+GQELNG NI V+ A D P
Sbjct:    58 TEARVMTNKVTGRSRGYGFVNFISEDSANSAISAMNGQELNGFNISVNVAKDWP 111

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

GO:0005840 "ribosome" evidence=IEA

GO:0006412 "translation" evidence=IEA;NAS

GO:0015935 "small ribosomal subunit" evidence=IEA

GO:0006354 "DNA-dependent transcription, elongation" evidence=RCA

GO:0005763 "mitochondrial small ribosomal subunit" evidence=IDA

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

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 57/121 (47%), Positives = 88/121 (72%)

Query:     1 MAFCGKLGMLVRQ------NGQAPKAS--LINAVRFMSQSQTKLFVGGLSWGTDDSSLKE 52
             MAF  K G +++Q      N Q   +S  L  A+R MS S  KLF+GG+++  D+ SL+E
Sbjct:     1 MAFLSKFGNILKQTTNKQLNAQVSLSSPSLFQAIRCMSSS--KLFIGGMAYSMDEDSLRE 58

Query:    53 AFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND 112
             AF+ +G++ + +VI +RE+G+SRGFGFVT+ S+E+ASSA  A+DG++L+GR ++V++AND
Sbjct:    59 AFTKYGEVVDTRVILDRETGRSRGFGFVTFTSSEAASSAIQALDGRDLHGRVVKVNYAND 118

Query:   113 R 113
             R
Sbjct:   119 R 119

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005524 "ATP binding" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

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

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

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

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

GO:0034968 "histone lysine methylation" evidence=RCA

TAIR|locus:2019622 GR-RBP5 "AT1G74230" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 55/115 (47%), Positives = 82/115 (71%)

Query:     1 MAFCGKLGMLVRQNGQ--APKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFG 58
             MAF  K+G L  Q        +S++ ++R MS S  K+FVGG+S+ TD+  L+EAFS +G
Sbjct:     1 MAFLSKVGRLFSQTSSHVTASSSMLQSIRCMSSS--KIFVGGISYSTDEFGLREAFSKYG 58

Query:    59 DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR 113
             ++ +AK+I +RE+G+SRGF FVT+ S E AS+A   +DGQ+L+GR IRV++A +R
Sbjct:    59 EVVDAKIIVDRETGRSRGFAFVTFTSTEEASNAMQ-LDGQDLHGRRIRVNYATER 112

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

GO:0005524 "ATP binding" evidence=IDA

GO:0005507 "copper ion binding" evidence=IDA

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

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

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 46/85 (54%), Positives = 65/85 (76%)

Query:    29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
             M+  + + FVGGL W TDD SL+ AFS +GD+ ++K+IT+RE+G+SRGFGFVT+ S+E+ 
Sbjct:     1 MADVEYRCFVGGLRWATDDQSLQNAFSKYGDVIDSKIITDRETGRSRGFGFVTFASDEAM 60

Query:    89 SSAQSAMDGQELNGRNIRVSFANDR 113
               A  AM+GQ+L+GRNI V+ A  R
Sbjct:    61 RQAIEAMNGQDLDGRNITVNEAQSR 85

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

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IDA

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

TAIR|locus:2049721 AT2G37220 [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 44/84 (52%), Positives = 62/84 (73%)

Query:    32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
             S  +++VG LSWG DD +L+  FS  G + EA+VI +R+SG+S+GFGFVTYDS++   +A
Sbjct:   202 SGNRVYVGNLSWGVDDMALESLFSEQGKVVEARVIYDRDSGRSKGFGFVTYDSSQEVQNA 261

Query:    92 QSAMDGQELNGRNIRVSFANDRPP 115
               ++DG +L+GR IRVS A  RPP
Sbjct:   262 IKSLDGADLDGRQIRVSEAEARPP 285

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

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

GO:0010319 "stromule" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

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

GO:0009534 "chloroplast thylakoid" evidence=IDA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009814 "defense response, incompatible interaction" evidence=RCA

GO:0019684 "photosynthesis, light reaction" evidence=RCA

GO:0042742 "defense response to bacterium" evidence=RCA

TAIR|locus:2077427 AT3G08000 [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 50/113 (44%), Positives = 74/113 (65%)

Query:     9 MLVRQNGQAPKASLINAVRFMSQSQT--------KLFVGGLSWGTDDSSLKEAFSNFGDI 60
             +LVR+    P+ S+ ++  F+ Q  T        KLF+GGLSW  D+ SLK+AFS+FG++
Sbjct:     8 LLVRRVSAIPQHSISSSFHFLPQFCTSSSASPSSKLFIGGLSWSVDEQSLKDAFSSFGEV 67

Query:    61 TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR 113
              E ++  ++ SG+SRGFGFV +     A SA+ AMDG+ L GR +R+SFA +R
Sbjct:    68 AEVRIAYDKGSGRSRGFGFVDFAEEGDALSAKDAMDGKGLLGRPLRISFALER 120

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2122009 RBP31 "AT4G24770" [Arabidopsis thaliana (taxid:3702)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 45/108 (41%), Positives = 66/108 (61%)

Query:     8 GMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVIT 67
             G L+  N  AP+ S       + +   +++VG L W  D+  L++ FS  G + EA+V+ 
Sbjct:   218 GRLLTVNKAAPRGSRPERAPRVYEPAFRVYVGNLPWDVDNGRLEQLFSEHGKVVEARVVY 277

Query:    68 ERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPP 115
             +RE+G+SRGFGFVT    +  + A SA+DGQ L GR IRV+ A +RPP
Sbjct:   278 DRETGRSRGFGFVTMSDVDELNEAISALDGQNLEGRAIRVNVAEERPP 325

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009579 "thylakoid" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0009631 "cold acclimation" evidence=IMP

GO:0016553 "base conversion or substitution editing" evidence=IMP

GO:0043489 "RNA stabilization" evidence=IMP

GO:0006396 "RNA processing" evidence=TAS

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

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 41/85 (48%), Positives = 60/85 (70%)

Query:    29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
             MS+ + + FVGGL+W T+D  L+  FS FGD+ ++K+I +RESG+SRGFGFVT+   ++ 
Sbjct:     1 MSEVEYRCFVGGLAWATNDEDLQRTFSQFGDVIDSKIINDRESGRSRGFGFVTFKDEKAM 60

Query:    89 SSAQSAMDGQELNGRNIRVSFANDR 113
               A   M+G+EL+GR I V+ A  R
Sbjct:    61 RDAIEEMNGKELDGRVITVNEAQSR 85

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0005618 "cell wall" evidence=IDA

GO:0045087 "innate immune response" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0005777 "peroxisome" evidence=IDA

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

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

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0048046 "apoplast" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0007623 "circadian rhythm" evidence=RCA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SVM8	RBG2_ARATH	No assigned EC number	0.5853	0.7755	0.7215	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pm.C_880007	SubName- Full=Putative uncharacterized protein; (131 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XV.2574.1	hypothetical protein (203 aa)			•						0.495
	gw1.232.53.1	hypothetical protein (203 aa)			•						0.492

---

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	147
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-39
smart00360	73	smart00360, RRM, RNA recognition motif	7e-28
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-27
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-25
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-24
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-23
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-23
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-23
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-21
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-21
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-20
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-20
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-19
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-19
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-18
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	8e-18
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-17
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-17
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-17
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-17
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-16
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-16
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-16
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-16
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-16
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-16
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-15
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-15
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-15
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-15
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-15
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-15
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	6e-15
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-15
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	9e-15
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-14
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-14
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-14
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-14
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	2e-14
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-14
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-14
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-14
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-14
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-14
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-14
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-14
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-14
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	7e-14
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-13
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-13
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	3e-13
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-13
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	4e-13
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-13
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-13
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-13
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	6e-13
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	6e-13
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	7e-13
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	7e-13
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	7e-13
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	8e-13
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-12
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-12
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-12
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	2e-12
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-12
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-12
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-12
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-12
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-12
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-12
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-12
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-12
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	7e-12
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	9e-12
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-11
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-11
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-11
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-11
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-11
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-11
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-11
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-11
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-11
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-11
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-11
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	3e-11
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-11
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	3e-11
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-11
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-11
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-11
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	4e-11
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	4e-11
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	5e-11
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-11
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	6e-11
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	7e-11
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	7e-11
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-11
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-10
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-10
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-10
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-10
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	2e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-10
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-10
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-10
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-10
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-10
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-10
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	5e-10
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-10
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-10
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	7e-10
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	8e-10
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	8e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	9e-10
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-09
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-09
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-09
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-09
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-09
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-09
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-09
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-09
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-09
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-09
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-09
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-09
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	4e-09
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	5e-09
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	5e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	6e-09
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	7e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	8e-09
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	8e-09
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	8e-09
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	9e-09
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	9e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-08
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-08
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-08
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-08
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	2e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-08
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	3e-08
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	3e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-08
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	5e-08
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	5e-08
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-08
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	7e-08
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	7e-08
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	9e-08
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	9e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-07
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	1e-07
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	1e-07
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
cd12644	90	cd12644, RRM_CFIm59, RNA recognition motif of pre-	2e-07
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	2e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-07
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-07
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-07
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	2e-07
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-07
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	3e-07
cd12643	77	cd12643, RRM_CFIm68, RNA recognition motif of pre-	3e-07
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-07
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-07
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-07
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-07
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-07
cd12667	92	cd12667, RRM3_RAVER1, RNA recognition motif 3 in v	4e-07
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	4e-07
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-07
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	6e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-07
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	9e-07
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-06
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	1e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	2e-06
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-06
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	2e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-06
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	2e-06
cd12535	86	cd12535, RRM_FUS_TAF15, RNA recognition motif in v	2e-06
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	2e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-06
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-06
cd12668	98	cd12668, RRM3_RAVER2, RNA recognition motif 3 foun	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-06
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	4e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	4e-06
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	5e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	7e-06
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	1e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-05
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	3e-05
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	3e-05
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	4e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	4e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	4e-05
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	5e-05
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	5e-05
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	5e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	6e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	7e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	7e-05
cd12364	81	cd12364, RRM_RDM1, RNA recognition motif of RAD52	7e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	8e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	9e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	9e-05
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	1e-04
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	1e-04
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	1e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-04
cd12558	76	cd12558, RRM3_RBM15B, RNA recognition motif 3 in p	2e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	2e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	2e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	2e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	3e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	4e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	4e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	4e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	5e-04
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	6e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	6e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	6e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	7e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	7e-04
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	7e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	8e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	8e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	8e-04
cd12339	71	cd12339, RRM2_SRSF1_4_like, RNA recognition motif	0.001
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.001
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.001
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.001
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.001
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	0.002
cd12374	85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	0.002
cd12497	74	cd12497, RRM3_RBM47, RNA recognition motif 3 in ve	0.002
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.002
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.002
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	0.003
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.003
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.003
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	0.004
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	0.004
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.004
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	0.004
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.004
cd12410	93	cd12410, RRM2_RRT5, RNA recognition motif 2 in yea	0.004

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

 Score =  130 bits (328), Expect = 1e-39
 Identities = 81/150 (54%), Positives = 105/150 (70%), Gaps = 13/150 (8%)

Query: 1   MAFCGKLGMLVRQN----GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSN 56
           MAFC KLG L+RQN    G  P  S++ ++R MS   TKLF+GGLSWGTDD+SL++AF++
Sbjct: 1   MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMS---TKLFIGGLSWGTDDASLRDAFAH 57

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPR 116
           FGD+ +AKVI +RE+G+SRGFGFV ++   +A++A S MDG+ELNGR+IRV+ ANDRP  
Sbjct: 58  FGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSA 117

Query: 117 SDGGYGGGNDGSYGGNRGGYRVNYRGGDDG 146
                GGG     GG  GG      GGD G
Sbjct: 118 PRAYGGGGGYSGGGGGYGG------GGDGG 141

Length = 144

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

 Score = 97.7 bits (244), Expect = 7e-28
 Identities = 31/73 (42%), Positives = 49/73 (67%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
            LFVG L   T +  L+E FS FG +   +++ ++E+GKS+GF FV ++S E A  A  A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 95  MDGQELNGRNIRV 107
           ++G+EL+GR ++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 97.5 bits (243), Expect = 1e-27
 Identities = 42/76 (55%), Positives = 53/76 (69%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
            LFVG LSW  DD  LK  F  FG +  A+VIT+RE+G+SRGFG+V ++S E A  A  A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 95  MDGQELNGRNIRVSFA 110
           MDG+EL+GR I V F+
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 92.3 bits (230), Expect = 1e-25
 Identities = 32/77 (41%), Positives = 51/77 (66%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
            L+VG L +   +  LK+ F  FG++T A+VIT+RE+G+SRGFGFV  ++ E A++A   
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 95  MDGQELNGRNIRVSFAN 111
           ++G +  GR + V+ A 
Sbjct: 61  LNGTDFGGRTLTVNEAR 77

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

>gnl|CDD|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 = 88.0 bits (218), Expect = 6e-24
 Identities = 37/78 (47%), Positives = 57/78 (73%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGLS+ T++ SL++ FS +G I+E  V+ +RE+ +SRGFGFVT+++ + A  A  A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 95  MDGQELNGRNIRVSFAND 112
           M+G+ ++GR IRV  A  
Sbjct: 62  MNGKSVDGRQIRVDQAGK 79

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

 Score = 85.8 bits (213), Expect = 3e-23
 Identities = 32/73 (43%), Positives = 50/73 (68%), Gaps = 1/73 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L   T +  L+E FS FG+I   +++ +++ GKS+GF FV ++S E A  A  A+
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 96  DGQELNGRNIRVS 108
           +G+EL+GR ++VS
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 85.7 bits (213), Expect = 4e-23
 Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L   T +  LK+ FS FG I   +++ + E+G+S+GF FV ++  E A  A  A+
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 96  DGQELNGRNIR 106
           +G+EL GR +R
Sbjct: 60  NGKELGGRELR 70

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

>gnl|CDD|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 = 85.4 bits (212), Expect = 7e-23
 Identities = 36/77 (46%), Positives = 51/77 (66%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            KLFV GLS  T +  L+  FS FG + E  ++ + E+G+SRGFGFVT++S E A +A  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 94  AMDGQELNGRNIRVSFA 110
            ++G+EL GR I+V  A
Sbjct: 62  DLNGKELEGRVIKVEKA 78

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

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

 Score = 81.5 bits (202), Expect = 2e-21
 Identities = 38/72 (52%), Positives = 51/72 (70%), Gaps = 4/72 (5%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA-- 91
           TK+FVGGL + T D SL++ FS FG+I EA VIT+R++GKSRG+GFVT+   ESA  A  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 92  --QSAMDGQELN 101
                +DG++ N
Sbjct: 61  DPNPIIDGRKAN 72

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

 Score = 80.3 bits (199), Expect = 5e-21
 Identities = 29/72 (40%), Positives = 45/72 (62%), Gaps = 5/72 (6%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+GGLSW T + SL+E FS +G++ +  ++ +  +G+SRGFGFVT+      SS    +
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTF---ADPSSVDKVL 57

Query: 96  DGQE--LNGRNI 105
             +   L+GR I
Sbjct: 58  AAKPHVLDGREI 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|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 79.0 bits (195), Expect = 2e-20
 Identities = 32/71 (45%), Positives = 51/71 (71%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS   D  +L+ AF+ FG+I++A+V+ + ++GKS+G+GFV++   E A +A  +M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 96  DGQELNGRNIR 106
           +GQ L GR IR
Sbjct: 62  NGQWLGGRAIR 72

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|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 = 78.0 bits (193), Expect = 4e-20
 Identities = 28/74 (37%), Positives = 47/74 (63%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
           FVG + +   +  L E FS  G +   +++T+R++GK +G+GF  ++  E+A+SA   ++
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 97  GQELNGRNIRVSFA 110
           G E NGR +RV FA
Sbjct: 62  GYEFNGRALRVDFA 75

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

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

 Score = 76.5 bits (189), Expect = 2e-19
 Identities = 31/73 (42%), Positives = 45/73 (61%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VGGL+   D+  L  AF  FGDI + ++  + E+ K RGF FV ++  E A++A   M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 96  DGQELNGRNIRVS 108
           +  EL GR IRV+
Sbjct: 61  NESELFGRTIRVN 73

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

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

 Score = 75.3 bits (186), Expect = 6e-19
 Identities = 30/75 (40%), Positives = 38/75 (50%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L + T D  L+E FS  G I    V+ ++ S K RGFG+VT+   E A  A    
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 96  DGQELNGRNIRVSFA 110
              +  GR I V FA
Sbjct: 62  KKTKFGGRKIHVEFA 76

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

 Score = 73.8 bits (182), Expect = 2e-18
 Identities = 32/77 (41%), Positives = 50/77 (64%), Gaps = 1/77 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T ++V  L    DD  LKE F  +G IT AKV+ + + GKS+GFGFV ++++E+A  A  
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVE 60

Query: 94  AMDGQELNGRNIRVSFA 110
            ++G+E+NG+ + V  A
Sbjct: 61  ELNGKEVNGKKLYVGRA 77

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

 Score = 72.3 bits (178), Expect = 8e-18
 Identities = 34/76 (44%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
            L+V  L    DD  L+E FS FG IT AKV+T+ E G+S+GFGFV + S E A+ A + 
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 95  MDGQELNGRNIRVSFA 110
           M+G+ + G+ + V+ A
Sbjct: 62  MNGRIIGGKPLYVALA 77

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

 Score = 71.9 bits (177), Expect = 1e-17
 Identities = 32/76 (42%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEA-KVITERESGKSRGFGFVTYDSNESASSAQSA 94
           LF+G L    D+  L + FS FG I +  K++ + ++G S+GF F++YDS E++ +A  A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 95  MDGQELNGRNIRVSFA 110
           M+GQ L  R I VS+A
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

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

 Score = 71.6 bits (176), Expect = 2e-17
 Identities = 32/69 (46%), Positives = 46/69 (66%), Gaps = 4/69 (5%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLF+GGLS+ T D SLK  FS +G+IT+  V+ +  + +SRGFGFVT+ S     +A +A
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 95 ----MDGQE 99
              +DG+E
Sbjct: 61 RPHKVDGRE 69

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

 Score = 70.7 bits (174), Expect = 3e-17
 Identities = 23/54 (42%), Positives = 36/54 (66%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
          KLFVGGL     +  L+E FS +G++   +++T++E+GK RGF FVT+D  +  
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPV 54

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 70.3 bits (173), Expect = 4e-17
 Identities = 32/75 (42%), Positives = 52/75 (69%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V GLS  T +  L+E FS +G I + +V+ ++++G+SRGFGFV ++S E A  A+  +
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 96  DGQELNGRNIRVSFA 110
           +G E++GR IRV ++
Sbjct: 62  NGMEIDGRRIRVDYS 76

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

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

 Score = 73.8 bits (180), Expect = 2e-16
 Identities = 36/89 (40%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
               LFVG L +   +  L+E F  FG +   +++ +RE+GKSRGF FV ++S ESA  A
Sbjct: 114 ENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173

Query: 92  QSAMDGQELNGRNIRVSFANDR-PPRSDG 119
              ++G+EL GR +RV  A     PRS+ 
Sbjct: 174 IEELNGKELEGRPLRVQKAQPASQPRSEL 202

Length = 306

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

 Score = 68.2 bits (167), Expect = 3e-16
 Identities = 30/72 (41%), Positives = 50/72 (69%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG LS+  D+ S+ EAF  +G+I+  ++ T+ +SG+ +GFG+V + S E+A +A  A+
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 96  DGQELNGRNIRV 107
            G +L GR +R+
Sbjct: 61  GGTDLLGRPVRL 72

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

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

 Score = 68.3 bits (167), Expect = 3e-16
 Identities = 30/74 (40%), Positives = 50/74 (67%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS    D++L  AFS F   ++A+V+ + +SG+SRG+GFV++ S + A +A + M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 96  DGQELNGRNIRVSF 109
           +G+ L  R IR ++
Sbjct: 62  NGKWLGSRPIRCNW 75

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

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

 Score = 67.8 bits (166), Expect = 4e-16
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGGL     +   KE FS FG + +A+++ + ++G+SRGFGFVT+D +ESA     +
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFD-SESAVERVFS 59

Query: 95  MDGQELNGRNIRVSFA 110
               EL G+ + V  A
Sbjct: 60  AGMLELGGKQVEVKRA 75

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

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

 Score = 67.7 bits (166), Expect = 4e-16
 Identities = 25/73 (34%), Positives = 42/73 (57%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG L +   +  L+  F  FG+I   ++  + E+G+S+G+GF+ +   E A  A   +
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 96  DGQELNGRNIRVS 108
           +G EL GR I+V 
Sbjct: 61  NGFELAGRPIKVG 73

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

>gnl|CDD|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 = 67.3 bits (165), Expect = 6e-16
 Identities = 25/62 (40%), Positives = 43/62 (69%)

Query: 47  DSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR 106
           D  L + F+ FG++  AKV  ++ +G+S+ FGFV+YD+ ESA +A  AM+G ++ G+ ++
Sbjct: 12  DQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLK 71

Query: 107 VS 108
           V 
Sbjct: 72  VQ 73

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

>gnl|CDD|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 = 66.7 bits (163), Expect = 1e-15
 Identities = 29/75 (38%), Positives = 46/75 (61%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG + +   +  LK+ FS  G +   +++ +RE+GK +G+GF  Y   E+A SA   +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 96  DGQELNGRNIRVSFA 110
           +G ELNGR +RV  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 66.1 bits (162), Expect = 2e-15
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 2/77 (2%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++FVGG+   T +  L++ FS FG + + K+IT+R +G S+G+GFVT+++ E A     A
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKIL-A 61

Query: 95  MDGQELNGRNIRVSFAN 111
           M      G+ + +  A 
Sbjct: 62  MGNLNFRGKKLNIGPAI 78

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

 Score = 66.1 bits (162), Expect = 2e-15
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +L V  L +   ++ LK+ FS FG + E  +  +   GK +GF FV + S   A  A   
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59

Query: 95  MDGQELNGRNIRVSFA 110
           ++G+++ GR + V +A
Sbjct: 60  VNGKKIKGRPVAVDWA 75

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

>gnl|CDD|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 = 65.3 bits (160), Expect = 4e-15
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFVG L     +  ++  F  +G+I E  +I ++++G+S+G  FV + S E A  A  A
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 95  MDGQELN---GRNIRV 107
           + G+       R ++V
Sbjct: 61  LHGKVTMPGASRPLQV 76

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

 Score = 65.4 bits (160), Expect = 4e-15
 Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 2/78 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG LSW  +   L+E F   G++ + + I + + G+S+GFG V + + E A  A    
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVR-IAQDDDGRSKGFGHVEFATEEGAQKA-LEK 59

Query: 96  DGQELNGRNIRVSFANDR 113
            G+EL GR IRV  A +R
Sbjct: 60  SGEELLGREIRVDLATER 77

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

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

 Score = 65.1 bits (159), Expect = 5e-15
 Identities = 24/77 (31%), Positives = 39/77 (50%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L V  L        L+  F   G I   K++ +R +G+S G+GFV Y     A  A +
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 94  AMDGQELNGRNIRVSFA 110
            ++G E+  + ++VS+A
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

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

 Score = 65.2 bits (159), Expect = 6e-15
 Identities = 29/78 (37%), Positives = 46/78 (58%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L++      L + FS+   I  A V+T+ E+G+SRG+GFVT+   E A  A + +
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 96  DGQELNGRNIRVSFANDR 113
             ++L+GR +R+  A  R
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

 Score = 65.1 bits (159), Expect = 6e-15
 Identities = 30/81 (37%), Positives = 45/81 (55%), Gaps = 3/81 (3%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFV GL +      L++ F   G +   +++T R SGK +G  +V Y++  SAS A   
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLK 62

Query: 95  MDGQELNGRNIRVSFANDRPP 115
           MDG E+  + I V+ +N  PP
Sbjct: 63  MDGTEIKEKTISVAISN--PP 81

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

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

 Score = 64.8 bits (158), Expect = 9e-15
 Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 1/74 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFVGGL+  T DS L+  F+ +G +TE  V+ +  + +SRGFGF+T+ S + A  A  A
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

Query: 95  MDGQELNGRNIRVS 108
                ++G  I + 
Sbjct: 64  Q-PHSIDGNQIELK 76

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

 Score = 69.5 bits (170), Expect = 1e-14
 Identities = 35/90 (38%), Positives = 49/90 (54%), Gaps = 1/90 (1%)

Query: 27  RFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
           R M      L+V  L     D  L+E FS  G+IT AKV+ + E G SRGFGFV + + E
Sbjct: 279 RKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPE 337

Query: 87  SASSAQSAMDGQELNGRNIRVSFANDRPPR 116
            A+ A + M G+ L G+ + V+ A  +  R
Sbjct: 338 EANRAVTEMHGRMLGGKPLYVALAQRKEQR 367

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

 Score = 68.8 bits (168), Expect = 2e-14
 Identities = 32/84 (38%), Positives = 49/84 (58%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KL+VG L +   +  L++ F  FGDI + ++  + E+G+S+GFGF+ +   E A  A   
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 95  MDGQELNGRNIRVSFANDRPPRSD 118
           M+G EL GR I+V +A D     D
Sbjct: 248 MNGFELAGRPIKVGYAQDSTYLLD 271

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

 Score = 63.7 bits (156), Expect = 2e-14
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  L    D+ +L + FS FG+I   KV T+ E+G S+G+GFV +++ E+A  A   +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 96  DGQELNGRNIRV 107
           +G  LN + + V
Sbjct: 64  NGMLLNDKKVFV 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 63.3 bits (155), Expect = 2e-14
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L VG L+   +   LKE FSN+G + +  +  +RE    RG+ +V ++S E A  A   M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 96  DGQELNGRNIRVS 108
           DG +++G+ + V 
Sbjct: 61  DGGQIDGQEVTVE 73

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

>gnl|CDD|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 = 63.5 bits (155), Expect = 2e-14
 Identities = 25/76 (32%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           L+VG L+W T D  L+ A +  G  D+   K    + +GKS+GF +V + S  +A++ + 
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 94  AMDGQELNGRNIRVSF 109
            ++G+E NG+   V++
Sbjct: 61  KLEGREFNGKKCVVTY 76

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

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 63.8 bits (156), Expect = 2e-14
 Identities = 34/86 (39%), Positives = 44/86 (51%), Gaps = 3/86 (3%)

Query: 31  QSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
            S+  LFV  L     D S L++ FS  G  T  ++     +G+ RGF FV Y + E A 
Sbjct: 1   HSRC-LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAP-NGQPRGFAFVEYATAEDAE 58

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPP 115
            AQ A++G  L G  IRVSF N   P
Sbjct: 59  EAQQALNGHSLQGSPIRVSFGNPGRP 84

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

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

 Score = 63.8 bits (156), Expect = 2e-14
 Identities = 21/72 (29%), Positives = 43/72 (59%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L++ T +S L+  F  +G I   +++ ++++GK RG+ F+ ++      +A    
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 96  DGQELNGRNIRV 107
           DG++++GR + V
Sbjct: 64  DGKKIDGRRVLV 75

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

 Score = 63.4 bits (154), Expect = 2e-14
 Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFVGGL     +  L E FS FG + +A+VI ++++GK RGFGFV + +++SA  A + 
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA-AV 59

Query: 95  MDGQELNGRNIRVSFA 110
           +    +NG  + V  A
Sbjct: 60  VKFHPINGHRVEVKKA 75

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 63.0 bits (154), Expect = 3e-14
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V  L     +  L+E FS +G +   +++  R   + RGF FV + S E A +A   +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLV--RNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 96  DGQELNGRNIR 106
           +G  L+GR +R
Sbjct: 59  NGLVLDGRTLR 69

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 = 62.7 bits (153), Expect = 4e-14
 Identities = 27/73 (36%), Positives = 43/73 (58%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LFV  L + T +  L+E F  FG+I+E  +  ++E+ +S+GF FV++   E A  A S 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 95  MDGQELNGRNIRV 107
           +DG    GR + V
Sbjct: 61  LDGSIFQGRLLHV 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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 62.7 bits (153), Expect = 5e-14
 Identities = 30/72 (41%), Positives = 41/72 (56%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GLS  T  + LK+ FS +G +  AK++T   S  +R FGFVT  S E A+     +
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 96  DGQELNGRNIRV 107
              EL+GR I V
Sbjct: 62  HRTELHGRVISV 73

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

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

 Score = 62.8 bits (153), Expect = 5e-14
 Identities = 27/76 (35%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGGL     ++ L++ FS FG +TE  V+ + E  + RGFGF+T++S +S       
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV-VN 62

Query: 95  MDGQELNGRNIRVSFA 110
               ++NG+ + V  A
Sbjct: 63  EHFHDINGKKVEVKRA 78

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 62.4 bits (152), Expect = 5e-14
 Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 3/76 (3%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+GGLSW T    L+E FS FG+I E  V+ +  + +SRGFGFVT+ S+ ++     A 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTF-SDPASVDKVLAQ 59

Query: 96  DGQELNGRNI--RVSF 109
              EL+G+ I  +V+F
Sbjct: 60  GPHELDGKKIDPKVAF 75

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. 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 = 75

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

 Score = 62.3 bits (152), Expect = 7e-14
 Identities = 26/72 (36%), Positives = 41/72 (56%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  L++ T    L+  F  +G++ +  +  +R + +SRGF FV +     A  A  AM
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 96  DGQELNGRNIRV 107
           DG+EL+GR +RV
Sbjct: 61  DGKELDGRELRV 72

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

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

 Score = 62.5 bits (152), Expect = 7e-14
 Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 3/72 (4%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTY-DSNESASSAQS 93
           KLFVGGLSW T   +L+  FS +G++ +  ++ ++ + +SRGFGFV + D N   +    
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 94  AMDGQELNGRNI 105
                 L+GR I
Sbjct: 61  G--PHTLDGRTI 70

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

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

 Score = 61.6 bits (150), Expect = 1e-13
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  L    D+S L + FS FG +T  KVI +  + K +G+GFVT  + E A SA +++
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 96  DGQELNGRNIRVSF 109
           +G  L GR ++VSF
Sbjct: 64  NGYRLGGRVLQVSF 77

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

 Score = 61.5 bits (150), Expect = 1e-13
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS-----S 90
           +F+  L +   +  LKE FS FG++  A+++ ++ +G S+G  FV + + ESA      +
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 91  AQSAMDGQELNGRNIRVSFA 110
             +   G  L+GR + V+ A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 60.9 bits (148), Expect = 3e-13
 Identities = 22/59 (37%), Positives = 33/59 (55%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           L V GL W T +  LK+ FS FG++   +V  + ++G+S+GFGFV +   E      S
Sbjct: 1  DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS 59

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 60.5 bits (147), Expect = 4e-13
 Identities = 22/54 (40%), Positives = 38/54 (70%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
          K+FVGGLS  T +  +K+ FS FG + +A ++ ++++ + RGFGFVT++S +  
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVV 54

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

 Score = 60.1 bits (146), Expect = 4e-13
 Identities = 23/53 (43%), Positives = 36/53 (67%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNES 87
          K+FVGGLS  T +  ++E F  FG+I E ++  ++++ K RGF F+T+DS E 
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEP 53

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

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

 Score = 60.1 bits (146), Expect = 4e-13
 Identities = 26/73 (35%), Positives = 43/73 (58%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LFV  L +   +  L++ FS FG+++E  V  +++SGKS+GF +V +   E A  A   
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 95  MDGQELNGRNIRV 107
           +DG+   GR I +
Sbjct: 64  LDGKVFQGRLIHI 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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 60.1 bits (146), Expect = 5e-13
 Identities = 26/78 (33%), Positives = 43/78 (55%)

Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +T L V  L        ++  FS+ G+I   K+I ++ +G+S G+GFV Y   E A  A 
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 93  SAMDGQELNGRNIRVSFA 110
           + ++G  L  + I+VS+A
Sbjct: 61  NTLNGLRLQNKTIKVSYA 78

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

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

 Score = 59.9 bits (145), Expect = 5e-13
 Identities = 26/66 (39%), Positives = 44/66 (66%), Gaps = 3/66 (4%)

Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS---SAQ 92
          +F+GGL+W T D SL+E F  FG++T+  V+ +  +G+SRGFGF+T+   +S +     +
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 93 SAMDGQ 98
            +DG+
Sbjct: 61 HILDGK 66

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

>gnl|CDD|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 = 59.9 bits (146), Expect = 6e-13
 Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 6/75 (8%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T ++VG L  G  +  L+  FS FG I E +V       K +G+ FV +D++E+A++A  
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF------KDKGYAFVRFDTHEAAATAIV 54

Query: 94  AMDGQELNGRNIRVS 108
           A++G  +NG+ ++ S
Sbjct: 55  AVNGTSINGQTVKCS 69

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

 Score = 59.9 bits (145), Expect = 6e-13
 Identities = 31/72 (43%), Positives = 46/72 (63%), Gaps = 5/72 (6%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVGGLSW T    LKE FS FG++ +  +  +  +G+SRGFGFV +   + A+S +  +
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLF---KDAASVEKVL 57

Query: 96  DGQE--LNGRNI 105
           D +E  L+GR I
Sbjct: 58  DQKEHKLDGRVI 69

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

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

 Score = 59.7 bits (144), Expect = 7e-13
 Identities = 33/79 (41%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGLS+ T D SL+E F  +G +T+  V+ + ++ +SRGFGFVTY   E   +A SA
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 95  MDGQELNGRNIRVSFANDR 113
               +++GR +    A  R
Sbjct: 64  RP-HKVDGRVVEPKRAVSR 81

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

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

 Score = 59.9 bits (145), Expect = 7e-13
 Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 5/80 (6%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITE---RESGK--SRGFGFVTYDSNESASS 90
           LFV  L++ T +  L +AF +      A+V T+   +  G+  S GFGFV + + E A +
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 91  AQSAMDGQELNGRNIRVSFA 110
           A  AMDG  L+G  + V F+
Sbjct: 63  ALKAMDGFVLDGHTLVVKFS 82

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

 Score = 59.6 bits (144), Expect = 7e-13
 Identities = 33/75 (44%), Positives = 51/75 (68%), Gaps = 3/75 (4%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV GLS  T + +LKE+F   G I  A+++T+R++G S+GFGFV + S E A +A+ AM
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 96  DGQELNGRNIRVSFA 110
           +  E++G  + + FA
Sbjct: 60  EDGEIDGNKVTLDFA 74

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

 Score = 60.1 bits (145), Expect = 8e-13
 Identities = 30/75 (40%), Positives = 48/75 (64%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V GLS  T +  L+E FS +G I +  ++ +++S +SRGF FV +++ + A  A+   
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 71

Query: 96  DGQELNGRNIRVSFA 110
           +G EL+GR IRV F+
Sbjct: 72  NGMELDGRRIRVDFS 86

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

 Score = 59.2 bits (144), Expect = 1e-12
 Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 6/77 (7%)

Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           + +LFVG L     +   KE FS +G+++E  +       K +GFGF+  D+  +A  A+
Sbjct: 1   RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAK 54

Query: 93  SAMDGQELNGRNIRVSF 109
           + +DG    GR +RV F
Sbjct: 55  AELDGIMRKGRQLRVRF 71

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

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

 Score = 59.2 bits (144), Expect = 1e-12
 Identities = 22/77 (28%), Positives = 43/77 (55%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            +++V  +     +  +K  F  FG I    +  + E+GK +G+GF+ Y++ +SA  A +
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 94  AMDGQELNGRNIRVSFA 110
           +M+  +L G+ +RV  A
Sbjct: 61  SMNLFDLGGQQLRVGKA 77

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

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

 Score = 59.2 bits (144), Expect = 1e-12
 Identities = 25/74 (33%), Positives = 39/74 (52%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L+  T D  L+  FS FG I   +VI ++++G S  + F+ +++ E    A   M
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 96  DGQELNGRNIRVSF 109
           D   ++ R I V F
Sbjct: 66  DNVLIDDRRIHVDF 79

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 58.6 bits (142), Expect = 2e-12
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T ++VG +   T  + L   F NFG I E +   +R      GF FV  D++E A+ A  
Sbjct: 1   TTVYVGNIPPYTTQADLIPLFQNFGYILEFRHQPDR------GFAFVKLDTHEQAAMAIV 54

Query: 94  AMDGQELNGRNIRVSFANDR 113
            + G  ++GR +R  +  DR
Sbjct: 55  QLQGFPVHGRPLRCGWGKDR 74

This subfamily corresponds to the RRM3 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. 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 RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 58.4 bits (142), Expect = 2e-12
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           +++ V  L     +  L+E F + G++T+ KV+  R+ GKSR FGFV + S E A  A  
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVK 59

Query: 94  AMDGQELNGRNIRVSFA 110
             +   ++   I V  A
Sbjct: 60  YFNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 58.3 bits (142), Expect = 2e-12
 Identities = 23/72 (31%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
           FVG L +  ++  L++ F + GD+   +++ +R++G  +GFG+V + + +S + A   ++
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLN 61

Query: 97  GQELNGRNIRVS 108
           G +L GR IRV 
Sbjct: 62  GIKLKGRKIRVK 73

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

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

 Score = 58.5 bits (141), Expect = 2e-12
 Identities = 32/79 (40%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGLS+ T D SL+  F  +G +T+  V+ +  + +SRGFGFVTY S E   +A +A
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 95  MDGQELNGRNIRVSFANDR 113
               +++GR +    A  R
Sbjct: 64  RP-HKVDGRVVEPKRAVSR 81

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

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

 Score = 58.0 bits (141), Expect = 2e-12
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V  L   T +  L+E FS +G++   K        K + + FV ++  + A  A   M
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAVKAMEEM 55

Query: 96  DGQELNGRNIRVSFA 110
           +G+EL G  I VS A
Sbjct: 56  NGKELEGSPIEVSLA 70

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

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

 Score = 58.4 bits (142), Expect = 4e-12
 Identities = 27/78 (34%), Positives = 42/78 (53%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG LS  T + +L+E FS +GDI   +++ +  +G S+G+ FV Y+    A  A    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 96  DGQELNGRNIRVSFANDR 113
               ++G  I V F  +R
Sbjct: 66  HKLVIDGSEIFVDFERER 83

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 57.7 bits (139), Expect = 4e-12
 Identities = 29/77 (37%), Positives = 46/77 (59%), Gaps = 3/77 (3%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+F+GGLSW T    L+E F  FG++ E  V+ +  + +SRGFGFVT+  +++      A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF-MDQAGVDKVLA 60

Query: 95  MDGQELNGRNI--RVSF 109
               EL+ + I  +V+F
Sbjct: 61  QSRHELDSKTIDPKVAF 77

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 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, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 57.7 bits (139), Expect = 4e-12
 Identities = 30/73 (41%), Positives = 48/73 (65%), Gaps = 5/73 (6%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGGLSW T    LK+ F+ FG++T+  +  +  +G+SRGFGF+ +   + ASS +  
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILF---KDASSVEKV 57

Query: 95  MDGQE--LNGRNI 105
           ++ +E  L+GR I
Sbjct: 58  LEQKEHRLDGRLI 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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 57.4 bits (138), Expect = 5e-12
 Identities = 31/75 (41%), Positives = 48/75 (64%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS       +K AF+ FG I++A+V+ +  +GKS+G+GFV++ +   A +A   M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 96  DGQELNGRNIRVSFA 110
            GQ L GR IR ++A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 61.7 bits (150), Expect = 6e-12
 Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             +FV  L    D+ +L + FS FG+I   KV T+ E+GKSRG+GFV ++  ESA +A  
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQ 147

Query: 94  AMDGQELNGRNIRV 107
            ++G  LN + + V
Sbjct: 148 KVNGMLLNDKEVYV 161

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

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

 Score = 57.0 bits (137), Expect = 7e-12
 Identities = 25/52 (48%), Positives = 38/52 (73%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          KLFVGG+   T++  L++ F  +G I   ++IT+R+SGK RGFGFVT+D ++
Sbjct: 2  KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHD 53

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

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 57.0 bits (137), Expect = 9e-12
 Identities = 25/48 (52%), Positives = 35/48 (72%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTY 82
          K+F+GGLSW T   SL++ FS FG+I E  V+ +  + +SRGFGFVT+
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which 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. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 60.9 bits (147), Expect = 1e-11
 Identities = 34/111 (30%), Positives = 58/111 (52%), Gaps = 5/111 (4%)

Query: 9   MLVRQNGQAPKASLINAVRFMSQSQ-----TKLFVGGLSWGTDDSSLKEAFSNFGDITEA 63
           +L++Q     +  L N  R   + Q      +++VG +S+   + +++ AF  FG I   
Sbjct: 78  VLLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSI 137

Query: 64  KVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
            +  +  +GK +GF FV Y+  E+A  A   M+GQ L GRNI+V   ++ P
Sbjct: 138 NMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMP 188

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

 Score = 56.1 bits (136), Expect = 1e-11
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  L +      LK+ F   G++  A V T+   G+S+GFG V ++S E A  A    
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 96  DGQELNGRNIRV 107
           +G +L GR + V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 56.2 bits (135), Expect = 1e-11
 Identities = 31/75 (41%), Positives = 48/75 (64%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS       +K AF+ FG I++A+V+ +  +GKS+G+GFV++ +   A +A   M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 96  DGQELNGRNIRVSFA 110
            GQ L GR IR ++A
Sbjct: 64  GGQWLGGRQIRTNWA 78

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

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

 Score = 56.5 bits (137), Expect = 1e-11
 Identities = 21/80 (26%), Positives = 44/80 (55%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV G+     +  + + F+ FG+I    +  +R +G  +G+  + Y++ + A +A   +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 96  DGQELNGRNIRVSFANDRPP 115
           +G+EL G+ I V +A  + P
Sbjct: 69  NGKELLGQTISVDWAFVKGP 88

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

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

 Score = 59.8 bits (145), Expect = 2e-11
 Identities = 30/98 (30%), Positives = 51/98 (52%), Gaps = 10/98 (10%)

Query: 14  NGQAPKASLINAVRFMSQSQ---------TKLFVGGLSWGTDDSSLKEAFSNFGDITEAK 64
           NG       +   RF+ + +         T L+V  L    ++  L+E F+ FG+IT A 
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA 209

Query: 65  VITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG 102
           V+ +  SG+SRGF FV ++ +E A+ A   M+G+++  
Sbjct: 210 VMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246

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|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 = 56.1 bits (136), Expect = 2e-11
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNF-GDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           ++L V  L     ++ LKE FS   G+IT+ K++   E GKSR   F+ Y + E A  A+
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLR-TEDGKSRRIAFIGYKTEEEAQKAK 59

Query: 93  SAMDGQELNGRNIRVSFA 110
              +   +N   I V FA
Sbjct: 60  DYFNNTYINTSKISVEFA 77

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|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 56.3 bits (136), Expect = 2e-11
 Identities = 28/72 (38%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            KLFVG +    ++  L+  F  FG I E  V+ ++ +G  +G  F+TY + ESA  AQS
Sbjct: 6   IKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQS 65

Query: 94  AMDGQE-LNGRN 104
           A+  Q+ L G N
Sbjct: 66  ALHEQKTLPGMN 77

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 56.1 bits (135), Expect = 2e-11
 Identities = 27/73 (36%), Positives = 44/73 (60%)

Query: 38  VGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG 97
           V GLS  T +  L+E FS +G +    V+ ++ +G+SRGF FV ++  + +  A    +G
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 98  QELNGRNIRVSFA 110
            EL+GR IRV ++
Sbjct: 64  MELDGRRIRVDYS 76

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

 Score = 55.7 bits (135), Expect = 2e-11
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE-----SGKSRGFGFVTYDSNESA 88
           T LFV  L++ T + +LK+ F   G +    +  +++        S G+GFV + S E+A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 89  SSAQSAMDGQELNGRNIRVSF 109
             A   + G  L+G  + +  
Sbjct: 61  QKALKRLQGTVLDGHALELKL 81

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

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 20/75 (26%), Positives = 42/75 (56%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++V  L +   ++ L + FS +G + +  ++ ++E+ KS+G  F+ +   E A     A+
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 96  DGQELNGRNIRVSFA 110
           + +EL GR ++ S A
Sbjct: 64  NNKELFGRTLKCSIA 78

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

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

 Score = 55.6 bits (134), Expect = 3e-11
 Identities = 21/72 (29%), Positives = 42/72 (58%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++G L  G  +  LK+ FS FG +   +V   +++G S+ +GF+ + + E A+ A  +M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 96  DGQELNGRNIRV 107
           +   L G+ ++V
Sbjct: 62  NNYLLMGKVLQV 73

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

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

 Score = 55.7 bits (135), Expect = 3e-11
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSN-FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +FVG L+    D  L+E F   +  +  AKV+ +  +G+S+G+GFV +   +    A + 
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 95  MDGQELNGRNIRVSFA 110
           M+G   + R +RVS A
Sbjct: 64  MNGVYCSSRPMRVSPA 79

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

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

 Score = 55.4 bits (134), Expect = 3e-11
 Identities = 24/57 (42%), Positives = 34/57 (59%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          KLFVG L W      LKE FS FG +    V  ++E+G S+G+GFV++ S +   +A
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENA 57

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

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

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 3/75 (4%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG LS+ T +  L+  F   G I   +++T  +SGK +GF FV +   E    A +A+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDF---EEIEFATNAL 57

Query: 96  DGQELNGRNIRVSFA 110
            G+ LNGR +RV + 
Sbjct: 58  KGKHLNGRALRVEYG 72

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 55.6 bits (135), Expect = 3e-11
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 40  GLSWGTDDSSLKEAFSNFGD--ITEAKVITERESGKSRGFGFVTYDSNESASSAQSA--- 94
           GL   T +  + +A S      I + ++I ++ +G SRGF FV + S E A+    A   
Sbjct: 9   GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 95  MDGQELNGRNIRVSFA 110
           +D   ++GR +RVS+A
Sbjct: 69  LDPFVIDGRVVRVSYA 84

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

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 55.4 bits (134), Expect = 3e-11
 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L++G LS    +  LK  F  +G+I    +I        RG  +V  ++ + A  A  
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQ 56

Query: 94  AMDGQELNGRNIRVSFA 110
            +   +L G+ I+V++A
Sbjct: 57  KLRNVKLAGKKIKVAWA 73

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

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

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 22/69 (31%), Positives = 39/69 (56%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LF+  L++   +  L++ FS +G ++E  +  ++ + K +GF FVTY   E A  A + 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 95  MDGQELNGR 103
           +DG    GR
Sbjct: 64  LDGTVFQGR 72

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 55.4 bits (133), Expect = 4e-11
 Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGG+   T++  L++ F  +G I   +V+ +R+SGK RGF FVT+D +++       
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKI-VV 60

Query: 95  MDGQELNGRNIRVSFA 110
                +NG N  V  A
Sbjct: 61  QKYHTINGHNCEVKKA 76

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 55.0 bits (132), Expect = 4e-11
 Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+GGLSW T    LK+ FS FG++ +  +  +  +G+SRGFGFV +  +ES        
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 96  DGQELNGRNI 105
           +  +LNG+ I
Sbjct: 61  E-HKLNGKVI 69

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

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

 Score = 55.0 bits (132), Expect = 5e-11
 Identities = 23/53 (43%), Positives = 37/53 (69%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNES 87
          K+FVGG+   T++  L++ F  +G I   +++T+R SGK RGF FVT+D ++S
Sbjct: 2  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 54

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

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

 Score = 54.5 bits (132), Expect = 6e-11
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 8/78 (10%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VGGL   T  + L+  F  FG I              R + ++ Y+S E+A +A+ A+
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYD------PGRNYAYIEYESIEAAQAAKEAL 54

Query: 96  DGQELNGRN--IRVSFAN 111
            G  L G    +RV FA+
Sbjct: 55  RGFPLGGPGRRLRVDFAD 72

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

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

 Score = 54.6 bits (132), Expect = 6e-11
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T +++ GL   T D  L++    FG I   K I ++++ K +G+GFV +DS E+A  A  
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 94  AMDGQELNGRNIRVSF 109
                 LNGR ++  F
Sbjct: 61  G-----LNGRGVQAQF 71

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

 Score = 54.4 bits (131), Expect = 7e-11
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +++VG +S+   + ++++AFS FG I    +  +  + K +GF FV Y+  E+A  A   
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 95  MDGQELNGRNIRV 107
           M+G  L GRNI+V
Sbjct: 62  MNGVMLGGRNIKV 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 54.5 bits (132), Expect = 7e-11
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++G L  G  +  L++ FS FG +T  ++   +++GKS+G+ FV ++S E A      M
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 96  DGQELNGRNIRVS 108
           +   L  R ++  
Sbjct: 62  NNYLLFERLLKCK 74

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

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

 Score = 58.0 bits (140), Expect = 9e-11
 Identities = 25/81 (30%), Positives = 47/81 (58%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  LS  TD++ L + F  FG +   K+I +  + + +G+GFV+  + + A+ A  ++
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 96  DGQELNGRNIRVSFANDRPPR 116
           +G  L  R ++VSF  ++  R
Sbjct: 332 NGYTLGNRVLQVSFKTNKAYR 352

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

 Score = 54.2 bits (131), Expect = 1e-10
 Identities = 24/79 (30%), Positives = 50/79 (63%), Gaps = 2/79 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L++G L    D++ +  AF+  G++T  K+I  +++GKS G+GFV + ++E+A  A  ++
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 96  DGQELNG--RNIRVSFAND 112
           +G+ +    +  R+++AN 
Sbjct: 62  NGKPIPNTQQRFRLNWANF 80

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

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFVG L   T    L+  F  +G +TE  V+        + +GFV  +  E A  A  A
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 95  MDGQELNGRNIRV 107
           ++G E  G+ I V
Sbjct: 53  LNGYEFMGKRINV 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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 53.9 bits (129), Expect = 1e-10
 Identities = 23/53 (43%), Positives = 33/53 (62%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNES 87
          K+F+GGLSW T    L E  S FG++ +  + T+  +G+SRGFGFV +    S
Sbjct: 1  KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAAS 53

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

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

 Score = 53.5 bits (129), Expect = 1e-10
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  L +      LKE F   G +  A +  ++E GKSRG G V ++    A  A S  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 96  DGQELNGRNIRV 107
           +GQ L  R +RV
Sbjct: 60  NGQMLFDRPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

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

 Score = 53.6 bits (128), Expect = 2e-10
 Identities = 29/72 (40%), Positives = 42/72 (58%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GLS  T  + LK  FS +G +  AKV+T   S  +R +GFVT  ++E A+   + +
Sbjct: 4   LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 96  DGQELNGRNIRV 107
              EL+GR I V
Sbjct: 64  HRTELHGRMISV 75

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

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 23/72 (31%), Positives = 44/72 (61%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++GGL +   +  +   FS +G+I +  ++ ++++GKS+GF F+ Y+   S   A   +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 96  DGQELNGRNIRV 107
           +G +L GR IRV
Sbjct: 72  NGIKLLGRTIRV 83

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

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

 Score = 53.4 bits (129), Expect = 2e-10
 Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 4/77 (5%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSR---GFGFVTYDSNESASSA 91
           +++V  L +  D+  L+  FS FG++   ++  +++  + R   GF FVT+    SA +A
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 92  QSAMDGQELNGRNIRVS 108
              ++G EL GR I VS
Sbjct: 62  LQ-LNGTELGGRKISVS 77

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

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

 Score = 53.5 bits (128), Expect = 2e-10
 Identities = 25/72 (34%), Positives = 45/72 (62%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+  L     D+ L + F  FG++  AKV  ++++  S+ FGFV+YD+ +SA +A  AM
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 96  DGQELNGRNIRV 107
           +G ++  + ++V
Sbjct: 67  NGFQIGTKRLKV 78

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

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

 Score = 53.3 bits (128), Expect = 2e-10
 Identities = 23/74 (31%), Positives = 48/74 (64%), Gaps = 3/74 (4%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++FVGG+ + T+++ L++ FS +G + E K++ +R +G S+G+GFVT+++ E A      
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQ- 61

Query: 95  MDGQELNGRNIRVS 108
            +   L  R+ +++
Sbjct: 62  -EANRLCFRDKKLN 74

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 52.5 bits (127), Expect = 2e-10
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 50  LKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF 109
           L + FS FG++ + K+       K  GF FV + + E+A  A   ++G    GR +RV +
Sbjct: 1   LYKLFSPFGNVEKIKL-----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 110 A 110
           +
Sbjct: 56  S 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 53.0 bits (128), Expect = 3e-10
 Identities = 24/74 (32%), Positives = 41/74 (55%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++FVG L     D  L  AFS +    +AKV+ ++ +GKS+G+GFV++        A   
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKE 67

Query: 95  MDGQELNGRNIRVS 108
           M+G+ +  R I++ 
Sbjct: 68  MNGKYVGNRPIKLR 81

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

 Score = 52.7 bits (127), Expect = 3e-10
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS       L E FS  G I E  +I  + +  +  F F+ ++  ++A+ A  + 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 96  DGQELNGRNIRVSF 109
           +   L  + + V +
Sbjct: 64  NHSMLKNKTMHVQY 77

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

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

 Score = 53.2 bits (127), Expect = 3e-10
 Identities = 29/78 (37%), Positives = 46/78 (58%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  LS   D+S L + F  FG +T  KVI +  + K +GFGFVT  + + A+ A +++
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 96  DGQELNGRNIRVSFANDR 113
           +G  L  R ++VSF   +
Sbjct: 64  NGYRLGDRVLQVSFKTSK 81

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

 Score = 52.4 bits (126), Expect = 5e-10
 Identities = 20/73 (27%), Positives = 33/73 (45%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LFVG L     +  LKE F  FG++ E ++ ++   G+   FGFV +D  E+     + 
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 95  MDGQELNGRNIRV 107
                     + V
Sbjct: 65  KPIYFRGDHRLNV 77

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 52.5 bits (126), Expect = 5e-10
 Identities = 28/76 (36%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAF-SNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +FVG LS   ++S L   F S F     AK++T+  +G SRG+GFV +        A   
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 95  MDGQELNGRNIRVSFA 110
           M G    GR +R+S A
Sbjct: 64  MQGVYCGGRPMRISTA 79

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 52.0 bits (125), Expect = 5e-10
 Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 2/72 (2%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
           ++G L+W   +  ++E F    +IT  ++ T++E+G+ +GFG V +   ES  +A   +D
Sbjct: 3   YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KLD 60

Query: 97  GQELNGRNIRVS 108
           G  L GR IR++
Sbjct: 61  GTVLCGRPIRIA 72

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

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

 Score = 51.9 bits (125), Expect = 6e-10
 Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L     +  L E F   G +   K+  +   GK + F FVT+    S   A   +
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 96  DGQELNGRNIRVS 108
           +G  L GR +R+ 
Sbjct: 63  NGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

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

 Score = 51.9 bits (125), Expect = 7e-10
 Identities = 20/63 (31%), Positives = 39/63 (61%), Gaps = 2/63 (3%)

Query: 50  LKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRV 107
           L+EAF+ FG+I +  V+ ++++ +S+G  +V +    SA+ A   M+G+ L G  + ++V
Sbjct: 19  LREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDTKPLKV 78

Query: 108 SFA 110
             A
Sbjct: 79  LIA 81

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

 Score = 51.5 bits (124), Expect = 8e-10
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 8/75 (10%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V G  +G  +  LK+AFS FG+I    +  E+E    +  GFVT++  ESA  A + +
Sbjct: 7   LYVHG--YGLTEEILKKAFSPFGNII--NISMEKE----KNCGFVTFEKMESADRAIAEL 58

Query: 96  DGQELNGRNIRVSFA 110
           +G  + G  ++VS A
Sbjct: 59  NGTTVQGVQLKVSLA 73

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

 Score = 51.8 bits (124), Expect = 8e-10
 Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 35  KLFVGGLSWGTDD-SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           KL +  L W       LK+ F  +G + EA +  +R  GK  GF FVT    ++A  A  
Sbjct: 2   KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKR-GGKLCGFAFVTMKKRKNAEIALE 60

Query: 94  AMDGQELNGRNIRVSFANDR 113
             +G E++GR + V +A  +
Sbjct: 61  NTNGLEIDGRPVAVDWAVQK 80

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

 Score = 51.4 bits (124), Expect = 9e-10
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 41  LSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL 100
           LS   D+  L+E F  FG I+   +  ++E+G+SRGF FVT+ + E A  A   ++G   
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGY 66

Query: 101 NGRNIRVSFA 110
           +   + V +A
Sbjct: 67  DNLILSVEWA 76

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L + T    L   F N G     +++T++++GKS+G  FV +D+ E+ + A   +
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALK-L 61

Query: 96  DGQELNGRNIRV 107
               L GR I V
Sbjct: 62  HHTLLKGRKINV 73

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

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

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 28/78 (35%), Positives = 47/78 (60%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  L+   D+S L + F  FG +T  KVI +  + K +GFGFVT  + + A+ A +++
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 96  DGQELNGRNIRVSFANDR 113
           +G  L  R ++VSF  ++
Sbjct: 66  NGYRLGDRVLQVSFKTNK 83

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

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 23/72 (31%), Positives = 47/72 (65%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VGG+ + + +  ++  FS  G+I E  ++T  ++G+ RG  F+T+ + E+A  A  A+
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA-LAL 59

Query: 96  DGQELNGRNIRV 107
           DG+++ GR ++V
Sbjct: 60  DGEDMGGRFLKV 71

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|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 = 51.4 bits (123), Expect = 1e-09
 Identities = 25/72 (34%), Positives = 44/72 (61%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+  L     D+ L + F  FG++  AKV  +R + +S+ FGFV++D+  SA +A  AM
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 96  DGQELNGRNIRV 107
           +G ++  + ++V
Sbjct: 67  NGFQIGMKRLKV 78

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

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

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T+L V  L +   +  L+E F   G++ + K+  +R SG+S G   V ++  E A  A  
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

Query: 94  AMDGQELNGRNIRVSF 109
             +G  L+G+ ++V  
Sbjct: 60  QFNGVLLDGQPMQVEL 75

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

 Score = 51.6 bits (123), Expect = 1e-09
 Identities = 28/78 (35%), Positives = 47/78 (60%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  LS  +D+S L + F  FG +   KVI +  + K +GFGFVT  + + A+ A +++
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 96  DGQELNGRNIRVSFANDR 113
           +G  L  R ++VSF  ++
Sbjct: 66  NGYRLGDRVLQVSFKTNK 83

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

 Score = 51.2 bits (122), Expect = 1e-09
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 2/82 (2%)

Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +T L V  L        L+  FS+ G++  AK+I ++ +G S G+GFV Y + + A  A 
Sbjct: 1   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 93  SAMDGQELNGRNIRVSFANDRP 114
           + ++G  L  + I+VS+A  RP
Sbjct: 61  NTLNGLRLQSKTIKVSYA--RP 80

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

 Score = 54.6 bits (131), Expect = 2e-09
 Identities = 27/84 (32%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           +S+T L V  L        ++  F++ G+I   K++ ++ +G+S G+GFV Y   E A  
Sbjct: 1   ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEK 60

Query: 91  AQSAMDGQELNGRNIRVSFANDRP 114
           A ++++G  L  + I+VS+A  RP
Sbjct: 61  AVNSLNGLRLQNKTIKVSYA--RP 82

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

 Score = 50.9 bits (121), Expect = 2e-09
 Identities = 24/60 (40%), Positives = 38/60 (63%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLF+GGLS+ T + SL+  +  +G +T+  V+ +  S +SRGFGFVT+       +A +A
Sbjct: 4  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

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

 Score = 50.7 bits (122), Expect = 2e-09
 Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  ++   +D  L+  F  FGDI    + T   + K RGF  V+Y    +A  A+ A+
Sbjct: 4   LFVRNINSNVEDEELRALFEQFGDIR--TLYT---ACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 96  DGQELNGRNIRVSFA 110
            G EL GR + + F+
Sbjct: 59  QGTELGGRKLDIHFS 73

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

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

 Score = 50.3 bits (120), Expect = 3e-09
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L     +  L E F   G +T+  +  ++E GK + FGFV +  +ES   A + +
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIALL 62

Query: 96  DGQELNGRNIRVS 108
           +G  L GR I+V 
Sbjct: 63  NGIRLYGRPIKVH 75

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

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

 Score = 50.5 bits (120), Expect = 3e-09
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L        LK  F + G+I   K++ ++ +G+S G+GFV Y   + A  A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
            + ++G  L  + I+VS+A  RP
Sbjct: 63  INTLNGLRLQTKTIKVSYA--RP 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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 50.2 bits (120), Expect = 4e-09
 Identities = 25/61 (40%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLFVG LS   +++ ++  F+ FG I E  V+ + ++G+SRG  FVT+ S + A +A  A
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIKA 61

Query: 95 M 95
          M
Sbjct: 62 M 62

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

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

 Score = 50.0 bits (119), Expect = 4e-09
 Identities = 30/73 (41%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++FV  L +      LKE FS  G +  A++  + E+GKS+G G V +DS ESA  A   
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEI--KMENGKSKGCGTVRFDSPESAEKACRL 58

Query: 95  MDGQELNGRNIRV 107
           M+G ++NGR I V
Sbjct: 59  MNGIKINGREIDV 71

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

 Score = 49.7 bits (119), Expect = 5e-09
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 2/76 (2%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +L V  + +   D  L++ F  FG I + ++I   E G S+GFGFVT+ ++  A  A+  
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFN-ERG-SKGFGFVTFANSADADRAREK 59

Query: 95  MDGQELNGRNIRVSFA 110
           + G  + GR I V+ A
Sbjct: 60  LHGTVVEGRKIEVNNA 75

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

 Score = 49.6 bits (119), Expect = 5e-09
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG L     +  L E FS  G I   K+I E     +  + FV Y  + SA++A   M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIRE---HGNDPYAFVEYYDHRSAAAALQTM 57

Query: 96  DGQELNGRNIRVSFA 110
           +G+ + G+ I+V++A
Sbjct: 58  NGRLILGQEIKVNWA 72

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

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

 Score = 49.5 bits (118), Expect = 6e-09
 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 2/79 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L+V GL        L++ FS +G I  ++++ ++ +G SRG GF+ +D    A  A  
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 94  AMDGQELNG--RNIRVSFA 110
            ++GQ+  G    I V FA
Sbjct: 61  GLNGQKPEGASEPITVKFA 79

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

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

 Score = 49.2 bits (117), Expect = 7e-09
 Identities = 21/52 (40%), Positives = 35/52 (67%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          K+FVGGLS  T    +K+ F  FG + +A ++ ++ + + RGFGFVT++S +
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52

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

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

 Score = 49.3 bits (117), Expect = 8e-09
 Identities = 26/78 (33%), Positives = 44/78 (56%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  L    D+  L + F  FG +T  KVI +  + K +GFGFVT  + E A+ A +++
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 96  DGQELNGRNIRVSFANDR 113
           +G  L  + ++VSF   +
Sbjct: 64  NGYRLGDKILQVSFKTSK 81

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

 Score = 49.3 bits (118), Expect = 8e-09
 Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L +  L     D   +  F   G +   K++ ++ +G S GFGFV Y S E A  A  
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 94  AMDGQELNGRNIRVSFANDRPP 115
            ++G +L  + I+V++A  RP 
Sbjct: 61  TLNGLQLQNKRIKVAYA--RPG 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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 49.3 bits (117), Expect = 8e-09
 Identities = 25/79 (31%), Positives = 42/79 (53%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L         K  F + G+I   K++ ++ +G+S G+GFV Y     A  A
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 92  QSAMDGQELNGRNIRVSFA 110
            + ++G +L  + I+VS+A
Sbjct: 62  INTLNGLKLQTKTIKVSYA 80

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 49.3 bits (118), Expect = 9e-09
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 8/83 (9%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAK--------VITERESGKSRGFGFVTYDSNES 87
           +FV  L   T +  L E F + G I   K        +  ++++G+ +G   VTYD   +
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 88  ASSAQSAMDGQELNGRNIRVSFA 110
           AS+A    + ++  G  I+VS A
Sbjct: 61  ASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 49.2 bits (118), Expect = 9e-09
 Identities = 31/80 (38%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 36  LFVGGLSWGTDDSSLKEAFSN-FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           LFVG L+   DD  L E FS  +     AKV+ + ++G SRG+GFV +        A + 
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALTE 62

Query: 95  MDGQE-LNGRNIRVSFANDR 113
           M G   L G+ IRVS A  +
Sbjct: 63  MQGASGLGGKPIRVSLAIPK 82

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

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA- 94
           +FV  L +   +  L++ FS  G+IT+ +++     GKS+G+ +V +   E+  S Q A 
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEF---ENEESVQEAL 57

Query: 95  -MDGQELNGRNIRVS 108
            +D + + GR + VS
Sbjct: 58  KLDRELIKGRPMFVS 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|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++ G        S +K  F   G + +  +++       +   F+T+++ E+A  A   +
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV----QPHAFITFENLEAAQLAIETL 57

Query: 96  DGQELNGRNIRV 107
           +G  ++G  I+V
Sbjct: 58  NGASVDGNCIKV 69

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

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 8/75 (10%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +L+V      T +S+++E FS +G + E K+I+         F FV ++S ESA  A+ +
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMIS--------NFAFVEFESLESAIRAKDS 52

Query: 95  MDGQELNGRNIRVSF 109
           + G+ LN   + V++
Sbjct: 53  VHGKVLNNNPLYVTY 67

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

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

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 26/75 (34%), Positives = 43/75 (57%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L VG L     D   +E  S FG +    ++    +G+S+G+GFV Y S  SA  A++ +
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 96  DGQELNGRNIRVSFA 110
           DG+++ GR ++V +A
Sbjct: 62  DGKQIGGRKLQVDWA 76

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

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVI---TERESGKSRGFGFVTYDSNESASS 90
           T L+VG L+    +  L + F  FG +   K++   TE E  ++R  GFV + +   A  
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 91  AQSAMDGQELNGRNIRVSFA 110
           A   +DG+++ G  +++ + 
Sbjct: 62  ALDELDGKDVMGYELKLGWG 81

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 48.4 bits (116), Expect = 1e-08
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
           FV  LS    +  L E FS  G + + ++I +R S +S+G  +V +   ES   A   + 
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLT 61

Query: 97  GQELNGRNIRV 107
           GQ L G+ I V
Sbjct: 62  GQRLLGQPIMV 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|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 25/75 (33%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T +FVGGL     +  L+  F  FG+I   K+      GK  G GFV +    +A +A  
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI----PPGK--GCGFVQFVHRAAAEAAIQ 55

Query: 94  AMDGQELNGRNIRVS 108
            + G  + G  IR+S
Sbjct: 56  QLQGTIIGGSRIRLS 70

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

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

 Score = 51.4 bits (123), Expect = 2e-08
 Identities = 20/103 (19%), Positives = 43/103 (41%)

Query: 8   GMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVIT 67
                 +  A     +     +  S+ ++++G L     +  +KE   +FGD+    +I 
Sbjct: 270 VSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIK 329

Query: 68  ERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           +  +G S+G+ F  Y        A +A++G++     + V  A
Sbjct: 330 DIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA 372

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

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

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 5/77 (6%)

Query: 35  KLFVGGL--SWGTDD--SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
            +FV G   S G DD   SL E FS+ G+IT   + T+RE+G S+GF ++ + S +    
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 91  AQSAMDGQELNGRNIRV 107
           A   +DG +L G N+ V
Sbjct: 61  ALE-LDGSDLGGGNLVV 76

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

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 47.7 bits (114), Expect = 2e-08
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           ++L V  L  G  +  L++ F  FG IT+ ++   ++ GK R FGFV Y + E A  A  
Sbjct: 1   SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALK 59

Query: 94  AMDGQELNGRNIRVSFA 110
             +   ++   I V   
Sbjct: 60  HFNNSFIDTSKITVEIC 76

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

>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 47.9 bits (115), Expect = 3e-08
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 49  SLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS 108
           SL   FS FG + +   I   ++ K RG  FV +   ESA++A  A+ G     + +R+ 
Sbjct: 19  SLYALFSQFGPVLD---IVASKTLKMRGQAFVVFKDVESATNALRALQGFPFYDKPMRIQ 75

Query: 109 FA 110
           +A
Sbjct: 76  YA 77

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 48.0 bits (115), Expect = 3e-08
 Identities = 21/75 (28%), Positives = 37/75 (49%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T +FVG +  G  D  +++     G +   K + +  +GK + FGF  ++  E A  A  
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 94  AMDGQELNGRNIRVS 108
            ++G EL G+ + V 
Sbjct: 61  LLNGLELGGKKLLVK 75

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

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

 Score = 47.2 bits (113), Expect = 4e-08
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 5/77 (6%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K++VG L        L++ F  +G +    V     +    GF FV ++    A  A  A
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVRA 55

Query: 95  MDGQELNGRNIRVSFAN 111
           +DG+ + G  +RV  + 
Sbjct: 56  LDGRRICGNRVRVELSR 72

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

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

 Score = 46.9 bits (112), Expect = 5e-08
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
           FVG L + T    L   F +   +   +++ ++E+ K +GF +V ++  ES   A    D
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEAL-EYD 62

Query: 97  GQELNGRNIRVSFA 110
           G   + R++RV  A
Sbjct: 63  GALFDDRSLRVDIA 76

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

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

 Score = 47.4 bits (112), Expect = 5e-08
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+  L     D  L + F  FG++  AKV  ++++  S+ FGFV+YD+  SA +A  AM
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 96  DGQELNGRNIRVSF 109
           +G ++  + ++V  
Sbjct: 70  NGFQIGMKRLKVQL 83

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

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

 Score = 47.0 bits (111), Expect = 5e-08
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L         +  F + G+I   K++ ++ +G+S G+GFV Y   + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
            + ++G  L  + I+VS+A  RP
Sbjct: 61  INTLNGLRLQTKTIKVSYA--RP 81

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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 46.6 bits (110), Expect = 7e-08
 Identities = 20/49 (40%), Positives = 33/49 (67%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYD 83
          K+FVGGLS  T    +K+ F  FG + +A ++ ++ + + RGFGFVT++
Sbjct: 5  KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which 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. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 47.1 bits (111), Expect = 7e-08
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GL        L++ FS +G I  ++++ ++ +G SRG GF+ +D    A  A   +
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 67

Query: 96  DGQELNGRN--IRVSFAND 112
           +GQ+  G    I V FAN+
Sbjct: 68  NGQKPPGATEPITVKFANN 86

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 46.5 bits (111), Expect = 9e-08
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           TKL V  L +G  D  +KE F+ FG + +A V  +R SG+S G   V ++    A  A  
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMK 59

Query: 94  AMDGQELNGRNIRVSF 109
             +G  L+GR +++  
Sbjct: 60  QYNGVPLDGRPMKIQL 75

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

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

 Score = 46.1 bits (110), Expect = 9e-08
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 6/61 (9%)

Query: 47  DSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR 106
           D  L++ F  FG + +  ++     GK+  +G+  Y   ESA  A + + G+E+NG  ++
Sbjct: 13  DYILEDVFCRFGGLIDVYLV----PGKN--YGYAKYADRESAERAITTLHGKEVNGVKLK 66

Query: 107 V 107
           V
Sbjct: 67  V 67

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

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

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVI---TERESGKSRGFGFVTYDSNESASSA 91
           +L++G L     +  L + FS +G I +   +   +    G+ RG+ FVT+++ E A  A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 92  QSAMDGQELNGRNIRVSFAN 111
             +++G+   G+ + V +A+
Sbjct: 61  LKSLNGKTALGKKLVVRWAH 80

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

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

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 4/76 (5%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVIT--ERESGKSRGFGFVTYDSNESASSAQS 93
           L+VG LS+ T +  + E FS  GDI   ++I   +R +    GF FV Y + E A +A  
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCGFCFVEYYTREDAENAVK 58

Query: 94  AMDGQELNGRNIRVSF 109
            ++G +L+ R IRV +
Sbjct: 59  YLNGTKLDDRIIRVDW 74

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

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

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 24/77 (31%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS-AQSA 94
           LFVGGLS    +S L+E FS FG +++ ++I ++++G  RGF ++   ++E+     +S 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 95  MDGQELNGRNIRVSFAN 111
           ++G +  G  +++  A 
Sbjct: 62  LNGTKWKGSVLKIEEAK 78

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 45.8 bits (108), Expect = 1e-07
 Identities = 22/52 (42%), Positives = 32/52 (61%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          K+FVGGLS  T +  +KE F  FG+I   ++  + ++ + RGF FVTY   E
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEE 52

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 38/72 (52%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GLS  T  + LK  F  +G +  AKV+T   S  ++ +G VT  S+   +   S +
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 96  DGQELNGRNIRV 107
              EL+G+ I V
Sbjct: 62  HRTELHGQQISV 73

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

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 20/77 (25%), Positives = 35/77 (45%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L+V  ++  T    L+  F  +G I +  +  +  + + RGF +V ++    A  A  
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 94  AMDGQELNGRNIRVSFA 110
            +D     GR I + FA
Sbjct: 61  YLDRTRFLGREIEIQFA 77

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 46.1 bits (109), Expect = 2e-07
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           ++VG  SW T D  L +   + G  D+ E K    R +G+S+G+  V   S  S      
Sbjct: 4   VYVGNFSWWTTDQQLIQVIRSVGVKDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 63

Query: 94  AMDGQELNGRNIRVSFAN 111
            + G+ LNG  + V  A 
Sbjct: 64  LLPGKVLNGEKVDVRPAT 81

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|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          +LFVG L    D+S LKE F +FG++ E ++ T+   GK   FGFV +D +E
Sbjct: 7  QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSE 58

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 22/75 (29%), Positives = 40/75 (53%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L+V  L     +  L++ F  +G+I +  ++ ++ +G  RG  FV YD  E A +A S
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 94  AMDGQELNGRNIRVS 108
           +++G    G  + +S
Sbjct: 61  SLNGTIPPGSTMPLS 75

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

 Score = 45.6 bits (107), Expect = 2e-07
 Identities = 23/64 (35%), Positives = 36/64 (56%)

Query: 32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          S+T L++ GL   T D  L +    +G I   K I ++ + K +G+GFV +DS  +A  A
Sbjct: 6  SKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKA 65

Query: 92 QSAM 95
           SA+
Sbjct: 66 VSAL 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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 45.4 bits (108), Expect = 2e-07
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GL        L+  FS +G I  ++++ +  +G SRG GF+ +D    A  A  A+
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 96  DGQELNGRN--IRVSFA 110
           +G    G    I V FA
Sbjct: 63  NGTIPPGATEPITVKFA 79

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

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

 Score = 45.3 bits (107), Expect = 2e-07
 Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +++LFVG L     +  +++ F  +G   E  +       K +GFGF+  ++   A  A+
Sbjct: 1   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEIFI------HKDKGFGFIRLETRTLAEIAK 54

Query: 93  SAMDGQELNGRNIRVSF 109
           + +D   L G+ +RV F
Sbjct: 55  AELDNMPLRGKQLRVRF 71

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L+    +  L++AF  FG +   K        K + + F+ +D  + A  A   M
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 55

Query: 96  DGQELNGRNIRVSFA 110
           +G+EL G NI + FA
Sbjct: 56  NGKELEGENIEIVFA 70

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 45.4 bits (107), Expect = 2e-07
 Identities = 19/52 (36%), Positives = 32/52 (61%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          K+FVGGLS  T +  ++E F  FG++   ++  + ++ K RGF F+T+   E
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEE 52

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

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

 Score = 45.1 bits (106), Expect = 3e-07
 Identities = 22/63 (34%), Positives = 36/63 (57%)

Query: 33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
          +T L++ GL  GT D  L +    +G I   K I ++ + K +G+GFV +DS  +A  A 
Sbjct: 1  KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 93 SAM 95
          +A+
Sbjct: 61 TAL 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|241087 cd12643, RRM_CFIm68, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

 Score = 45.1 bits (107), Expect = 3e-07
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           L+VG L+W T D  L EA  + G  D+ E K    R +G+S+GF  +   S  S+     
Sbjct: 2   LYVGNLTWWTTDQDLTEAIQSIGVNDLLEIKFFENRANGQSKGFALIVLGSESSSRKLMD 61

Query: 94  AMDGQELNGRN 104
            +  +EL+G+N
Sbjct: 62  KLPKKELHGQN 72

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

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

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            K+FVG L+    +  L++ FS FG++T+  +         R F FVT+   E A S   
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYI-----PKPFRAFAFVTFADPEVAQSLCG 55

Query: 94  AMDGQELNGRNIRVSFA 110
             +   + G ++ VS A
Sbjct: 56  --EDHIIKGVSVHVSNA 70

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 44.9 bits (106), Expect = 3e-07
 Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFVG L     +  ++  F  +G + E  +I        + +GFV  D   +A  A   
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 95  MDGQELNGRNIRV 107
           +   +L+G  I V
Sbjct: 54  LHHYKLHGVAINV 66

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 44.9 bits (106), Expect = 3e-07
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LFVG L     +   K+ F  +G+ +E  +       + RGFGF+  +S   A  A++ 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 56

Query: 95  MDGQELNGRNIRVSF 109
           +DG  L  R +R+ F
Sbjct: 57  LDGTILKNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 45.1 bits (106), Expect = 3e-07
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 2/77 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GL        L++ FS +G I  ++++ ++ +G SRG GF+ +D    A  A   +
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 64

Query: 96  DGQELNGRN--IRVSFA 110
           +GQ+ +G    I V FA
Sbjct: 65  NGQKPSGAAEPITVKFA 81

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 45.0 bits (106), Expect = 3e-07
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GL        +++ FS +G I  ++++ ++ +G SRG GF+ +D    A  A   +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 96  DGQELNGRN--IRVSFAN 111
           +GQ+  G    I V FAN
Sbjct: 64  NGQKPLGAAEPITVKFAN 81

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241111 cd12667, RRM3_RAVER1, RNA recognition motif 3 in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 19/46 (41%), Positives = 25/46 (54%)

Query: 70  ESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPP 115
           + G+ +GF  + Y+S E A   Q   DG  L G +IRVSF    PP
Sbjct: 39  QDGQLKGFAVLEYESAEMAEMVQQQADGLSLAGSHIRVSFCAPGPP 84

This subgroup corresponds to the RRM3 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 = 92

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESG--KSRGFGFVTYDSNESASSAQ 92
          K+FVG +     +  L+E F  +G + +  V+ +R     +S+G  FVT+ + ++A  AQ
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 93 SAM 95
          +A+
Sbjct: 63 NAL 65

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>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 = 44.5 bits (106), Expect = 4e-07
 Identities = 18/73 (24%), Positives = 36/73 (49%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+F+GGL     +  +KE   +FG +    ++ +  +G S+G+ F  Y        A + 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 95  MDGQELNGRNIRV 107
           ++G +L  + + V
Sbjct: 62  LNGMQLGDKKLTV 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 44.2 bits (105), Expect = 5e-07
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
           FVG + +GT    L+E F + G I    ++ ++ +G+ +GF ++ +    S  +A   ++
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LLN 61

Query: 97  GQELNGRNIRVS 108
             E  GR I+V+
Sbjct: 62  ESEFRGRQIKVT 73

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

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

 Score = 44.4 bits (106), Expect = 5e-07
 Identities = 18/72 (25%), Positives = 35/72 (48%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG L     ++ L E FS  G +   +V  +  + +S G+ +V + +   A  A   +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 96  DGQELNGRNIRV 107
           +   + G+ IR+
Sbjct: 62  NFDVIKGKPIRI 73

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

 Score = 44.4 bits (104), Expect = 6e-07
 Identities = 21/64 (32%), Positives = 37/64 (57%)

Query: 32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          S+T L++ GL  GT D  L +    +G I   K I ++ + + +G+GFV +DS  +A  A
Sbjct: 3  SKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62

Query: 92 QSAM 95
           +++
Sbjct: 63 VASL 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 46.7 bits (111), Expect = 8e-07
 Identities = 23/87 (26%), Positives = 42/87 (48%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG L     ++ L + F  FG +   +V  +  + +S G+G+V + +   A  A   M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 96  DGQELNGRNIRVSFANDRPPRSDGGYG 122
           + + L G+ IR+ ++   P     G G
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVG 89

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

 Score = 43.8 bits (104), Expect = 8e-07
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           TKL V  + +      L+E FS FG +   + + ++  G  RGF FV + + + A +A  
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 94  AMDGQELNGRNIRVSFA 110
           A+    L GR++ + +A
Sbjct: 60  ALKSTHLYGRHLVLEYA 76

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

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

 Score = 44.1 bits (105), Expect = 9e-07
 Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 15/70 (21%)

Query: 34 TKLFVGGLSWGTDDSSLKEAFSNFGD---------ITEAKVITERES------GKSRGFG 78
          T+L +  L    D+  LKE F              I + K++ + +       GKS+G+G
Sbjct: 1  TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 79 FVTYDSNESA 88
          FV + ++E A
Sbjct: 61 FVEFTNHEHA 70

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

 Score = 43.3 bits (102), Expect = 1e-06
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG L     +  LK+ F   G +   K+I ++ + K   +GFV Y  +  A  A   +
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 96  DGQELNGRNIRVSFA 110
           +G+++    IRV++A
Sbjct: 60  NGRQIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++FV  L +      LK+ F+  G +  A +  E  +GKS+G G V ++S E A  A   
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRM 58

Query: 95  MDGQELNGRNIRV 107
           M+G +LNGR I V
Sbjct: 59  MNGYKLNGREIDV 71

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 13/78 (16%)

Query: 36  LFVGGLSWGTDDSSLKEA----FSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           L+VGG+  G+    ++E     F  +GDI + +V+       S+G  FV Y    SA  A
Sbjct: 4   LYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRVLP------SKGIAFVRYKYRASAEFA 57

Query: 92  QSAMDGQELNGR---NIR 106
           + AM  Q L+G    N+R
Sbjct: 58  KEAMADQSLDGGEVLNVR 75

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GL        L+  FS FG I  ++++++  +G S+G GF+ +D  + A  A   +
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 96  DGQELNG--RNIRVSFAND 112
           +G   +G    I V FAN+
Sbjct: 152 NGTTPSGCTEPITVKFANN 170

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 23/63 (36%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLFVG L+    +  ++E FS +G + +  ++ + E  +SRG  FV Y S E A +A  A
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 95 MDG 97
          ++G
Sbjct: 60 LNG 62

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 18/50 (36%), Positives = 35/50 (70%), Gaps = 1/50 (2%)

Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN 85
          +FVGG+    D++ ++  F+ +G + E K+IT+R +G S+G+GFV++  +
Sbjct: 8  VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDD 56

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

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 42.6 bits (100), Expect = 2e-06
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LFVG L     +   K+ F+ +G+  E  +       K +GFGF+  +S   A  A++ 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56

Query: 95  MDGQELNGRNIRVSF 109
           +D   + GR +RV F
Sbjct: 57  LDDTPMRGRQLRVRF 71

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

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

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L +      LKE F +  DI   ++ + ++ G S+G  ++ + +   A  A    
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDI---RLPSGKD-GSSKGIAYIEFKTEAEAEKALEEK 61

Query: 96  DGQELNGRNIRVSF 109
            G E++GR+I V +
Sbjct: 62  QGAEVDGRSIVVDY 75

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

 Score = 42.5 bits (100), Expect = 2e-06
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            K+FVG +S       L+  F  FG + E   +        + + FV  +  E A +A  
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIE 52

Query: 94  AMDGQELNGRNIRV 107
           A++G+E+ GR I V
Sbjct: 53  ALNGKEVKGRRINV 66

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

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

 Score = 42.9 bits (102), Expect = 2e-06
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 50 LKEAFSNFGDITEAKV-ITERESGKSRGFGFVTYDSNESASSAQSAMDG 97
          L++ FS FG      + +   E+GK++G+ FV + + E A  A  A++G
Sbjct: 24 LRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNG 72

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

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 42.7 bits (100), Expect = 2e-06
 Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++ GG++ G  +  +++ FS FG I E +V  ++      G+ FV ++S+ESA+ A  ++
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPDK------GYSFVRFNSHESAAHAIVSV 56

Query: 96  DGQELNGRNIR 106
           +G  + G  ++
Sbjct: 57  NGTTIEGHVVK 67

This subgroup corresponds to the RRM3 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 = 74

>gnl|CDD|240979 cd12535, RRM_FUS_TAF15, RNA recognition motif in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 28/82 (34%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAK--------VITERESGKSRGFGFVTYDSNES 87
           +FV GL       S+ + F   G I   K        + T+RE+GK +G   V++D   S
Sbjct: 5   IFVQGLGEDVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 64

Query: 88  ASSAQSAMDGQELNGRNIRVSF 109
           A +A    DG+E +G  I+VSF
Sbjct: 65  AKAAIDWFDGKEFSGNPIKVSF 86

This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. . Length = 86

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

 Score = 42.7 bits (100), Expect = 2e-06
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           + +FV  L +      LKE FS  G +  A ++ +++ GKSRG G VT++    A  A S
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAIS 59

Query: 94  AMDGQELNGRNIRV 107
             +GQ L  R + V
Sbjct: 60  MFNGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
            LFV  L +   + SL   FS FG +  A  + ++ +G+++G GFV +    + ++ 
Sbjct: 2  FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNAC 59

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 42.8 bits (100), Expect = 2e-06
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG LS    +  + + FS  G     K+ITE  S     + FV +  +  A++A +AM
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59

Query: 96  DGQELNGRNIRVSFA 110
           +G+++ G+ ++V++A
Sbjct: 60  NGRKILGKEVKVNWA 74

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and 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 = 81

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

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 3/50 (6%)

Query: 47 DSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
          +  L+E F  FGDI    ++ ++ +G+S+GFG+V +      S A  A++
Sbjct: 14 EEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF---HKPSQAAVALE 60

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

>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 66  ITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF-ANDRPPRS 117
           + + E     GF  V Y++ E A   Q AMDG  + G  I++SF A   P RS
Sbjct: 35  LAQDEGSCVGGFAVVEYETAEQAEEVQLAMDGTTIKGSRIQLSFCAPGAPGRS 87

This subgroup corresponds to the RRM3 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 98

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

 Score = 44.7 bits (105), Expect = 4e-06
 Identities = 22/91 (24%), Positives = 51/91 (56%), Gaps = 1/91 (1%)

Query: 18  PKAS-LINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRG 76
           P+A  +I+ V+  ++   +++V  +     ++ +K  F  FG+I + ++         +G
Sbjct: 188 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKG 247

Query: 77  FGFVTYDSNESASSAQSAMDGQELNGRNIRV 107
           +GF+ Y++ +S S A ++M+  +L G+ +RV
Sbjct: 248 YGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 17/52 (32%), Positives = 31/52 (59%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          K+FVGGL+    +  ++E F  FG+I   ++  + ++ K RGF F+T+   +
Sbjct: 6  KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEED 57

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L++ GL        +++ FS FG I  ++V+ ++ +G SRG  F+ +D    A  A ++ 
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 96  DGQELNGRN--IRVSFA 110
           +G +  G +  I V FA
Sbjct: 63  NGHKPPGSSEPITVKFA 79

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 41.9 bits (98), Expect = 4e-06
 Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L+    +  L+++FS FG +   K        K + + FV ++  ++A  A   M
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEERDAAVRAMDEM 55

Query: 96  DGQELNGRNIRVSFA 110
           +G+E+ G  I +  A
Sbjct: 56  NGKEIEGEEIEIVLA 70

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 41.8 bits (99), Expect = 5e-06
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VG L     +  L E F   G +    +  +R +   +G+GFV + S E A  A   M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 96  DGQELNGRNIRVS 108
           +  +L G+ IRV+
Sbjct: 61  NMIKLYGKPIRVN 73

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

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

 Score = 41.5 bits (97), Expect = 7e-06
 Identities = 19/71 (26%), Positives = 41/71 (57%), Gaps = 6/71 (8%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++ GG++ G  +  +++ FS FG I E +V  E      +G+ F+ + ++ESA+ A  ++
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSV 56

Query: 96  DGQELNGRNIR 106
           +G  + G  ++
Sbjct: 57  NGTTIEGHVVK 67

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

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAK-------VITERESGKSRGFGFVTYDSNESA 88
           +++ GL     + SL E F   G I   K        I   +  + +G   VTYD   +A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 89  SSAQSAMDGQELNGRNIRVSF 109
            +A    +G E  G  I+VS 
Sbjct: 61  QAAIEWFNGYEFRGNKIKVSL 81

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

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 40.8 bits (95), Expect = 2e-05
 Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+G +S   +++ ++  FS FG I E +++     G SRG  FVT+ +   A +A  A
Sbjct: 3   KLFIGMVSKKCNENDIRVMFSPFGQIEECRIL-RGPDGLSRGCAFVTFTTRAMAQTAIKA 61

Query: 95  M-DGQELNG--RNIRVSFAN 111
           M   Q + G    I V FA+
Sbjct: 62  MHQAQTMEGCSSPIVVKFAD 81

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 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 two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 18/64 (28%), Positives = 32/64 (50%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLFVG +     +  ++  F   G++ E  +I ++ +G  +G  FV Y + + A  A  A
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 95 MDGQ 98
          +  Q
Sbjct: 61 LHNQ 64

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

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

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L     +  + E F   G + + K+  +++ GK + F FV +    S   A + +
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 96  DGQELNGRNIRV 107
           +G +L GR + +
Sbjct: 63  NGIKLYGRPLNI 74

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 28/72 (38%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  L +      LKE FS  G +  A  I E + GKSRG G VT++    A  A S  
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRAD-IKEDKDGKSRGMGTVTFEQPIEAVQAISMF 61

Query: 96  DGQELNGRNIRV 107
           +GQ L  R + V
Sbjct: 62  NGQFLFDRPMHV 73

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 39.6 bits (92), Expect = 3e-05
 Identities = 17/55 (30%), Positives = 33/55 (60%)

Query: 57  FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN 111
           FG++    ++    +G S+G+GFV Y   +SA+ A+S + G++L  R + V + +
Sbjct: 23  FGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLGKQLGSRTLYVHWTD 77

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

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           L++G L    D++ +K AF++ G  +   K+I  + +G   G+ FV +    +A      
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 95  MDGQELNGRNIRVSF 109
           ++G+ + G N    F
Sbjct: 62  LNGKPIPGSNPPKRF 76

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  LS+   + SL+E F     I        + +G+ +G+ FV ++S E A  A ++ 
Sbjct: 4   LVVNNLSYSASEDSLQEVFEKATSIR-----IPQNNGRPKGYAFVEFESAEDAKEALNSC 58

Query: 96  DGQELNGRNIRVSF 109
           +  E+ GR+IR+ F
Sbjct: 59  NNTEIEGRSIRLEF 72

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L     +  L+ AF  +G + +   I     G+   + FV + + + A  A+ AM
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDV-DIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 96  DGQELNGRNIRVSF 109
            GQ +    I++ +
Sbjct: 64  SGQYIGRNQIKIGY 77

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

>gnl|CDD|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 = 39.4 bits (92), Expect = 4e-05
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 9/76 (11%)

Query: 36  LFVGGLS-WGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           LFV G     T +  +++ F  FG +    +         + F FV ++ +E A+ A  A
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI--------RKTFAFVEFEDSEDATKALEA 53

Query: 95  MDGQELNGRNIRVSFA 110
           + G  ++G  + V F 
Sbjct: 54  LHGSRIDGSVLTVEFV 69

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

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

 Score = 39.5 bits (92), Expect = 4e-05
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
          +LFVG L    D S LKE F  +G++ E ++      GK   FGFV +D +E
Sbjct: 5  QLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSE 53

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

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 39.2 bits (92), Expect = 5e-05
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 50 LKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          L++AFS FG++  A VI + + G+S G G V +     A +A
Sbjct: 16 LEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRKPGAQAA 56

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)

 Score = 39.2 bits (91), Expect = 5e-05
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+G L     ++ L+ AF  FG ITE   I     G++  +GF+ +++ + A  A+ AM
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVD-IKRPGRGQTSTYGFLKFENLDMAHRAKLAM 68

Query: 96  DGQELNGRNIRVSFANDRP 114
            G+ L    I++ +    P
Sbjct: 69  SGKVLRRNPIKIGYGKATP 87

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

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

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VG + +G     L+  F   G +    ++ ++ SG  +GF ++ +   ES  +A  A+
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-AL 60

Query: 96  DGQELNGRNIRV 107
           D     GR I+V
Sbjct: 61  DESLFRGRQIKV 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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 38.9 bits (91), Expect = 6e-05
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 3/72 (4%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD 96
            VGG+     +  LKE FSN G++T  ++  +R+   S  F FV +   ESA SA + + 
Sbjct: 4   HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH--SARFAFVEFADAESALSALN-LS 60

Query: 97  GQELNGRNIRVS 108
           G  L G  +RVS
Sbjct: 61  GTLLGGHPLRVS 72

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 38.5 bits (90), Expect = 7e-05
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+G L   T  S L+EAF  FG+I +   I  ++ G +  + F+ Y    S   A   M
Sbjct: 5   LFIGNLEKTTTYSDLREAFERFGEIID---IDIKKQGGNPAYAFIQYADIASVVKAMRKM 61

Query: 96  DGQELNGRNIRV 107
           DG+ L    +++
Sbjct: 62  DGEYLGNNRVKL 73

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

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

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLFVG LS    +  ++  F  FG I E  ++   + G S+G  FV + S+  A +A +A
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSHAEAQAAINA 61

Query: 95 MDG 97
          + G
Sbjct: 62 LHG 64

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

>gnl|CDD|240810 cd12364, RRM_RDM1, RNA recognition motif of RAD52 motif-containing protein 1 (RDM1) and similar proteins

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 7/80 (8%)

Query: 36  LFVGGLSWGTDDS----SLKEAFSNFGDITEAKVITERESGKSRGF-GFVTYDSNESASS 90
           L+V G+S    +     SL  AFS FG +   KV     +  + GF  FV + S  +AS 
Sbjct: 3   LYVWGISPKLTEEEIYESLCSAFSQFGLLYSVKVF-PNAAVATPGFYAFVKFYSARAASR 61

Query: 91  AQSAMDGQEL-NGRNIRVSF 109
           AQ A +G+ L  G  ++V F
Sbjct: 62  AQKACNGKWLFQGSPLKVRF 81

This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. . Length = 81

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

 Score = 38.6 bits (90), Expect = 8e-05
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 36  LFVGGLSWGTDDSSLKEA----FSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           +FV  L     D  L+ A    FS +G +   KV       + R + FV + +++ A +A
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKV---LRDWRQRPYAFVQFTNDDDAKNA 61

Query: 92  QSAMDGQELNGRNIRVSFA 110
            +   G  L+GR+IR   A
Sbjct: 62  LAKGQGTILDGRHIRCERA 80

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

 Score = 38.3 bits (90), Expect = 9e-05
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 45  TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN 104
            D S +++ F  +G+I   +  + R   K+R F +V + S ESA++A + ++G+   G  
Sbjct: 12  FDQSDIRDLFEQYGEILSIRFPSLR-FNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYK 70

Query: 105 IRVSFAN 111
           + V  ++
Sbjct: 71  LVVKISD 77

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

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

 Score = 38.8 bits (90), Expect = 9e-05
 Identities = 21/77 (27%), Positives = 37/77 (48%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           + LFV  ++  T    L+  F  +G I +  V  +  + + RGF +V ++    A  A  
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 94  AMDGQELNGRNIRVSFA 110
            +D + + GR I + FA
Sbjct: 61  NLDRKWICGRQIEIQFA 77

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

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

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           ++  +FV G   GT +  L + FS FG +    VI +++ G    +  V +DS E     
Sbjct: 1   AERSVFVSGFKRGTSEEQLMDYFSAFGPVMN--VIMDKDKGV---YAIVEFDSKEGVDKV 55

Query: 92  QSAMDGQELNGRNIRV 107
            S      LNG  +RV
Sbjct: 56  LSE-PQHTLNGHRLRV 70

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

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

 Score = 38.3 bits (90), Expect = 1e-04
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 55  SNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF 109
           S FG +   KV          G  +V + + E+A     A++G+  +GR I   +
Sbjct: 33  SKFGPVEHIKVDKN----SPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQITAEY 83

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

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 22/89 (24%), Positives = 34/89 (38%), Gaps = 18/89 (20%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDI---------------TEAKVITERESGKSRGF--G 78
           +FVG L   T    LK+ F  FG I                +     +++    +     
Sbjct: 3   VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62

Query: 79  FVTYDSNESASSAQSAMDGQELNGRNIRV 107
           +V +   ESA  A   ++G E  G +IRV
Sbjct: 63  YVVFKEEESAEKA-LKLNGTEFEGHHIRV 90

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FV  L+    +  L E FS  G + + + I +R S +S+G  +V +  +  +     A+
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEF-YDVESVIKALAL 150

Query: 96  DGQELNGRNIRV 107
            GQ L GR I V
Sbjct: 151 TGQMLLGRPIIV 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|241002 cd12558, RRM3_RBM15B, RNA recognition motif 3 in putative RNA-binding protein 15B (RBM15B) from vertebrate

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T+L+VGGL   T  ++L   F  FG I     +      K   F ++ Y+S ++A +A +
Sbjct: 3   TRLWVGGLGPNTSLAALAREFDRFGSIRTIDYV------KGDSFAYIQYESLDAAQAACA 56

Query: 94  AMDGQELNG--RNIRVSFA 110
            M G  L G  R +RV FA
Sbjct: 57  QMRGFPLGGPDRRLRVDFA 75

This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 76

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGD-ITEAKVITERESG-KSRGFGFVTYDSNESASSA 91
            +LFVGG+        + E FS   + + +  V    +   K+RGF FV Y+S+ +A+ A
Sbjct: 2   CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61

Query: 92  QSA-MDGQ-ELNGRNIRVSFA 110
           +   + G+  L G  + V +A
Sbjct: 62  RRKLVPGRILLWGHEVAVDWA 82

This subfamily corresponds to the RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

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

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           TK+ V  L +      ++  FS++G +   +V  ++    +RGF FV + + + A +A +
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRV-PKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 94  AMDGQELNGRNIRVSFA 110
           A+    L GR + + +A
Sbjct: 60  ALKDTHLLGRRLVLQYA 76

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

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

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++++G L +   +  ++  F  +G I        RE     GFGFV ++    A  A   
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 95  MDGQELNGRNIRVSFA 110
           ++G+EL G  + V  A
Sbjct: 53  LNGKELCGERVIVEHA 68

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

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

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 49  SLKEAF-SNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV 107
            LK+ F    G++T  ++  + E GKSRG G V +   ES   A   M+  EL GR + V
Sbjct: 15  DLKDLFREKVGEVTYVELF-KDEEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 8/73 (10%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVG +   T    L+  F  +G +    V+        R F FV      +A  A   
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53

Query: 95  MDGQELNGRNIRV 107
           ++G+EL+GR + V
Sbjct: 54  LNGRELHGRKLVV 66

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

>gnl|CDD|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 37.3 bits (86), Expect = 2e-04
 Identities = 19/75 (25%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG LS    ++ + + FS  G     K+I +  +  +  + FV +  +  A+++ +AM
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMD--TAGNDPYCFVEFFEHRHAAASLAAM 59

Query: 96  DGQELNGRNIRVSFA 110
           +G+++ G+ ++V++A
Sbjct: 60  NGRKIMGKEVKVNWA 74

This subgroup corresponds to the RRM1 of 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 functions 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 = 74

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

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VG + +G+    L+  FS  G I    ++ ++ SG  +G+ ++ + + +S  +A  A+
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA-VAL 60

Query: 96  DGQELNGRNIRV 107
           D     GR I+V
Sbjct: 61  DESSFRGRVIKV 72

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|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 = 37.5 bits (88), Expect = 3e-04
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 50  LKEAFSNFGDITEAKVI-TERESGKSRGFG--FVTYDSNESASSAQSAMDGQELNGRNIR 106
           +KE    +G +    +   E E     G G  FV +   E A  AQ A+ G++ +GR + 
Sbjct: 28  VKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTVV 87

Query: 107 VS 108
            S
Sbjct: 88  AS 89

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

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 9/69 (13%)

Query: 35  KLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           ++FVG L+        L+E FS +G I    +         +G+GFV +D+ E A +A +
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

Query: 94  AMDGQELNG 102
             +G+E+ G
Sbjct: 54  GENGREIAG 62

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITE---AKVITERESGKSRGFGFVTYDSNESASS 90
           +K+ V  + +      L+E FS FG++      K +T    G  RGFGFV + + + A  
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGT--GSHRGFGFVDFITKQDAKR 58

Query: 91  AQSAM-DGQELNGR 103
           A  A+     L GR
Sbjct: 59  AFKALCHSTHLYGR 72

This subgroup corresponds to the RRM6 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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 20/77 (25%), Positives = 37/77 (48%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T LFV  ++  T    L+  F  +G I +  V  +  + + RGF ++ ++    A  A  
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 94  AMDGQELNGRNIRVSFA 110
            ++ + + GR I + FA
Sbjct: 61  NLNRKWVCGRQIEIQFA 77

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

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            K+ +  +        L    S +G +   + +  +    +     VTY+S E A  A +
Sbjct: 1   RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATV---NVTYESPEQAQQAVN 57

Query: 94  AMDGQELNGRNIRVSFAND 112
            ++G E  G  ++VS+  D
Sbjct: 58  KLNGHEYEGSKLKVSYIPD 76

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 13/34 (38%), Positives = 21/34 (61%)

Query: 67  TERESGKSRGFGFVTYDSNESASSAQSAMDGQEL 100
            +  +GKS+GF +VTY +  SA  A+  ++G E 
Sbjct: 33  RDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFEY 66

This subfamily corresponds to the RRM3 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 = 75

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA- 94
           L+VG L     +  + E F  +G +   K++ +R S       FV +   +SA  A +A 
Sbjct: 2   LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKAHNAV 60

Query: 95  --MDGQEL 100
             M  ++L
Sbjct: 61  NKMGDRDL 68

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

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

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+G L     +  L+ AF  +G I E  VI     G+   + F+ + + + A  A+ AM
Sbjct: 11  LFIGNLDHNVSEVELRRAFDKYGIIEEV-VIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 96  DGQELNGRNIRVSFA 110
            G+ +    I++ + 
Sbjct: 70  SGRVIGRNPIKIGYG 84

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

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

 Score = 36.5 bits (84), Expect = 6e-04
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T++FVG +     +  L   F   G I + +++ +  SG++RG+ F+T+   E+A  A  
Sbjct: 2   TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

Query: 94  AMDGQEL-NGRNIRV 107
             D  E+  G+++ V
Sbjct: 62  LCDNYEIRPGKHLGV 76

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

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

 Score = 36.2 bits (84), Expect = 6e-04
 Identities = 14/60 (23%), Positives = 27/60 (45%)

Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
          ++V  L        LK  FS +G +    +   + +G  +GF F+ +++ E A  A   +
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

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

 Score = 36.0 bits (84), Expect = 6e-04
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 7/74 (9%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+  L   T    L+  F+ F    E +++        RG  FV +++ E A+ A  A+
Sbjct: 5   LFLQNLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQAL 58

Query: 96  DGQELN-GRNIRVS 108
            G ++  G  +++S
Sbjct: 59  QGFKITPGHAMKIS 72

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

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

 Score = 36.1 bits (83), Expect = 6e-04
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T++FVG +     +  L   F   G I + +++ +  +G +RG+ FVT+ + E+A  A  
Sbjct: 2   TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

Query: 94  AMDGQEL-NGRNIRV 107
             +  E+  G++I V
Sbjct: 62  LYNNHEIRPGKHIGV 76

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 38.4 bits (89), Expect = 7e-04
 Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 17/103 (16%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNF--GDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           L+V  L   T +  ++++FS F  G +   K        K R + FV ++  E A  A  
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVK--------KIRDYAFVHFEDREDAVKAMD 287

Query: 94  AMDGQELNGRNIRVSFAN-------DRPPRSDGGYGGGNDGSY 129
            ++G+EL G  I V+ A         R  R  GG G     + 
Sbjct: 288 ELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAAR 330

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|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 36.1 bits (84), Expect = 7e-04
 Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 47  DSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR 106
           +   ++   +FG  +  +V++ R  GK +   F T+D+ ++AS A S +   ++ G+ + 
Sbjct: 13  EDDKEDLLKHFG-ASSVRVMSRR--GKLKNTAFATFDNEQAASQALSRLHQLKILGKRLV 69

Query: 107 VSFA 110
           V +A
Sbjct: 70  VEYA 73

This subfamily corresponds to the RRM1 of 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 repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), 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. . Length = 73

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

 Score = 35.8 bits (83), Expect = 7e-04
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 37  FVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE---SGKSRGFGFVTYDSNESASSAQS 93
           ++G L +   +  +KE F     +  + V   RE    G+ RGFG+  ++  +S   A S
Sbjct: 5   YLGNLPYDVTEEDIKEFFR---GLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 94  AMDGQELNGRNIRVSFA 110
            ++ + L  R IRV  A
Sbjct: 62  -LNDESLKNRRIRVDIA 77

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 28/116 (24%), Positives = 46/116 (39%), Gaps = 14/116 (12%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L+V  L     D  L   F  +G I +  ++ ++ +G  RG  FV ++  E A  A S
Sbjct: 194 TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS 253

Query: 94  AMDG--------------QELNGRNIRVSFANDRPPRSDGGYGGGNDGSYGGNRGG 135
           A++                E +G+     + +     + G  G GN G  GG+   
Sbjct: 254 ALNNVIPEGGSQPLTVRLAEEHGKAKAHHYMSQMGHGNMGNMGHGNMGMAGGSGMN 309

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 36.0 bits (84), Expect = 8e-04
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 11/57 (19%)

Query: 50  LKEAFSNFGDITEAKVITERESG-KSRGFGFVTYDSNESASSAQSAMDGQELNGRNI 105
           L + FS +G + E  +I E+ +G ++     V +DS ESA +A+ A     LNGRNI
Sbjct: 18  LHQVFSPYGAV-EKILIFEKNTGVQA----LVQFDSVESAENAKKA-----LNGRNI 64

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

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

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAK--------VITERESGKSRGFGFVTYDSNES 87
           ++V GL+       L + F + G +   K        + T++E+GK +G   V+Y+   S
Sbjct: 3   IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYEDPPS 62

Query: 88  ASSAQSAMDGQELNGRNIRVS 108
           A +A    DG++  G  ++VS
Sbjct: 63  AKAAVEWFDGKDFQGSKLKVS 83

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

>gnl|CDD|240785 cd12339, RRM2_SRSF1_4_like, RNA recognition motif 2 in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 25/70 (35%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 38  VGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG 97
           V GL  G     LK+     GD+T A V  ++E     G G V + S E    A   +DG
Sbjct: 5   VSGLPEGASWQDLKDFGRQAGDVTYADVDRDQE-----GEGVVEFTSQEDMERALRKLDG 59

Query: 98  QELNGRNIRV 107
            E  GR +RV
Sbjct: 60  TEFRGRRVRV 69

This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 71

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L+VGGL     +  L++ F  FG+I    V+  ++        FVT+ + E+A  A  
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC------AFVTFTTREAAEKAAE 55

Query: 94  AMDGQE-LNGRNIRV 107
            +  +  +NGR +++
Sbjct: 56  RLFNKLIINGRRLKL 70

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++ GL     +  L   FS +G +    V+ +R+    RG   V +D  E+A +A + M
Sbjct: 10  VWLDGLDESVTEQYLTRHFSRYGPVV--HVVIDRQ----RGQALVFFDKVEAAQAAVNEM 63

Query: 96  DGQELNGRNIRVSF 109
            G++L GR ++V F
Sbjct: 64  KGRKLGGRKLQVDF 77

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 77

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 35.8 bits (82), Expect = 0.001
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
          T L++  L    D+  L+     FG +   +++ +  SG SRG GF   +S E   +  S
Sbjct: 1  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIS 59

Query: 94 AMDGQ 98
            +G+
Sbjct: 60 HFNGK 64

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is 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 = 85

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
          T L++  L    D+  L+     FG +   +++ +  SG SRG GF   +S E   +  +
Sbjct: 1  TNLYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIIT 59

Query: 94 AMDGQ 98
            +G+
Sbjct: 60 HFNGK 64

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is 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 = 86

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

 Score = 36.8 bits (84), Expect = 0.002
 Identities = 21/96 (21%), Positives = 42/96 (43%)

Query: 19  KASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFG 78
              L      + +    L+VG L   T +  L + F + GDI  A +   ++    +   
Sbjct: 211 AKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRS 270

Query: 79  FVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP 114
           FV  ++++ A  + S  + +++ GR  R +F+  R 
Sbjct: 271 FVGNEASKDALESNSRGNKKKILGRGPRKAFSQPRL 306

Length = 306

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 51  KEAFSNFGDITEAKVITERESGKSRGFG-FVTYDSNESASSAQSAMDGQELNGRNIRVSF 109
           +E    +G +    V     S        FV +   + A  A  A++G+   GR +   F
Sbjct: 24  EEECEKYGKVLNVIVHEVASSEADDAVRIFVEFSDADEAIKAVRALNGRFFGGRKVTARF 83

Query: 110 AN 111
            +
Sbjct: 84  YD 85

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|240941 cd12497, RRM3_RBM47, RNA recognition motif 3 in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 10/77 (12%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNF--GDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           L+V  L   T + ++K+ F  F  G +   K        K R + FV + S E A  A +
Sbjct: 4   LYVRNLMIETSEDTIKKTFGQFNPGCVERVK--------KIRDYAFVHFTSREDAVHAMN 55

Query: 94  AMDGQELNGRNIRVSFA 110
            ++G EL G  I V+ A
Sbjct: 56  NLNGTELEGSCIEVTLA 72

This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V  L   T + ++K  F+ F        + ER   K R + FV + + E A +A S M
Sbjct: 4   LYVRNLMISTTEETIKAEFNKF-----KPGVVERVK-KLRDYAFVHFFNREDAVAAMSVM 57

Query: 96  DGQELNGRNIRVSFA 110
           +G+ ++G +I V+ A
Sbjct: 58  NGKCIDGASIEVTLA 72

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 10/84 (11%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++++G LS+   +  ++  F  +G I E  +          G+GFV +D    A  A   
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEVDL--------KNGYGFVEFDDLRDADDAVYE 52

Query: 95  MDGQELNGRNIRVSFANDRPPRSD 118
           ++G++L G   RV   + R PR D
Sbjct: 53  LNGKDLCGE--RVIVEHARGPRRD 74

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 16/62 (25%), Positives = 32/62 (51%)

Query: 50  LKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF 109
            +E    +G+I    ++    +G S+G+GFV Y   +SAS A+  + G++L    +   +
Sbjct: 16  FEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLGKQLGESTLFAQW 75

Query: 110 AN 111
            +
Sbjct: 76  MD 77

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +++VG L     +  +++ F  +G I     I  +   +   F FV ++    A  A   
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKA---IDLKNRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 95  MDGQELNGRNIRVSF 109
            DG + +G  +RV F
Sbjct: 58  RDGYDFDGYRLRVEF 72

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++FVG +     +  L   F   G I E +++ E  SG++RG+ FV Y + E A  A   
Sbjct: 3   EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIRI 61

Query: 95  MDGQELN-GRNIRV 107
           ++  E+  G+ I V
Sbjct: 62  LNNYEIRPGKFIGV 75

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 34.2 bits (78), Expect = 0.003
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K++VG L  G     L+ AFS +G +    +     +    GF FV ++    A  A   
Sbjct: 1   KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 55

Query: 95  MDGQELNGRNIRVSFANDRPPR 116
           +DG+ + G  +RV  +   P R
Sbjct: 56  LDGKVICGSRVRVELSTGMPRR 77

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

>gnl|CDD|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 34.2 bits (78), Expect = 0.003
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 8/76 (10%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++F+G L+    +  ++  F  +G I        R+    RGFGFV +D    A  A   
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRI--------RDIDLKRGFGFVEFDDPRDADDAVYE 52

Query: 95  MDGQELNGRNIRVSFA 110
           +DG+EL    + +  A
Sbjct: 53  LDGKELCNERVTIEHA 68

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          ++VG +   T  S L++ F  FG+I E   +  R+ G +  +GFVTY     A  A
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEI-EEITLHFRDDGDN--YGFVTYRYACDAFRA 57

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 34.3 bits (78), Expect = 0.004
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          L V  LS    +  L+EAFS FG +  A VI + + G+S G G V + S  +A  A
Sbjct: 2  LSVRNLSPYVSNELLEEAFSQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKA 56

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

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

 Score = 34.4 bits (80), Expect = 0.004
 Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 11/87 (12%)

Query: 33  QTKL-FVGGLS-WGTDDSSLK--EAFSNFGDITEAKVITERESGKSRGFG-----FVTYD 83
           Q  L +V GL     D+  LK  E F  +G I   K++  R +  +   G     +VTY 
Sbjct: 4   QRNLVYVVGLPPRLADEEVLKKPEYFGQYGKIK--KIVINRNTSYNGSQGPSASAYVTYS 61

Query: 84  SNESASSAQSAMDGQELNGRNIRVSFA 110
             E A     A+DG  L+GR ++ SF 
Sbjct: 62  RKEDALRCIQAVDGFYLDGRLLKASFG 88

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

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 7/63 (11%)

Query: 46  DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVT-YDSNESASSAQSAMDGQELNGRN 104
            D  L+  FS FG++   K I  RE+       FV  YD   +A +A  A++G+   G  
Sbjct: 14  SDQELRSLFSQFGEV---KDI--RETPLRPSQKFVEFYDIR-AAEAALDALNGRPFLGGR 67

Query: 105 IRV 107
           ++V
Sbjct: 68  LKV 70

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

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

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 39  GGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ 98
           GGL  G     L   F  +G + +  +      GK   + FV+Y S E A++A  A++G+
Sbjct: 9   GGLGNGVSREELLRVFEKYGTVEDLVMPP----GKP--YCFVSYSSIEDAAAAYDALNGK 62

Query: 99  ELN 101
           EL 
Sbjct: 63  ELE 65

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K++VG L    + + L+ AF  +G +    V     +    GF FV ++    A+ A   
Sbjct: 6   KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 60

Query: 95  MDGQELNGRNIRVSFAN 111
           +DG+ L G  +RV  +N
Sbjct: 61  LDGRTLCGCRVRVELSN 77

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

>gnl|CDD|240856 cd12410, RRM2_RRT5, RNA recognition motif 2 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 12/85 (14%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGF---------VTY 82
           S+  ++ G L     D  L+E F ++      ++   R     R             VT 
Sbjct: 1   SKDTVYCGKLPKKVTDEDLREFFKDYN---PQEIWIFRTRKSKRNPLQLHRHFTAALVTL 57

Query: 83  DSNESASSAQSAMDGQELNGRNIRV 107
           D+ E+      ++  ++LNG+ I +
Sbjct: 58  DTEETLDEIIESLKSKKLNGKKISL 82

This subfamily corresponds to the RRM2 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 = 93

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	147
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.94
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.86
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.72
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
KOG0122	270	consensus Translation initiation factor 3, subunit	99.72
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.66
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.65
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.65
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.63
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.62
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.62
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.61
PLN03120	260	nucleic acid binding protein; Provisional	99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.59
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.58
smart00362	72	RRM_2 RNA recognition motif.	99.57
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.57
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.54
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
smart00360	71	RRM RNA recognition motif.	99.53
PLN03121	243	nucleic acid binding protein; Provisional	99.53
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.52
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.52
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.52
PLN03213	759	repressor of silencing 3; Provisional	99.51
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.51
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.5
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.5
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.48
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.48
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.48
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.47
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.46
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.46
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.45
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.44
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.41
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.4
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.4
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.37
smart00361	70	RRM_1 RNA recognition motif.	99.33
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.33
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.32
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.3
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.3
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.29
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.25
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.19
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.19
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.17
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.16
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.16
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.15
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.12
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.1
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	99.07
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.06
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.06
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.04
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.03
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.98
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.97
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.95
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.94
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.92
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.81
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.78
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.77
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.75
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.71
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.68
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.66
KOG0226	290	consensus RNA-binding proteins [General function p	98.64
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.62
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.62
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.37
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.36
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.27
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.21
KOG0151	877	consensus Predicted splicing regulator, contains R	98.21
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.2
KOG4210	285	consensus Nuclear localization sequence binding pr	98.2
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	98.15
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.15
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.06
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.06
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.04
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.03
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.97
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.95
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.82
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.82
KOG3152	278	consensus TBP-binding protein, activator of basal	97.79
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.77
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.72
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.69
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.59
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.54
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.54
KOG2314	698	consensus Translation initiation factor 3, subunit	97.48
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.43
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.31
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.17
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.12
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.09
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.92
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.82
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.76
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.75
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.55
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.55
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.16
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.11
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.07
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.05
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.89
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.84
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.76
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.71
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.63
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.62
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.49
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	95.44
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.22
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.64
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.57
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	94.06
KOG2135	526	consensus Proteins containing the RNA recognition	93.85
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.62
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.45
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.23
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	93.19
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.13
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	89.11
KOG4210	285	consensus Nuclear localization sequence binding pr	88.51
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	83.64
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	83.23
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	80.8
smart00596	69	PRE_C2HC PRE_C2HC domain.	80.12

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

Probab=99.94  E-value=1.6e-25  Score=148.88  Aligned_cols=117  Identities=55%  Similarity=0.940  Sum_probs=99.6

Q ss_pred             CcccccchhhhhccCCCCCchhhHH-hhhCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEE
Q 032111            1 MAFCGKLGMLVRQNGQAPKASLINA-VRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGF   79 (147)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~af   79 (147)
                      |++|.+|.-++++......+..... ........++|||.|||+.+++++|+++|.+||.|..+.++.++.++++++|||
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaF   80 (144)
T PLN03134          1 MAFCNKLGGLLRQNISSNGNVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGF   80 (144)
T ss_pred             CchhhhhhhhhcccccCCCCCccccccccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEE
Confidence            8899999999998755433222222 222345567999999999999999999999999999999999999999999999


Q ss_pred             EEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCCCCCC
Q 032111           80 VTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPRS  117 (147)
Q Consensus        80 v~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~~~~~  117 (147)
                      |+|.+.++|++|++.|++..|.++.|+|+++..++...
T Consensus        81 V~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~~~  118 (144)
T PLN03134         81 VNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPSAP  118 (144)
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCCCC
Confidence            99999999999999999999999999999998765543

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

Probab=99.86  E-value=1.6e-21  Score=123.65  Aligned_cols=115  Identities=30%  Similarity=0.451  Sum_probs=99.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+||+..+++++|.++|..+|.|..|.+-.++.+..++|||||+|.+.++|+.|+..++++.+..++|.+.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            34556899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 032111          109 FANDRPPRSDGGYGGGNDGSYGGNRGGYRVNYRGGDDGF  147 (147)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  147 (147)
                      |+-.....    ++-|++-++|.-+..++..+..+||||
T Consensus       112 ~D~GF~eG----RQyGRG~sGGqVrde~r~d~D~~rggy  146 (153)
T KOG0121|consen  112 WDAGFVEG----RQYGRGKSGGQVRDEYRTDYDPGRGGY  146 (153)
T ss_pred             ccccchhh----hhhcCCCCCCeechhhhhhcCcccCcc
Confidence            98876543    222233355666778888888888887

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.80  E-value=1.6e-18  Score=129.98  Aligned_cols=82  Identities=27%  Similarity=0.541  Sum_probs=75.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~  109 (147)
                      ..++|||.|||+.+++++|+++|.+||.|..+.++.++.+++++++|||+|.+.++|++||+.|++..+.+  ++|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            34689999999999999999999999999999999998899999999999999999999999999998865  6899998


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      ++..
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            8754

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.75  E-value=1.8e-17  Score=124.89  Aligned_cols=83  Identities=29%  Similarity=0.512  Sum_probs=78.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      +.+|||.|||+++++++|+++|.+||.|..++++.+..++.++|||||+|.+.++|.+||..||+..+.|+.|+|.+...
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            34799999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          113 RPP  115 (147)
Q Consensus       113 ~~~  115 (147)
                      ++.
T Consensus       349 ~~~  351 (352)
T TIGR01661       349 KAY  351 (352)
T ss_pred             CCC
Confidence            754

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.72  E-value=1.2e-16  Score=93.39  Aligned_cols=70  Identities=41%  Similarity=0.792  Sum_probs=66.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      |||+|||+++++++|+++|.+||.+..+.+..+ .++..+++|||+|.+.++|++|++.|++..+.++.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999887 6788899999999999999999999999999999875

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=7e-17  Score=121.22  Aligned_cols=83  Identities=25%  Similarity=0.475  Sum_probs=77.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||.|||+++++++|+++|..+|.|..|+++.+..++++++||||+|.+.++|++||+.|++..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34466899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      +++
T Consensus       183 ~a~  185 (346)
T TIGR01659       183 YAR  185 (346)
T ss_pred             ccc
Confidence            764

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=8.8e-17  Score=121.12  Aligned_cols=83  Identities=30%  Similarity=0.579  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +..+|||+|||..+++++|+++|.+||.|..|+++.++.+++++|||||+|.+.++|++||+.|++..+.++.|.|++++
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            543

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=99.72  E-value=6.5e-17  Score=112.91  Aligned_cols=82  Identities=29%  Similarity=0.523  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +..+|.|.||+.++++.+|+++|..+|.|.++.+.+++.|+.++|||||.|.+.++|.+||+.|++.-++.-.|.|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            55789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            75

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

Probab=99.71  E-value=2.7e-16  Score=104.88  Aligned_cols=78  Identities=32%  Similarity=0.609  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .+.|||+||+..++..+|+..|..||.|..|-+-..+     .|||||+|++..+|+.|+..|++..|+|..|.|++++.
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4799999999999999999999999999888665543     47999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          113 RPP  115 (147)
Q Consensus       113 ~~~  115 (147)
                      .+.
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            654

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

Probab=99.70  E-value=5.9e-16  Score=122.18  Aligned_cols=75  Identities=29%  Similarity=0.540  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF--GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..++|||+||++++++++|+++|++|  |.|.+|.+++        +||||+|.+.++|++||+.||+..|.++.|+|.+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  9999987654        4999999999999999999999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +++..
T Consensus       304 Akp~~  308 (578)
T TIGR01648       304 AKPVD  308 (578)
T ss_pred             ccCCC
Confidence            97643

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.

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

Probab=99.66  E-value=9.6e-16  Score=103.33  Aligned_cols=79  Identities=23%  Similarity=0.484  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||.++.+.+|+++|.+||.|..|.+...   ...-.||||+|++..+|+.||.--++..+.+..|+|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4589999999999999999999999999999987543   2234699999999999999999999999999999999987


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      .-
T Consensus        82 gg   83 (241)
T KOG0105|consen   82 GG   83 (241)
T ss_pred             CC
Confidence            54

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

Probab=99.65  E-value=7.7e-16  Score=105.34  Aligned_cols=79  Identities=34%  Similarity=0.615  Sum_probs=75.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .+|.|.||.+-|+.++|..+|++||.|-.|.|++|..|..++|||||.|....+|+.|+++|++..|+|+.|.|++++-
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            5789999999999999999999999999999999999999999999999999999999999999999999999998863

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.65  E-value=3e-15  Score=87.74  Aligned_cols=70  Identities=34%  Similarity=0.757  Sum_probs=63.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      |||+|||+.+++++|.++|..+|.|..+.+..++. +..+++|||+|.+.++|.+|+..+++..+.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            78999999999999999999999999999999866 88999999999999999999999988999998874

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 ....

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

Probab=99.63  E-value=8e-15  Score=105.14  Aligned_cols=85  Identities=28%  Similarity=0.631  Sum_probs=79.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .++=+||||.-|++++++..|+..|+.||.|+.|.|++++.|++++|||||+|...-++..|.+..++.+|+++.|.|.+
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            34557999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      ...+.
T Consensus       178 ERgRT  182 (335)
T KOG0113|consen  178 ERGRT  182 (335)
T ss_pred             ccccc
Confidence            76543

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

Probab=99.62  E-value=6.4e-17  Score=108.56  Aligned_cols=112  Identities=22%  Similarity=0.480  Sum_probs=90.6

Q ss_pred             CcccccchhhhhccCCCCCchh--hHHhhhCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEE
Q 032111            1 MAFCGKLGMLVRQNGQAPKASL--INAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFG   78 (147)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~a   78 (147)
                      |..+..+..+.+.+........  ....+..-.+..-|||+|||++.|+.+|.-+|++||.|..|.+++|+.||+++|||
T Consensus         1 mnplt~vk~i~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFa   80 (219)
T KOG0126|consen    1 MNPLTNVKNIQKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFA   80 (219)
T ss_pred             CchhHHHHHHHHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceE
Confidence            4444555555444322222111  23456666677899999999999999999999999999999999999999999999


Q ss_pred             EEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           79 FVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        79 fv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      |+.|++..+..-|+..||++.|.|+.|+|.....
T Consensus        81 FLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   81 FLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             EEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            9999999999999999999999999999987543

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

Probab=99.62  E-value=6.3e-15  Score=116.77  Aligned_cols=83  Identities=23%  Similarity=0.491  Sum_probs=78.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+++++++|+++|+.||.|..+++.+++.+++++|||||+|.+.++|.+||+.||+..+.|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            44789999999999999999999999999999999998889999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      .++
T Consensus       283 ~pP  285 (612)
T TIGR01645       283 TPP  285 (612)
T ss_pred             CCc
Confidence            643

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.

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

Probab=99.61  E-value=3.5e-15  Score=118.19  Aligned_cols=83  Identities=33%  Similarity=0.612  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||+|||+++++++|+++|.+||.|..|.++.++.+++++|||||+|.+.++|++||..||+..+.|+.|+|.+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      ...
T Consensus       184 p~~  186 (612)
T TIGR01645       184 PSN  186 (612)
T ss_pred             ccc
Confidence            543

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.59  E-value=1.9e-14  Score=102.74  Aligned_cols=77  Identities=23%  Similarity=0.364  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+.+++++|+++|..||.|.+|.++.+..   .++||||+|.+.++++.||. |++..|.|+.|.|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            47999999999999999999999999999999988753   46899999999999999996 999999999999999875


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      .
T Consensus        80 ~   80 (260)
T PLN03120         80 Y   80 (260)
T ss_pred             C
Confidence            4

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

Probab=99.59  E-value=1.5e-14  Score=115.26  Aligned_cols=78  Identities=26%  Similarity=0.536  Sum_probs=75.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      +|||+|||.++++++|.++|.++|.|..|+++++..+++++|||||+|.+.++|++|++.++...+.++.|+|.|+..
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            799999999999999999999999999999999998999999999999999999999999999999999999999764

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

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

Probab=99.59  E-value=4.8e-15  Score=103.14  Aligned_cols=77  Identities=42%  Similarity=0.818  Sum_probs=72.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ++|||++|+|++..+.|+++|++||.|++..++.|+.+++++||+||+|.+.++|.+|++. .+-.|+|++..|.++.
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            5899999999999999999999999999999999999999999999999999999999995 4578999998888764

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

Probab=99.58  E-value=9.2e-15  Score=93.91  Aligned_cols=84  Identities=25%  Similarity=0.547  Sum_probs=78.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      .+..|||.++..++++++|.+.|..||.|+.+.+..+..++..+|||+|+|.+.++|++|+..+|+..+.+.+|.|.|+-
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      ...+
T Consensus       151 v~gp  154 (170)
T KOG0130|consen  151 VKGP  154 (170)
T ss_pred             ecCC
Confidence            5443

>smart00362 RRM_2 RNA recognition motif

Probab=99.57  E-value=4.9e-14  Score=81.79  Aligned_cols=72  Identities=44%  Similarity=0.768  Sum_probs=66.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +|+|.|||..+++++|+++|.+||.+..+.+..++  +.+++++||+|.+.++|++|+..+++..+.++.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999888765  6778999999999999999999999999999888763

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

Probab=99.57  E-value=1.5e-14  Score=104.88  Aligned_cols=81  Identities=30%  Similarity=0.594  Sum_probs=74.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|+|+|||+...+-||+.+|++||.|.+|+++.+.  ..+|||+||+|++.++|++|-++||+..+.|++|.|..+
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            345789999999999999999999999999999999863  568899999999999999999999999999999999988


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ..+
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            654

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

Probab=99.57  E-value=4e-14  Score=111.45  Aligned_cols=82  Identities=23%  Similarity=0.502  Sum_probs=77.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ....+|||+|||..+++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|..||..|++..+.++.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34579999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             cC
Q 032111          111 ND  112 (147)
Q Consensus       111 ~~  112 (147)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            64

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

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

Probab=99.57  E-value=3.4e-14  Score=110.57  Aligned_cols=80  Identities=39%  Similarity=0.772  Sum_probs=76.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ..+|||+|||..+++++|+++|.+||.|..|.++.+..++++++||||+|.+.++|.+|+..|++..+.|+.|.|.++..
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            57999999999999999999999999999999999988889999999999999999999999999999999999999763

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.

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

Probab=99.54  E-value=8.2e-14  Score=108.44  Aligned_cols=82  Identities=29%  Similarity=0.460  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .....+|||.|||..+++++|+++|.++|.|..|.++.++.+++++|||||+|.+.++|++||. |++..+.+++|.|..
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3446799999999999999999999999999999999998999999999999999999999998 899999999999987


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      ...
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            653

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.

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

Probab=99.53  E-value=6e-14  Score=111.84  Aligned_cols=82  Identities=39%  Similarity=0.648  Sum_probs=76.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ....+|||.||++.+++++|+++|++||.|..++++.+ .++.++||+||+|.+.++|.+|+..||+..+.|++|.|.++
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            45578999999999999999999999999999999998 67899999999999999999999999999999999999998


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ..+
T Consensus       362 ~~k  364 (562)
T TIGR01628       362 QRK  364 (562)
T ss_pred             cCc
Confidence            754

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

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

Probab=99.53  E-value=6e-14  Score=110.94  Aligned_cols=80  Identities=28%  Similarity=0.484  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNIRVS  108 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l~v~  108 (147)
                      +...++|||+|||+++++++|+++|+++|.|..++++.+ .++++++||||+|.+.++|++||+.|++..+. ++.|.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            445689999999999999999999999999999999999 78999999999999999999999999999884 6666665


Q ss_pred             ee
Q 032111          109 FA  110 (147)
Q Consensus       109 ~~  110 (147)
                      ++
T Consensus       134 ~S  135 (578)
T TIGR01648       134 IS  135 (578)
T ss_pred             cc
Confidence            43

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.

>smart00360 RRM RNA recognition motif

Probab=99.53  E-value=1.2e-13  Score=79.89  Aligned_cols=71  Identities=39%  Similarity=0.798  Sum_probs=65.6

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           38 VGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        38 v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      |.|||..+++++|+++|.++|.|..+.+..++.++.++++|||+|.+.++|.+|+..+++..+.++.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57899999999999999999999999998887778899999999999999999999999999999888763

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.53  E-value=1.6e-13  Score=96.72  Aligned_cols=79  Identities=16%  Similarity=0.208  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ...+.+|||+||++.+++++|+++|..+|.|..|.++++..   ..++|||+|.+.++++.|+. |++..|.++.|.|..
T Consensus         2 ~~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~   77 (243)
T PLN03121          2 YPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAVL-LSGATIVDQRVCITR   77 (243)
T ss_pred             CCCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEe
Confidence            34568999999999999999999999999999999998743   34799999999999999996 999999999999987


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      ...
T Consensus        78 ~~~   80 (243)
T PLN03121         78 WGQ   80 (243)
T ss_pred             Ccc
Confidence            653

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

Probab=99.52  E-value=5.1e-14  Score=99.94  Aligned_cols=81  Identities=43%  Similarity=0.779  Sum_probs=78.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ..|||+-|..+++.++|++.|.+||.|...++++|..|+|++||+||.|.+.++|+.||..|++.=|.+|.|+..|+..+
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRK  142 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRK  142 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999877


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      +
T Consensus       143 p  143 (321)
T KOG0148|consen  143 P  143 (321)
T ss_pred             c
Confidence            6

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

Probab=99.52  E-value=2.5e-13  Score=96.47  Aligned_cols=82  Identities=28%  Similarity=0.605  Sum_probs=75.8

Q ss_pred             hhhCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           26 VRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        26 ~~~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      ....+++.++||++||+..+++++|++.|..||.|.+|++.+++      ||+||.|.++|.|.+||..+|+.++.|+.+
T Consensus       157 ~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~V  230 (321)
T KOG0148|consen  157 YNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLV  230 (321)
T ss_pred             hccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEE
Confidence            44567788999999999999999999999999999999998874      799999999999999999999999999999


Q ss_pred             EEEeecCC
Q 032111          106 RVSFANDR  113 (147)
Q Consensus       106 ~v~~~~~~  113 (147)
                      +|.|.+..
T Consensus       231 kCsWGKe~  238 (321)
T KOG0148|consen  231 RCSWGKEG  238 (321)
T ss_pred             EEeccccC
Confidence            99998754

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

Probab=99.52  E-value=1.6e-14  Score=99.89  Aligned_cols=86  Identities=40%  Similarity=0.664  Sum_probs=80.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +....++|||++|..++++.-|...|-+||.|..|.++.|..++++++|+||+|...++|.+||..||+.++.|+.|+|.
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            34456899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++++..
T Consensus        86 ~AkP~k   91 (298)
T KOG0111|consen   86 LAKPEK   91 (298)
T ss_pred             ecCCcc
Confidence            998653

>PLN03213 repressor of silencing 3; Provisional

Probab=99.51  E-value=1.3e-13  Score=105.11  Aligned_cols=78  Identities=23%  Similarity=0.464  Sum_probs=70.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCH--HHHHHHHHHhcCCeeCCeEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN--ESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~--~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...-+|||+||++.+++++|...|..||.|..+.+++  .++  +|||||+|.+.  .++.+||..|++..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            3457999999999999999999999999999999984  445  89999999987  78999999999999999999999


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      .+++
T Consensus        84 KAKP   87 (759)
T PLN03213         84 KAKE   87 (759)
T ss_pred             eccH
Confidence            8764

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

Probab=99.51  E-value=1.4e-13  Score=103.40  Aligned_cols=82  Identities=26%  Similarity=0.467  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee-CCeEEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL-NGRNIRVS  108 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~-~g~~l~v~  108 (147)
                      +.-++-|||+.||.++.+++|.-+|++.|.|-.++++.++.++.++|||||.|.+.++|++||+.||+.+| .|+.|.|+
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999999999988 58888887


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      .+.
T Consensus       160 ~Sv  162 (506)
T KOG0117|consen  160 VSV  162 (506)
T ss_pred             Eee
Confidence            653

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

Probab=99.50  E-value=1.2e-13  Score=103.80  Aligned_cols=78  Identities=28%  Similarity=0.479  Sum_probs=72.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .+...+.|||+||+.++|++.|+++|.+||.|++|+.++|        ||||.|.+.++|.+||+.+|+..|.|..|.|.
T Consensus       255 ~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvt  326 (506)
T KOG0117|consen  255 TMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVT  326 (506)
T ss_pred             hhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEE
Confidence            5556788999999999999999999999999999988766        99999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++++..
T Consensus       327 LAKP~~  332 (506)
T KOG0117|consen  327 LAKPVD  332 (506)
T ss_pred             ecCChh
Confidence            998753

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

Probab=99.50  E-value=2.2e-13  Score=83.82  Aligned_cols=80  Identities=20%  Similarity=0.432  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +....-+||.|||+.+|.++..++|.+||.|..|++-..+.   .+|.|||.|++..+|.+|+++|.+..+.++.+.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            34457899999999999999999999999999998876544   368899999999999999999999999999999987


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      ..+
T Consensus        92 yq~   94 (124)
T KOG0114|consen   92 YQP   94 (124)
T ss_pred             cCH
Confidence            654

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

Probab=99.48  E-value=4.8e-13  Score=101.90  Aligned_cols=81  Identities=27%  Similarity=0.458  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...+|||.|||.+++..+|+++|..||.|+...+......++..+|+||+|.+.++++.+|.+ +-..+.+++|.|+..+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            445699999999999999999999999999987776554455558999999999999999996 5678899999999877


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      +.
T Consensus       366 ~~  367 (419)
T KOG0116|consen  366 PG  367 (419)
T ss_pred             cc
Confidence            54

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.48  E-value=1e-12  Score=76.55  Aligned_cols=74  Identities=39%  Similarity=0.814  Sum_probs=67.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +|+|.|||..+++++|+++|..+|.|..+.+..+..+ ..++++||+|.+.++|..|+..+++..+.++.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4889999999999999999999999999988876543 6788999999999999999999999999999988764

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).

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

Probab=99.48  E-value=3.3e-13  Score=101.48  Aligned_cols=79  Identities=24%  Similarity=0.464  Sum_probs=72.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhc-cCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSN-FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      .+.+||+|||++..|++|++++.+ -|.|.+|.+..| ..+|+++.|.|+|.++|.+++|++.|+...+.+++|.|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            345999999999999999999975 678999999988 679999999999999999999999999999999999999876


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      .
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            4

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

Probab=99.47  E-value=9.5e-14  Score=93.36  Aligned_cols=81  Identities=28%  Similarity=0.475  Sum_probs=77.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ....+|||+||+..++++.|+++|-+.|.|..+.++++..+.+++||||++|.+.++|+=|++.|+..++.|++|+|..+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~ka   86 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKA   86 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEec
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             c
Q 032111          111 N  111 (147)
Q Consensus       111 ~  111 (147)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            6

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

Probab=99.46  E-value=2.5e-13  Score=104.01  Aligned_cols=82  Identities=33%  Similarity=0.720  Sum_probs=78.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      +.|||+|+|+++++++|.++|.+.|.|..++++.|..+++++||+|++|.+.+++..|++.|++.++.+++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             CC
Q 032111          114 PP  115 (147)
Q Consensus       114 ~~  115 (147)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

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

Probab=99.46  E-value=7.2e-13  Score=95.28  Aligned_cols=79  Identities=42%  Similarity=0.811  Sum_probs=76.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..+|||+|||+++++++|.++|.++|.+..+.+..++.+++.+++|||+|.+.+++..|+..+++..+.++.|.|.+..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999998899999999999999999999999999999999999999965

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

Probab=99.45  E-value=5.8e-13  Score=94.34  Aligned_cols=84  Identities=30%  Similarity=0.570  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+..+.+.|.=||..+++++++.+|...|.|++|++++|+-++.+.||+||.|..+++|++|+..||+..+..+.|+|++
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            44556788888999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      +++.
T Consensus       118 ARPS  121 (360)
T KOG0145|consen  118 ARPS  121 (360)
T ss_pred             ccCC
Confidence            9864

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

Probab=99.44  E-value=1.4e-12  Score=102.37  Aligned_cols=78  Identities=19%  Similarity=0.350  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+.++|||.|||+ .+++++|+++|+.||.|..|+++.++     +++|||+|.+.++|+.||..||+..|.|++|+|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3567999999998 69999999999999999999998763     47999999999999999999999999999999998


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      ++..
T Consensus       348 s~~~  351 (481)
T TIGR01649       348 SKQQ  351 (481)
T ss_pred             cccc
Confidence            8653

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).

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

Probab=99.41  E-value=2.5e-12  Score=100.88  Aligned_cols=76  Identities=16%  Similarity=0.256  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEEEee
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM--DGQELNGRNIRVSFA  110 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~~~~~~g~~l~v~~~  110 (147)
                      .++|||+|||+.+++++|+++|++||.|..+.++.+      +++|||+|.+.++|++|+..|  ++..+.|++|.|.++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            478999999999999999999999999999988754      469999999999999999975  678999999999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      ..+.
T Consensus        76 ~~~~   79 (481)
T TIGR01649        76 TSQE   79 (481)
T ss_pred             CCcc
Confidence            7653

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).

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

Probab=99.40  E-value=3.6e-12  Score=90.37  Aligned_cols=83  Identities=35%  Similarity=0.546  Sum_probs=77.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ..+..|||=||.+++++.-|+++|.+||.|..|++++|..+.+.+||+||.+.+.++|..||..||+..+.++.|.|.+.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999886


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ..+
T Consensus       356 tnk  358 (360)
T KOG0145|consen  356 TNK  358 (360)
T ss_pred             cCC
Confidence            654

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

Probab=99.40  E-value=7.4e-13  Score=99.29  Aligned_cols=84  Identities=29%  Similarity=0.562  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee---CCeEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL---NGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~---~g~~l~  106 (147)
                      ..+.-.+||+-||..++|.+|+++|++||.|.+|.+++|+.++.++|+|||.|.+.++|.+|+..||+...   ..++|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            34456899999999999999999999999999999999999999999999999999999999999998744   347888


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      |+++...
T Consensus       111 vk~Ad~E  117 (510)
T KOG0144|consen  111 VKYADGE  117 (510)
T ss_pred             ecccchh
Confidence            8887653

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

Probab=99.39  E-value=2.2e-12  Score=99.33  Aligned_cols=82  Identities=29%  Similarity=0.586  Sum_probs=75.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.+.|+|+|||+.+...+|+.+|+.||.|..|.+++. ..++-+|||||.|.+..+|..||+.+|+.+|.|++|.|.|+.
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k-~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRK-KDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccC-CCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            3688999999999999999999999999999999865 557777999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      ++.
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
T ss_pred             ccc
Confidence            654

>PF13893 RRM_5: RNA recognition motif

Probab=99.37  E-value=7.4e-12  Score=70.15  Aligned_cols=56  Identities=39%  Similarity=0.797  Sum_probs=50.1

Q ss_pred             HHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           50 LKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        50 l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      |.++|++||.|..+.+..++     +++|||+|.+.++|++|++.||+..+.|++|+|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999887653     469999999999999999999999999999999985

(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=99.33  E-value=1.5e-11  Score=72.03  Aligned_cols=61  Identities=23%  Similarity=0.567  Sum_probs=53.6

Q ss_pred             HHHHHHHhh----ccCCeeEEE-EEecCCC--CccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           47 DSSLKEAFS----NFGDITEAK-VITERES--GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        47 ~~~l~~~f~----~~g~i~~~~-~~~~~~~--~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      +++|+++|.    +||.|.++. ++.++.+  +.++|++||+|.+.++|.+|+..||+..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            467888888    999999985 6666555  888999999999999999999999999999999876

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

Probab=99.33  E-value=3.8e-12  Score=90.58  Aligned_cols=89  Identities=29%  Similarity=0.488  Sum_probs=82.3

Q ss_pred             hhCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           27 RFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        27 ~~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ...-+++|.|||=.||.+..+.+|.+.|..||.|.+.++..|..|..+++|+||.|.+..+++.||..||++.|..++|+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLK  358 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLK  358 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhh
Confidence            34557889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 032111          107 VSFANDRPP  115 (147)
Q Consensus       107 v~~~~~~~~  115 (147)
                      |.+.+++..
T Consensus       359 VQLKRPkda  367 (371)
T KOG0146|consen  359 VQLKRPKDA  367 (371)
T ss_pred             hhhcCcccc
Confidence            998877653

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

Probab=99.32  E-value=3.6e-12  Score=95.65  Aligned_cols=84  Identities=32%  Similarity=0.594  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCe-e--CCeEEEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQE-L--NGRNIRVS  108 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~-~--~g~~l~v~  108 (147)
                      ..+.+||+-|+..++|++++++|.+||.|++|.++++ ..+.++|++||.|.+.+.|..||+.||+.. +  +..+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            3578999999999999999999999999999999998 568999999999999999999999999883 3  56789999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++....++
T Consensus       202 FADtqkdk  209 (510)
T KOG0144|consen  202 FADTQKDK  209 (510)
T ss_pred             ecccCCCc
Confidence            99876554

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

Probab=99.30  E-value=6.8e-12  Score=92.30  Aligned_cols=84  Identities=32%  Similarity=0.537  Sum_probs=78.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +.++...+||..|.+-++.++|.-+|+.||.|..|.++++..++.+..||||+|.+.+++++|.-+|++..|.++.|+|.
T Consensus       235 ~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD  314 (479)
T KOG0415|consen  235 VKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD  314 (479)
T ss_pred             cCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence            44566899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      ++.+
T Consensus       315 FSQS  318 (479)
T KOG0415|consen  315 FSQS  318 (479)
T ss_pred             hhhh
Confidence            7653

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

Probab=99.30  E-value=2.7e-12  Score=94.82  Aligned_cols=78  Identities=35%  Similarity=0.664  Sum_probs=75.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ++|||+.|.+++.++.|+..|..||.|++|.+.+|+.|+++++||||+|+-.|.|+-|++.||+..+.|+.|+|.+..
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999997654

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

Probab=99.29  E-value=6.1e-12  Score=90.29  Aligned_cols=72  Identities=28%  Similarity=0.607  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ..+||+|||.++++.+|+.+|++||.|.+|.++++        |+||..++.+.++.||..||+.+|.|..|.|+-++++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            46899999999999999999999999999999876        9999999999999999999999999999999988766

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

Probab=99.25  E-value=2.1e-11  Score=90.14  Aligned_cols=102  Identities=21%  Similarity=0.423  Sum_probs=87.0

Q ss_pred             hccCCCCCchhhHHhhhCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHH
Q 032111           12 RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA   91 (147)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a   91 (147)
                      ++++.+......+........-.+|||..+.++.+++||+..|+.||.|.+|.+-+.....+++||+|++|.+.++...|
T Consensus       189 rPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eA  268 (544)
T KOG0124|consen  189 RPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEA  268 (544)
T ss_pred             CCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHH
Confidence            33444444455555555556668999999999999999999999999999999999988899999999999999999999


Q ss_pred             HHHhcCCeeCCeEEEEEeecCC
Q 032111           92 QSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        92 i~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      |..||-+.+.|..|+|-.+-.+
T Consensus       269 iasMNlFDLGGQyLRVGk~vTP  290 (544)
T KOG0124|consen  269 IASMNLFDLGGQYLRVGKCVTP  290 (544)
T ss_pred             hhhcchhhcccceEecccccCC
Confidence            9999999999999999776543

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

Probab=99.19  E-value=3.7e-11  Score=92.50  Aligned_cols=76  Identities=37%  Similarity=0.724  Sum_probs=72.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +||+||..++++..|+.+|+.||.|..|.+.++..++..+||+|++|.+.+.|.+|+..||+++|.|+.|+|..-.
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            8999999999999999999999999999999998899999999999999999999999999999999999987644

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

Probab=99.19  E-value=8.8e-11  Score=80.60  Aligned_cols=81  Identities=21%  Similarity=0.408  Sum_probs=72.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF-GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...-+++..+|..+.+.++..+|.++ |.+..+++.+++.||.++|||||+|++.+.|+-|.+.||+..+.++.|.|.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34568899999999999999999998 67788888899999999999999999999999999999999999999988765


Q ss_pred             cC
Q 032111          111 ND  112 (147)
Q Consensus       111 ~~  112 (147)
                      .+
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            43

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

Probab=99.17  E-value=2.1e-10  Score=90.53  Aligned_cols=76  Identities=17%  Similarity=0.412  Sum_probs=61.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhcc------------CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcC
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNF------------GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG   97 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~------------g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~   97 (147)
                      .....+|||+|||+.+++++|+++|.++            ..|..+.+      .+.++||||+|.+.++|..||. |++
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCC
Confidence            3456789999999999999999999875            12233322      3346899999999999999996 999


Q ss_pred             CeeCCeEEEEEeecC
Q 032111           98 QELNGRNIRVSFAND  112 (147)
Q Consensus        98 ~~~~g~~l~v~~~~~  112 (147)
                      ..+.|+.|+|.....
T Consensus       245 ~~~~g~~l~v~r~~~  259 (509)
T TIGR01642       245 IIYSNVFLKIRRPHD  259 (509)
T ss_pred             eEeeCceeEecCccc
Confidence            999999999976543

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

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

Probab=99.16  E-value=1.9e-10  Score=80.03  Aligned_cols=76  Identities=30%  Similarity=0.559  Sum_probs=69.6

Q ss_pred             eEEEcCCCCCCCHHHHHH----HhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKE----AFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +|||.||+..+..++|+.    +|++||.|..|...   .+.+.+|-|||.|.+.+.|-.|+..|+|+.+.|++++|.++
T Consensus        11 TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen   11 TLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             eEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            999999999999998877    99999999998665   35778899999999999999999999999999999999998


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ++.
T Consensus        88 ~s~   90 (221)
T KOG4206|consen   88 KSD   90 (221)
T ss_pred             cCc
Confidence            754

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

Probab=99.16  E-value=1.2e-10  Score=89.92  Aligned_cols=83  Identities=35%  Similarity=0.568  Sum_probs=77.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ++.||||++||+.++.++|.++|+..|.|..+.++.++.+..++||+||.|.-.+++++|++.+.+..|.|+.|.|..+.
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~   83 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAK   83 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccc
Confidence            34899999999999999999999999999999999998888899999999999999999999999999999999999887


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      .+.
T Consensus        84 ~R~   86 (678)
T KOG0127|consen   84 KRA   86 (678)
T ss_pred             ccc
Confidence            653

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

Probab=99.15  E-value=9.1e-11  Score=79.15  Aligned_cols=87  Identities=34%  Similarity=0.620  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITE-AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+..+||.||.+++++..|.+.|+.+|.+.. .+++++..++..++++|+.|.+.+.+.+|+..+++..+..+++.|.
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            344578999999999999999999999998755 4788888999999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++.....+
T Consensus       173 ya~k~~~k  180 (203)
T KOG0131|consen  173 YAFKKDTK  180 (203)
T ss_pred             EEEecCCC
Confidence            99865443

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

Probab=99.12  E-value=3.4e-10  Score=85.85  Aligned_cols=79  Identities=37%  Similarity=0.648  Sum_probs=71.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ..|||.||++.++..+|.++|..||.|.+|++..+.. + ++|| ||+|.+.++|.+||..+|+..+.++.|.|.....+
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            4499999999999999999999999999999998854 4 8899 99999999999999999999999999999876654


Q ss_pred             CC
Q 032111          114 PP  115 (147)
Q Consensus       114 ~~  115 (147)
                      +.
T Consensus       154 ~e  155 (369)
T KOG0123|consen  154 EE  155 (369)
T ss_pred             hh
Confidence            43

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

Probab=99.10  E-value=2.7e-10  Score=86.03  Aligned_cols=77  Identities=30%  Similarity=0.554  Sum_probs=68.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ++...++|+|+|||.++||+.|++-|.++|.|.+..++   ..+++++  .|.|.++++|++|+..|++.++.++.|+|.
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            44566899999999999999999999999999988774   4466765  899999999999999999999999999998


Q ss_pred             ee
Q 032111          109 FA  110 (147)
Q Consensus       109 ~~  110 (147)
                      +.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            63

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

Probab=99.07  E-value=2.8e-09  Score=65.90  Aligned_cols=79  Identities=15%  Similarity=0.255  Sum_probs=68.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC----CeEEE
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNF--GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN----GRNIR  106 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~----g~~l~  106 (147)
                      ++||.|+|||...+.+.|.+++.+.  |....+.++.|..+..+.|||||.|.+.+.+.+..+.+++..+.    .+.+.
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            4789999999999999999998663  56778888999888999999999999999999999999999884    45667


Q ss_pred             EEeec
Q 032111          107 VSFAN  111 (147)
Q Consensus       107 v~~~~  111 (147)
                      |.+|+
T Consensus        81 i~yAr   85 (97)
T PF04059_consen   81 ISYAR   85 (97)
T ss_pred             EehhH
Confidence            77765

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

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

Probab=99.06  E-value=1.5e-10  Score=91.53  Aligned_cols=81  Identities=25%  Similarity=0.525  Sum_probs=75.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .+.|+|.|||+..+-.+++.+|..||.+..|+++.....+.++|||||+|-+..+|.+|+..|..+.+.|+.|.++|++.
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            46899999999999999999999999999999988756677899999999999999999999999999999999999875


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      .
T Consensus       693 d  693 (725)
T KOG0110|consen  693 D  693 (725)
T ss_pred             c
Confidence            3

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

Probab=99.06  E-value=3.2e-10  Score=81.60  Aligned_cols=77  Identities=29%  Similarity=0.589  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +...++++|+||.+.++..+++..|++||.+..+.++++        |+||.|.-.++|..|+.-|++.++.|++++|.+
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            445689999999999999999999999999999999876        999999999999999999999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +.++-
T Consensus       147 stsrl  151 (346)
T KOG0109|consen  147 STSRL  151 (346)
T ss_pred             ecccc
Confidence            88753

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

Probab=99.04  E-value=8.8e-10  Score=88.08  Aligned_cols=78  Identities=23%  Similarity=0.515  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .+||||+.|+..+++.+|.++|++||.|.+|.++..      +++|||.+...++|++|+.+|.+..+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            478999999999999999999999999999988764      56999999999999999999999999999999999987


Q ss_pred             CCCC
Q 032111          113 RPPR  116 (147)
Q Consensus       113 ~~~~  116 (147)
                      +..+
T Consensus       495 ~G~k  498 (894)
T KOG0132|consen  495 KGPK  498 (894)
T ss_pred             CCcc
Confidence            6543

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

Probab=99.03  E-value=2e-09  Score=79.14  Aligned_cols=75  Identities=23%  Similarity=0.530  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC-eeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ-ELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~-~~~g~~l~v~~~  110 (147)
                      .-.++||++|...+++.+|++.|.+||.|.++.+...+      +.|||+|.+.++|+.|.+++-+. .|+|.+|.|.|.
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            34689999999999999999999999999999887763      48999999999999988865544 669999999999


Q ss_pred             cC
Q 032111          111 ND  112 (147)
Q Consensus       111 ~~  112 (147)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            87

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

Probab=99.00  E-value=1.6e-09  Score=84.38  Aligned_cols=82  Identities=35%  Similarity=0.530  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ..++.+||.+|...+...+|+.+|.+||.|.-.+++.+..+...++|+||++.+.++|.++|..||.++|.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34567999999998888999999999999999989888778888899999999999999999999999999999999887


Q ss_pred             cC
Q 032111          111 ND  112 (147)
Q Consensus       111 ~~  112 (147)
                      +.
T Consensus       483 KN  484 (940)
T KOG4661|consen  483 KN  484 (940)
T ss_pred             cc
Confidence            63

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

Probab=99.00  E-value=2.2e-09  Score=81.49  Aligned_cols=75  Identities=25%  Similarity=0.487  Sum_probs=69.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ..+||+   +.+++..|.++|..+|.+.++++.++. +  +.|||||.|.+.++|++||..||-..+.|++|+|.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            357887   889999999999999999999999997 6  9999999999999999999999999999999999998754


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      +
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            3

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

Probab=98.98  E-value=2.8e-09  Score=84.45  Aligned_cols=76  Identities=30%  Similarity=0.570  Sum_probs=68.7

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCC---ccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESG---KSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +||.||++.++.+++...|..+|.|..+.|...+...   .+.||+||+|.+.++|++|+..|+++.++|+.|.|+++.
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999999999999999999999999887654332   244999999999999999999999999999999999988

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

Probab=98.97  E-value=2.5e-09  Score=79.02  Aligned_cols=81  Identities=31%  Similarity=0.638  Sum_probs=74.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ...|||++||..+++++++++|.+|+.|..+.++.|..+...++|+||.|.+.+++++++. ..-+.|+++.+.|+.+.+
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeeccc
Confidence            4589999999999999999999999999999999999999999999999999999999987 566799999999999887


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      +.
T Consensus       176 k~  177 (311)
T KOG4205|consen  176 KE  177 (311)
T ss_pred             hh
Confidence            64

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

Probab=98.95  E-value=6.6e-09  Score=74.17  Aligned_cols=80  Identities=29%  Similarity=0.541  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...+|+|.|||+.+++++|+++|.+|+.+..+.+-.+ ..+.+.|.|-|.|...++|++|++.|++..++|+++++....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            3378999999999999999999999997777766555 678899999999999999999999999999999999887764


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      +
T Consensus       161 ~  161 (243)
T KOG0533|consen  161 S  161 (243)
T ss_pred             C
Confidence            3

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

Probab=98.94  E-value=7.2e-09  Score=73.89  Aligned_cols=86  Identities=22%  Similarity=0.422  Sum_probs=78.0

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ..+.+.+.+||+|+.+.++.++++..|+.+|.+..+.++.++..+.+++|+||+|.+.+..+.++. |++..+.+..+.+
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            345567899999999999999999999999999999999998888899999999999999999999 9999999999999


Q ss_pred             EeecCCC
Q 032111          108 SFANDRP  114 (147)
Q Consensus       108 ~~~~~~~  114 (147)
                      .+.....
T Consensus       175 t~~r~~~  181 (231)
T KOG4209|consen  175 TLKRTNV  181 (231)
T ss_pred             eeeeeec
Confidence            8876543

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

Probab=98.92  E-value=1.9e-09  Score=79.65  Aligned_cols=84  Identities=40%  Similarity=0.768  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.+.+||++|+++++++.|++.|.+||.|..+.+++++.++.+++|+||+|++.+...++|.. ....|.++.|.++.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            568999999999999999999999999999999999999999999999999999999998883 4578999999999888


Q ss_pred             CCCCC
Q 032111          112 DRPPR  116 (147)
Q Consensus       112 ~~~~~  116 (147)
                      ++...
T Consensus        84 ~r~~~   88 (311)
T KOG4205|consen   84 SREDQ   88 (311)
T ss_pred             Ccccc
Confidence            76543

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

Probab=98.81  E-value=2.7e-08  Score=76.22  Aligned_cols=82  Identities=22%  Similarity=0.391  Sum_probs=69.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ......-|.+.+|||++|+++|++||+.+ .|..+.+.+  .+++..|-|||+|.+.+++++|++ .+...+..+.|.|-
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf   81 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVF   81 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEE
Confidence            34455788899999999999999999987 477765554  568899999999999999999999 58888899999998


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      .+...+
T Consensus        82 ~~~~~e   87 (510)
T KOG4211|consen   82 TAGGAE   87 (510)
T ss_pred             ccCCcc
Confidence            876543

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

Probab=98.78  E-value=1.2e-07  Score=66.31  Aligned_cols=85  Identities=19%  Similarity=0.349  Sum_probs=66.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEe-cCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC---CeEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVIT-ERESGKSRGFGFVTYDSNESASSAQSAMDGQELN---GRNI  105 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~-~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~---g~~l  105 (147)
                      +...+++||.+||.++...+|..+|..+-.-+...+.. ++.....+-++|+.|.+.+.|++|+..|||..|+   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            34468999999999999999999999885544443332 2222223469999999999999999999999995   6789


Q ss_pred             EEEeecCCC
Q 032111          106 RVSFANDRP  114 (147)
Q Consensus       106 ~v~~~~~~~  114 (147)
                      +|+++++-.
T Consensus       111 hiElAKSNt  119 (284)
T KOG1457|consen  111 HIELAKSNT  119 (284)
T ss_pred             EeeehhcCc
Confidence            999987643

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

Probab=98.77  E-value=1.7e-08  Score=70.78  Aligned_cols=72  Identities=28%  Similarity=0.652  Sum_probs=65.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ..+||++||+.+.+.+|..||.+||.+..+.+..        +|+||+|.+..+|+.|+..|++..|.+-.+.|+++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            4689999999999999999999999999887653        48999999999999999999999999888888888754

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

Probab=98.75  E-value=5.3e-08  Score=71.76  Aligned_cols=79  Identities=29%  Similarity=0.425  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDIT--------EAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN  104 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~  104 (147)
                      .+.|||.|||.++|.+++.++|.++|.|.        .|++.++. .|+.+|=+++.|...++++-|+..|++..+.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            35699999999999999999999999663        36777774 4999999999999999999999999999999999


Q ss_pred             EEEEeecC
Q 032111          105 IRVSFAND  112 (147)
Q Consensus       105 l~v~~~~~  112 (147)
                      |+|+.++-
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99998863

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

Probab=98.71  E-value=3.4e-08  Score=70.71  Aligned_cols=81  Identities=31%  Similarity=0.567  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee-C--CeEEEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL-N--GRNIRVS  108 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~-~--g~~l~v~  108 (147)
                      +.+++||+-|...-.|++++.+|..||.|.++.+.+. ..+.++|++||.|.+..+|+.||..||+..- -  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg-~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG-PDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC-CCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            5689999999999999999999999999999988876 5688999999999999999999999998743 2  3568888


Q ss_pred             eecCC
Q 032111          109 FANDR  113 (147)
Q Consensus       109 ~~~~~  113 (147)
                      ++...
T Consensus        97 ~ADTd  101 (371)
T KOG0146|consen   97 FADTD  101 (371)
T ss_pred             eccch
Confidence            87654

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

Probab=98.68  E-value=6e-08  Score=74.33  Aligned_cols=80  Identities=20%  Similarity=0.353  Sum_probs=64.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .....|.+++||+.|++++|.+||+..-.+....++.....+++++.|||.|++.+.+++|+.. |...|..+.|.|..+
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            3456899999999999999999999876555522233335577999999999999999999994 878898899988765


Q ss_pred             c
Q 032111          111 N  111 (147)
Q Consensus       111 ~  111 (147)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            3

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

Probab=98.66  E-value=8.4e-08  Score=71.01  Aligned_cols=83  Identities=27%  Similarity=0.439  Sum_probs=73.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDIT--------EAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGR  103 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~  103 (147)
                      ...+|||-+||..+++++|.++|.+++.|.        .|.+.+++.|++.++-|.|.|.+...|+.|+.-+++..+.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            346899999999999999999999998663        355677889999999999999999999999999999999999


Q ss_pred             EEEEEeecCCC
Q 032111          104 NIRVSFANDRP  114 (147)
Q Consensus       104 ~l~v~~~~~~~  114 (147)
                      .|+|.++..+.
T Consensus       145 ~ikvs~a~~r~  155 (351)
T KOG1995|consen  145 TIKVSLAERRT  155 (351)
T ss_pred             Cchhhhhhhcc
Confidence            99998887654

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

Probab=98.64  E-value=3e-08  Score=70.34  Aligned_cols=84  Identities=29%  Similarity=0.556  Sum_probs=75.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+..+||.+-|..+++.+.|-..|.+|-.-..-++++++.+++++||+||.|.+.+++..|+..|++..++.++|++..
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            34568899999999999999999999997777778899999999999999999999999999999999999999998876


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      ..++
T Consensus       267 S~wk  270 (290)
T KOG0226|consen  267 SEWK  270 (290)
T ss_pred             hhHH
Confidence            5544

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

Probab=98.62  E-value=3.8e-08  Score=76.37  Aligned_cols=70  Identities=27%  Similarity=0.470  Sum_probs=62.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ...+|+|.|||..+++++|..+|+.||.|..|+....     .++.+||+|.+..+|++|++.|++..+.++.|+
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4578999999999999999999999999998765443     357999999999999999999999999998877

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

Probab=98.62  E-value=1.5e-08  Score=70.41  Aligned_cols=78  Identities=17%  Similarity=0.310  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...+|||.|+...++++.|.++|-+.|.|.++.++.++ .++.+ ||||+|.++....-|++.+|+..+.+..+.+++..
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            34799999999999999999999999999999887764 45566 99999999999999999999999999888887654

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

Probab=98.37  E-value=3.2e-06  Score=63.85  Aligned_cols=76  Identities=20%  Similarity=0.424  Sum_probs=67.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           33 QTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        33 ~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...|.|.||.. .+|.+.|..+|..||.|.+|++..++.     .-|+|.+.+...|+-|+..|++..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            36778888864 589999999999999999999988754     369999999999999999999999999999999987


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            54

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

Probab=98.36  E-value=4.5e-07  Score=70.71  Aligned_cols=83  Identities=27%  Similarity=0.539  Sum_probs=76.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .+.....|||++||...++.++++++..+|.+....++.+..++-+++|||.+|.+......|++.||+..+.+.+|.|.
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            34456789999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      .+-
T Consensus       365 ~A~  367 (500)
T KOG0120|consen  365 RAI  367 (500)
T ss_pred             hhh
Confidence            764

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.27  E-value=2.7e-06  Score=53.58  Aligned_cols=70  Identities=24%  Similarity=0.436  Sum_probs=43.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC-----eeCCeEEEEE
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ-----ELNGRNIRVS  108 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~-----~~~g~~l~v~  108 (147)
                      ..|.|.+++..++.++|++.|.+++.|..|.+.....      .++|.|.+.+.|++|+..+...     .+.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            4678888999999999999999999999988876533      7999999999999999977654     4455555544


Q ss_pred             e
Q 032111          109 F  109 (147)
Q Consensus       109 ~  109 (147)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            3

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

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

Probab=98.21  E-value=5.5e-07  Score=69.95  Aligned_cols=82  Identities=26%  Similarity=0.449  Sum_probs=74.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .+.+..++|+.-|+..++..+|.+||...|.|..|.++.+..++.++|.+||+|.+.+....||. |.|..+.|.+|.|.
T Consensus       175 eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq  253 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQ  253 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEec
Confidence            34566788888888889999999999999999999999999999999999999999999999997 89999999999887


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      ...
T Consensus       254 ~sE  256 (549)
T KOG0147|consen  254 LSE  256 (549)
T ss_pred             ccH
Confidence            654

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

Probab=98.21  E-value=3.5e-06  Score=67.50  Aligned_cols=82  Identities=23%  Similarity=0.459  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCC---CCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE---SGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      .+..+.+||.||++.++++.|...|..||.|..++++....   ....+-.+||.|-+..++++|++.|++..+..+.++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            34567899999999999999999999999998888775421   223345799999999999999999999999999999


Q ss_pred             EEeec
Q 032111          107 VSFAN  111 (147)
Q Consensus       107 v~~~~  111 (147)
                      +-|.+
T Consensus       251 ~gWgk  255 (877)
T KOG0151|consen  251 LGWGK  255 (877)
T ss_pred             ecccc
Confidence            98875

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

Probab=98.20  E-value=4.8e-06  Score=61.87  Aligned_cols=76  Identities=22%  Similarity=0.482  Sum_probs=65.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+||+||-|.+|+++|.+.+...|  .+..+++..+..++.++|||+|..-+..+.++.|+.|...+|.|+.-.|.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            34699999999999999999988766  46667777788899999999999999999999999999999988765554

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.20  E-value=2.1e-06  Score=63.26  Aligned_cols=83  Identities=31%  Similarity=0.589  Sum_probs=73.2

Q ss_pred             CCeEE-EcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           33 QTKLF-VGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        33 ~~~i~-v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..+++ +.+++..+++++|+..|...+.|..++++.+..++..+++++++|.+......++.. ....+.++++.+....
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            35566 899999999999999999999999999999999999999999999999999999886 7778888888888887


Q ss_pred             CCCCC
Q 032111          112 DRPPR  116 (147)
Q Consensus       112 ~~~~~  116 (147)
                      .++..
T Consensus       263 ~~~~~  267 (285)
T KOG4210|consen  263 PRPKS  267 (285)
T ss_pred             CCccc
Confidence            66443

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

Probab=98.15  E-value=5.3e-05  Score=51.85  Aligned_cols=63  Identities=29%  Similarity=0.395  Sum_probs=56.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN  101 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~  101 (147)
                      ....|.|++||+..+|++|++...+.|.|.+..+.++       +++.|+|...++++=|+..|....+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            3468999999999999999999999999999988877       48999999999999999999987664

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

Probab=98.15  E-value=4.6e-06  Score=58.52  Aligned_cols=65  Identities=22%  Similarity=0.382  Sum_probs=52.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      ...++||.||..++++++|+.+|..|-....+++..  ..+.  ..||++|.+.+.|..||..|++..+
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~--~~g~--~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA--RGGM--PVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec--CCCc--ceEeecHHHHHHHHHHHHHhhccee
Confidence            345899999999999999999999986554444422  2222  4899999999999999999998766

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

Probab=98.06  E-value=3.2e-06  Score=59.43  Aligned_cols=73  Identities=34%  Similarity=0.515  Sum_probs=62.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +....+.+.|.+++..+.+++|.+.|..+|.+......        ..++||+|.+.+++.+|+..|++..+.++.|.+.
T Consensus        95 p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~  166 (216)
T KOG0106|consen   95 PSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVE  166 (216)
T ss_pred             cccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh--------ccccceeehhhhhhhhcchhccchhhcCceeeec
Confidence            34556789999999999999999999999988444332        2489999999999999999999999999999984


Q ss_pred             e
Q 032111          109 F  109 (147)
Q Consensus       109 ~  109 (147)
                      .
T Consensus       167 ~  167 (216)
T KOG0106|consen  167 K  167 (216)
T ss_pred             c
Confidence            4

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

Probab=98.06  E-value=3e-05  Score=54.34  Aligned_cols=78  Identities=27%  Similarity=0.529  Sum_probs=66.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNIRV  107 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l~v  107 (147)
                      ...+...+++.|||.+++.+.+..+|.+|.....++++...     .+.|||+|.+...+..|...+++..+. ...+.|
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            34556789999999999999999999999988999887653     369999999999999999999999886 677777


Q ss_pred             Eeec
Q 032111          108 SFAN  111 (147)
Q Consensus       108 ~~~~  111 (147)
                      ..++
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            6653

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.04  E-value=3.3e-05  Score=62.06  Aligned_cols=79  Identities=19%  Similarity=0.335  Sum_probs=66.3

Q ss_pred             CCCC-eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQT-KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~-~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..++ .|-+.|+|+.++-+||.+||..|-.+..-.+++-...++.+|.|.|.|++.++|.+|...|++..|..+.+++.+
T Consensus       864 ~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3445 677889999999999999999997654433444446799999999999999999999999999999998887754

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.03  E-value=3.7e-05  Score=45.97  Aligned_cols=68  Identities=29%  Similarity=0.481  Sum_probs=45.7

Q ss_pred             CeEEEcCCCCCCCHHHH----HHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           34 TKLFVGGLSWGTDDSSL----KEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l----~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ..++|.|||.+.+...|    ++++..+| .|..|  .        .+.|+|.|.+.+.|++|.+.|++..+-|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            36899999998877654    55566665 45554  1        1479999999999999999999999999999998


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            864

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

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

Probab=97.97  E-value=0.00019  Score=54.02  Aligned_cols=69  Identities=17%  Similarity=0.298  Sum_probs=56.6

Q ss_pred             cCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEeecC
Q 032111           39 GGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVSFAND  112 (147)
Q Consensus        39 ~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~~~~  112 (147)
                      -|--+.+|.+.|..++...|.|.+|.+.+..  +   --|.|+|++.+.|++|...||+..|+.  -.|+|+++++
T Consensus       128 lNp~YpItvDVly~Icnp~GkVlRIvIfkkn--g---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP  198 (494)
T KOG1456|consen  128 LNPQYPITVDVLYTICNPQGKVLRIVIFKKN--G---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKP  198 (494)
T ss_pred             ecCccccchhhhhhhcCCCCceEEEEEEecc--c---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCc
Confidence            4555678899999999999999999887652  2   359999999999999999999998854  4577777764

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

Probab=97.95  E-value=1.8e-05  Score=59.53  Aligned_cols=79  Identities=18%  Similarity=0.293  Sum_probs=65.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCC-eeE--EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGD-ITE--AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~-i~~--~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ....|.+++||++.+-++|.+||..|.. |..  |.++.+ ..|...|.|||+|.+.+.|..|+.+.+++....+.|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            3568999999999999999999999864 333  555555 568888999999999999999999999887778888886


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      .+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            543

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.82  E-value=8.5e-05  Score=55.20  Aligned_cols=78  Identities=24%  Similarity=0.429  Sum_probs=61.1

Q ss_pred             CeEEEcCCCCCCCHHH------HHHHhhccCCeeEEEEEecCCC---CccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 032111           34 TKLFVGGLSWGTDDSS------LKEAFSNFGDITEAKVITERES---GKSRGFGFVTYDSNESASSAQSAMDGQELNGRN  104 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~------l~~~f~~~g~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~  104 (147)
                      .-+||-+||+.+..++      -.++|.+||.|..|.+.+....   ....--.||.|.+.++|.++|+..++..++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            4589999998876665      2678999999999977554211   112234599999999999999999999999999


Q ss_pred             EEEEeec
Q 032111          105 IRVSFAN  111 (147)
Q Consensus       105 l~v~~~~  111 (147)
                      |+..+..
T Consensus       195 lkatYGT  201 (480)
T COG5175         195 LKATYGT  201 (480)
T ss_pred             EeeecCc
Confidence            9997643

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

Probab=97.82  E-value=0.00018  Score=53.48  Aligned_cols=80  Identities=20%  Similarity=0.395  Sum_probs=61.5

Q ss_pred             CCCCCeEEEcCCCC----CCC-------HHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC
Q 032111           30 SQSQTKLFVGGLSW----GTD-------DSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ   98 (147)
Q Consensus        30 ~~~~~~i~v~nlp~----~~~-------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~   98 (147)
                      +...++|.+.|+-.    +.+       .++|.+-+.+||.|.+|.+.-..    +.|.+.|.|.+.++|..+|+.|+|.
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~h----PdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRH----PDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccC----CCceeEEEeCChHHHHHHHHHhcCe
Confidence            34457888888721    223       24556668899999999775332    3589999999999999999999999


Q ss_pred             eeCCeEEEEEeecCC
Q 032111           99 ELNGRNIRVSFANDR  113 (147)
Q Consensus        99 ~~~g~~l~v~~~~~~  113 (147)
                      .|.|++|..+.....
T Consensus       338 ~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  338 WFDGRQLTASIWDGK  352 (382)
T ss_pred             eecceEEEEEEeCCc
Confidence            999999998876543

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.79  E-value=1.3e-05  Score=57.20  Aligned_cols=72  Identities=19%  Similarity=0.365  Sum_probs=59.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCC--------C----ccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES--------G----KSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~--------~----~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      .-.||+++||+.+....|+++|..||.|-+|.+.....+        +    +.-..++|+|.+...|.++...||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            357999999999999999999999999999877654333        1    2224578999999999999999999999


Q ss_pred             CCeE
Q 032111          101 NGRN  104 (147)
Q Consensus       101 ~g~~  104 (147)
                      .|+.
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            8864

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

Probab=97.77  E-value=2.2e-05  Score=59.52  Aligned_cols=77  Identities=19%  Similarity=0.364  Sum_probs=62.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC--eeCCeEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ--ELNGRNIR  106 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~--~~~g~~l~  106 (147)
                      +..+.+.|.++|||++++|+++.+++.+||.|..+.+...++      -||++|.+.++|...+..+...  .+.+++|.
T Consensus        24 ~~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~y   97 (492)
T KOG1190|consen   24 MAEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIY   97 (492)
T ss_pred             ccCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCccee
Confidence            344678899999999999999999999999999998876543      6999999999988866654443  45677888


Q ss_pred             EEeec
Q 032111          107 VSFAN  111 (147)
Q Consensus       107 v~~~~  111 (147)
                      |.++.
T Consensus        98 iq~sn  102 (492)
T KOG1190|consen   98 IQYSN  102 (492)
T ss_pred             ehhhh
Confidence            87754

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

Probab=97.72  E-value=0.00035  Score=52.64  Aligned_cols=77  Identities=18%  Similarity=0.331  Sum_probs=67.1

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+++.++|-+|... ++.+.|-.+|-.||.|++|++++.+.     +-|.|++.+..+.++|+..|++..+-|.+|.|+.
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccCccccceEEEee
Confidence            45678888898754 66778999999999999999998654     6899999999999999999999999999999988


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      ++.
T Consensus       360 SkQ  362 (494)
T KOG1456|consen  360 SKQ  362 (494)
T ss_pred             ccc
Confidence            764

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

Probab=97.69  E-value=4.7e-05  Score=58.01  Aligned_cols=79  Identities=15%  Similarity=0.278  Sum_probs=60.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEec---CCCCc----------cceEEEEEeCCHHHHHHHHHHh
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITE---RESGK----------SRGFGFVTYDSNESASSAQSAM   95 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~---~~~~~----------~~g~afv~f~~~~~a~~ai~~l   95 (147)
                      ..-+.++|.+.|||.+-..+.|.++|..+|.|..|++...   +.+..          .+-.|+|+|.+.+.|.+|.+.|
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            3346789999999999888999999999999999998765   22211          2457999999999999999988


Q ss_pred             cCCeeCCeEEEE
Q 032111           96 DGQELNGRNIRV  107 (147)
Q Consensus        96 ~~~~~~g~~l~v  107 (147)
                      +....+..-++|
T Consensus       307 ~~e~~wr~glkv  318 (484)
T KOG1855|consen  307 NPEQNWRMGLKV  318 (484)
T ss_pred             chhhhhhhcchh
Confidence            655443333333

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

Probab=97.59  E-value=0.00031  Score=55.18  Aligned_cols=62  Identities=16%  Similarity=0.368  Sum_probs=49.9

Q ss_pred             HHHHhhccCCeeEEEEEecCC---CCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           50 LKEAFSNFGDITEAKVITERE---SGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        50 l~~~f~~~g~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ++.-+.+||.|..|.++++..   ..-..|-.||+|.+.+++++|++.|+|.+|.++.+.+.+..
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            344466889999998887622   22345779999999999999999999999999999888754

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

Probab=97.54  E-value=0.0003  Score=38.67  Aligned_cols=52  Identities=25%  Similarity=0.396  Sum_probs=40.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHH
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ   92 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai   92 (147)
                      +.|-|.+.+++.. +.+...|.++|.|..+.+...      ....+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            4677888887665 455668889999999877632      238999999999999985

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.54  E-value=0.00085  Score=37.98  Aligned_cols=54  Identities=19%  Similarity=0.284  Sum_probs=45.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhcc---CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHh
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNF---GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM   95 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~---g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l   95 (147)
                      ..|+|.++. +.+.++|+.+|..|   ....+|.|+.|.       .|-|.|.+.+.|.+||..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            578999986 47778999999998   246789999884       5999999999999998754

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

Probab=97.48  E-value=0.00075  Score=53.35  Aligned_cols=76  Identities=25%  Similarity=0.406  Sum_probs=60.1

Q ss_pred             CCeEEEcCCCCCCCH------HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEE
Q 032111           33 QTKLFVGGLSWGTDD------SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNI  105 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~------~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l  105 (147)
                      ...|.|.|+|---..      .-|..+|+++|.+..+.++.+.. ++.+||.|++|.+..+|+.|++.|||..+. .+..
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            457889999853221      24567899999999998887755 458999999999999999999999999884 5666


Q ss_pred             EEEe
Q 032111          106 RVSF  109 (147)
Q Consensus       106 ~v~~  109 (147)
                      .|..
T Consensus       137 ~v~~  140 (698)
T KOG2314|consen  137 FVRL  140 (698)
T ss_pred             Eeeh
Confidence            6643

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

Probab=97.43  E-value=0.00054  Score=53.46  Aligned_cols=67  Identities=24%  Similarity=0.301  Sum_probs=60.7

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhh-ccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHH
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFS-NFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA   94 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~   94 (147)
                      ..-++.+||||++||.-++-++|-.+|. -||.|..+-+-.|++-..++|-+=|.|.+.++-.+||.+
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            3456778999999999999999999998 699999999988888888999999999999999999984

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

Probab=97.31  E-value=0.0025  Score=42.21  Aligned_cols=77  Identities=23%  Similarity=0.416  Sum_probs=50.9

Q ss_pred             hCCCCCCeEEEcCCC----C--CCCH---HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC
Q 032111           28 FMSQSQTKLFVGGLS----W--GTDD---SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ   98 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp----~--~~~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~   98 (147)
                      .+-++..+|.|.=+.    .  ...+   .+|.+.|.+||.+.=+++..+        --+|+|.+-+.|.+|+. +++.
T Consensus        22 ~~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~   92 (146)
T PF08952_consen   22 SQGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGI   92 (146)
T ss_dssp             ----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCS
T ss_pred             hcCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCc
Confidence            344455677665333    1  1222   256777889998877777654        47999999999999999 8999


Q ss_pred             eeCCeEEEEEeecCC
Q 032111           99 ELNGRNIRVSFANDR  113 (147)
Q Consensus        99 ~~~g~~l~v~~~~~~  113 (147)
                      +++|+.|+|++.++-
T Consensus        93 ~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   93 QVNGRTLKIRLKTPD  107 (146)
T ss_dssp             EETTEEEEEEE----
T ss_pred             EECCEEEEEEeCCcc
Confidence            999999999886654

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.17  E-value=0.0019  Score=48.95  Aligned_cols=74  Identities=20%  Similarity=0.255  Sum_probs=56.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccC----CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFG----DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g----~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .|.+++||+++++.++.+||..-.    ..+.|.+++. .+++..|-|||.|..+++|+.|+.+ |...+.-+.|.+..+
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFRS  240 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHH
Confidence            466789999999999999997432    3345545544 5688899999999999999999995 766666666665443

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.12  E-value=0.004  Score=38.80  Aligned_cols=76  Identities=25%  Similarity=0.287  Sum_probs=49.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEE-EEecC------CCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE-E
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAK-VITER------ESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN-I  105 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~-~~~~~------~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~-l  105 (147)
                      ..|.|-+.|+. ....+.+.|++||.|.+.. +..+.      ..........|.|.+..+|++||. .|+..+.|.. +
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEEE
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEEE
Confidence            56778888877 5577889999999986653 00000      000112378999999999999999 5999998754 4


Q ss_pred             EEEeec
Q 032111          106 RVSFAN  111 (147)
Q Consensus       106 ~v~~~~  111 (147)
                      -|.+.+
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            576663

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.

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

Probab=97.09  E-value=0.004  Score=37.30  Aligned_cols=57  Identities=21%  Similarity=0.305  Sum_probs=42.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   96 (147)
                      ++..||--..|.++...||.++|..||.| .|.++.+.       .|||.....+.+..++..+.
T Consensus         7 ~RdHVFhltFPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    7 SRDHVFHLTFPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             SGCCEEEEE--TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             CcceEEEEeCchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            33455544599999999999999999976 56677663       79999999999999988776

; 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.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.92  E-value=0.00081  Score=54.42  Aligned_cols=79  Identities=18%  Similarity=0.090  Sum_probs=63.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITE-AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      +...+..|||..||..+++.++.++|.....|+. |.+... .+++.++.|||+|...+++..|...-+...+.-+.|+|
T Consensus       430 P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv  508 (944)
T KOG4307|consen  430 PGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRV  508 (944)
T ss_pred             CCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEe
Confidence            4456788999999999999999999998777766 555443 56788899999999988888888766666677777887


Q ss_pred             E
Q 032111          108 S  108 (147)
Q Consensus       108 ~  108 (147)
                      .
T Consensus       509 ~  509 (944)
T KOG4307|consen  509 D  509 (944)
T ss_pred             e
Confidence            5

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

Probab=96.82  E-value=0.008  Score=47.15  Aligned_cols=65  Identities=26%  Similarity=0.592  Sum_probs=49.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCC---Cccce---EEEEEeCCHHHHHHHHHHhc
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES---GKSRG---FGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g---~afv~f~~~~~a~~ai~~l~   96 (147)
                      .-.+.|||++||++++|+.|...|..||.+ .|.++.....   .-++|   |+|+.|+++..+..-|....
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            345789999999999999999999999964 4556532111   12456   99999999888888776544

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

Probab=96.76  E-value=0.0015  Score=53.83  Aligned_cols=79  Identities=23%  Similarity=0.342  Sum_probs=68.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ...++|+|+|+..|.+.++.++...|.+..+.++.. ..++++|.++|.|.+..++.++....+...+....+.|..+++
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            357899999999999999999999999988877665 4689999999999999999999888887777777777777665

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

Probab=96.75  E-value=0.0081  Score=44.14  Aligned_cols=63  Identities=21%  Similarity=0.321  Sum_probs=49.7

Q ss_pred             HHHHHHhhccCCeeEEEEEecCCCCcc-ceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           48 SSLKEAFSNFGDITEAKVITERESGKS-RGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        48 ~~l~~~f~~~g~i~~~~~~~~~~~~~~-~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .++++-+++||.|..|.+..++..... ..-.||+|...++|.+|+-.||+..|.|+.+..++.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            467888999999998876655332222 234799999999999999999999999998876654

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

Probab=96.55  E-value=0.0015  Score=46.92  Aligned_cols=54  Identities=26%  Similarity=0.431  Sum_probs=43.4

Q ss_pred             ccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           56 NFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        56 ~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +||.|+.+.+..+ --....|=++|.|...++|++|++.||+.-+.|++|.+.+.
T Consensus        92 kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   92 KYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             Hhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            7898888755432 12233567999999999999999999999999999988764

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.55  E-value=0.032  Score=45.79  Aligned_cols=62  Identities=13%  Similarity=0.209  Sum_probs=45.5

Q ss_pred             CCCCCHHHHHHHhhccCCe-----eEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           42 SWGTDDSSLKEAFSNFGDI-----TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        42 p~~~~~~~l~~~f~~~g~i-----~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ...++..+|..++..-+.|     -.|.+..        .|.||+.. ...+...+..|.+..+.++.|.|+.++.
T Consensus       496 ~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~--------~~s~v~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        496 DDGVEVRHIVGAIANEGDISSRYIGNIKLFA--------SHSTIELP-KGMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             ccCCCHHHHHHHHHhhcCCChhhCCcEEEeC--------CceEEEcC-hhhHHHHHHHhccccccCCceEEEECCC
Confidence            3457778888877665544     3344433        28899987 4668889999999999999999998753

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=96.16  E-value=0.072  Score=33.80  Aligned_cols=68  Identities=18%  Similarity=0.207  Sum_probs=48.1

Q ss_pred             CCeEEEcCCCCCC-CHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           33 QTKLFVGGLSWGT-DDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        33 ~~~i~v~nlp~~~-~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      ...+.+-.+|+.+ +.++|..+...+- .|..++++++..  .++-.+++.|.+.+.|......+||+.++.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3455555555554 4455555555443 577788888643  356789999999999999999999998854

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

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

Probab=96.11  E-value=0.014  Score=46.15  Aligned_cols=79  Identities=16%  Similarity=0.215  Sum_probs=51.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhh-ccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC----CeEEEE
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFS-NFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN----GRNIRV  107 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~----g~~l~v  107 (147)
                      .+++.|.|+|...|..-|....+ ..+.-.++.++.|-.+.++.|||||.|.+.+++..+.++.|++.+.    .+.+.+
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            34455555554433332222221 2345566777777677788899999999999999999999999763    344566


Q ss_pred             Eeec
Q 032111          108 SFAN  111 (147)
Q Consensus       108 ~~~~  111 (147)
                      .|++
T Consensus       468 tYAr  471 (549)
T KOG4660|consen  468 TYAR  471 (549)
T ss_pred             ehhh
Confidence            6654

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

Probab=96.07  E-value=0.0067  Score=48.45  Aligned_cols=74  Identities=20%  Similarity=0.333  Sum_probs=57.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee---CCeEEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF-GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL---NGRNIRV  107 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~---~g~~l~v  107 (147)
                      ..+.|+|.||-.-.|.-+|+.++... |.|... |+-.     .+..|||.|.+.++|.+...+||+..|   +.+.|-+
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDk-----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDK-----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-HHHH-----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            45689999998889999999999864 455544 4432     234799999999999999999999988   4566666


Q ss_pred             Eeec
Q 032111          108 SFAN  111 (147)
Q Consensus       108 ~~~~  111 (147)
                      .+..
T Consensus       517 df~~  520 (718)
T KOG2416|consen  517 DFVR  520 (718)
T ss_pred             eecc
Confidence            6643

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

Probab=96.05  E-value=0.00034  Score=57.45  Aligned_cols=65  Identities=28%  Similarity=0.394  Sum_probs=56.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ   98 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~   98 (147)
                      .++|++||++.+.+.+|...|..++.+..+++......+..+|+||++|...+.+.+|+......
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~  732 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSC  732 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhh
Confidence            46899999999999999999999998888777655677889999999999999999999955543

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

Probab=95.89  E-value=0.014  Score=48.71  Aligned_cols=75  Identities=31%  Similarity=0.494  Sum_probs=64.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~  108 (147)
                      ...+.+++.+|+..+....+...|..||.|..|.+-+..      .||++.|.+...++.|+..|-+..|.+  +.+.|.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq------~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ------PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC------cceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            345789999999999999999999999999988775543      499999999999999999999999965  567777


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      ++.
T Consensus       527 la~  529 (975)
T KOG0112|consen  527 LAS  529 (975)
T ss_pred             ccc
Confidence            765

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.84  E-value=0.0085  Score=46.14  Aligned_cols=75  Identities=24%  Similarity=0.413  Sum_probs=57.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC-eeCCeEEEEEeecC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ-ELNGRNIRVSFAND  112 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~-~~~g~~l~v~~~~~  112 (147)
                      ..+|++||.+..+..++..+|.....-..-.++..      .+|+||+..+..-+.+|++.+++. ++.|.++.+...-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            36899999999999999999987532111112221      369999999999999999999877 67888888887765


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      +.
T Consensus        76 kk   77 (584)
T KOG2193|consen   76 KK   77 (584)
T ss_pred             HH
Confidence            44

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.76  E-value=0.029  Score=44.71  Aligned_cols=69  Identities=13%  Similarity=0.217  Sum_probs=52.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC--eeCCeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ--ELNGRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~--~~~g~~l~  106 (147)
                      ..++.|.|+-||..+..++++.+|..-.  .+..|.+-.+.       -.||+|++.++|+.|.+.|...  +|.|++|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            4567788899999999999999998632  45566665553       3799999999999998876532  56666653

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.71  E-value=0.024  Score=40.92  Aligned_cols=62  Identities=27%  Similarity=0.440  Sum_probs=54.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   96 (147)
                      ..|||.||+.-++.+.+.+.|+.|+.|..-.++.| ..++..+-.+|+|...-.+.+|+..+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            67999999999999999999999999988666665 457788899999999999999999764

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.63  E-value=0.021  Score=43.55  Aligned_cols=75  Identities=16%  Similarity=0.233  Sum_probs=57.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCC---CccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES---GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..|-|.||.+.++.++++.+|.-.|.|..+.|+.....   ....-.|||.|.+.+.+..| ++|.++.+-+.-|.|-.
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~va-QhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVA-QHLTNTVFVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHH-hhhccceeeeeeEEEEe
Confidence            37889999999999999999999999999887653221   22345899999998887766 45788887776655543

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.62  E-value=0.019  Score=39.54  Aligned_cols=80  Identities=15%  Similarity=0.114  Sum_probs=48.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhc-cCCe---eEEEEEec--CCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC---
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSN-FGDI---TEAKVITE--RESGKSRGFGFVTYDSNESASSAQSAMDGQELNG---  102 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~-~g~i---~~~~~~~~--~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g---  102 (147)
                      ....|.|++||+.++++++.+.+.. ++.-   ..+.-...  ........-|||.|.+.+++...+..+++..|.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            3468999999999999998886555 3322   33331121  1111223579999999999999999999987743   


Q ss_pred             --eEEEEEeec
Q 032111          103 --RNIRVSFAN  111 (147)
Q Consensus       103 --~~l~v~~~~  111 (147)
                        ....|+++-
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence              334555553

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=95.49  E-value=0.1  Score=30.47  Aligned_cols=59  Identities=25%  Similarity=0.414  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHhhccCC-----eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           43 WGTDDSSLKEAFSNFGD-----ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        43 ~~~~~~~l~~~f~~~g~-----i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ..++..+|..++...+.     |-.|.+...        |+||+... +.++.++..|++..+.|+++.|+.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45677888888877643     445555433        89998875 5888999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=95.44  E-value=0.024  Score=42.65  Aligned_cols=6  Identities=50%  Similarity=1.370  Sum_probs=2.8

Q ss_pred             CCCCCC
Q 032111          142 GGDDGF  147 (147)
Q Consensus       142 ~~~~g~  147 (147)
                      |||+||
T Consensus       455 ggrg~y  460 (465)
T KOG3973|consen  455 GGRGGY  460 (465)
T ss_pred             CCCccc
Confidence            344444

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.22  E-value=0.0066  Score=45.22  Aligned_cols=78  Identities=24%  Similarity=0.410  Sum_probs=57.7

Q ss_pred             CeEEEcCCCCCCCHHHH---HHHhhccCCeeEEEEEecCC---CCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           34 TKLFVGGLSWGTDDSSL---KEAFSNFGDITEAKVITERE---SGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l---~~~f~~~g~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .-+||-+|+.....+.+   .+.|.+||.|..|.+..+..   .......++|+|...++|..+|...++..+.++.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            45778888877655544   34688999999987766541   1123345999999999999999999999888887666


Q ss_pred             Eeec
Q 032111          108 SFAN  111 (147)
Q Consensus       108 ~~~~  111 (147)
                      .+..
T Consensus       158 ~~gt  161 (327)
T KOG2068|consen  158 SLGT  161 (327)
T ss_pred             hhCC
Confidence            5543

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.64  E-value=0.19  Score=39.23  Aligned_cols=68  Identities=13%  Similarity=0.253  Sum_probs=57.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      ...|.|-.+|..++..||..|+..+- .|..++++++...  ++-..++.|.+.++|......+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            67899999999999999999988754 5888999986432  34579999999999999999999998864

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.57  E-value=0.43  Score=31.70  Aligned_cols=72  Identities=22%  Similarity=0.247  Sum_probs=50.2

Q ss_pred             CCeEEEcCCCCCC----CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           33 QTKLFVGGLSWGT----DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        33 ~~~i~v~nlp~~~----~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      -.+|.|+=|..++    +...+...++.||.|.+|.+.=.       ..|.|.|.+..+|=+|+.+++. ...|..+.+.
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            3567776444433    22344555778999999865422       3699999999999999998885 5667777777


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      |-..
T Consensus       158 Wqqr  161 (166)
T PF15023_consen  158 WQQR  161 (166)
T ss_pred             cccc
Confidence            7554

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

Probab=94.06  E-value=0.05  Score=45.38  Aligned_cols=74  Identities=30%  Similarity=0.391  Sum_probs=59.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee--CCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL--NGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~--~g~~l~v~~~~  111 (147)
                      .+.++.|.+-..+...|..+|.+||.+......++-.      .|.|+|.+.+.|..|+++|+|+.+  -|-+.+|.+++
T Consensus       299 p~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak  372 (1007)
T KOG4574|consen  299 PKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAK  372 (1007)
T ss_pred             chhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecc
Confidence            3445556666778888999999999999987767643      799999999999999999999976  46678888877


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      .-
T Consensus       373 ~~  374 (1007)
T KOG4574|consen  373 TL  374 (1007)
T ss_pred             cc
Confidence            53

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

Probab=93.85  E-value=0.043  Score=42.88  Aligned_cols=68  Identities=25%  Similarity=0.383  Sum_probs=53.2

Q ss_pred             EcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           38 VGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        38 v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      +.-.|+. -+.++|...|.+||.|..|.+-...      ..|.|+|.+..+|-.|.. .++..|+++.|+|.|-++
T Consensus       377 lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  377 LEKSPFGLNTIADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhccCCCCchHhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            3333443 3557899999999999998775442      269999999999977766 588999999999999875

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

Probab=93.62  E-value=0.32  Score=36.11  Aligned_cols=68  Identities=24%  Similarity=0.300  Sum_probs=49.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE-EEEEeec
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN-IRVSFAN  111 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~-l~v~~~~  111 (147)
                      |.|-+.|+.-. .-|...|.+||.|.+......-      -+-+|.|.+..+|++||. .++..|++.. |-|+.+.
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ng------NwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNG------NWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeecCCCC------ceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            44456665433 5677889999998876554221      278999999999999999 5999887654 4566543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.45  E-value=0.068  Score=43.35  Aligned_cols=73  Identities=15%  Similarity=0.241  Sum_probs=60.1

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .+.++..++||+|+...+..+-++.++..+|.|..+..  .       -|+|.+|..+.....|+..++...+++..+.+
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr--~-------~fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~  105 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKR--D-------KFGFCEFLKHIGDLRASRLLTELNIDDQKLIE  105 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhh--h-------hhcccchhhHHHHHHHHHHhcccCCCcchhhc
Confidence            34456689999999999999999999999998766432  2       18999999999999999999988888877766


Q ss_pred             Ee
Q 032111          108 SF  109 (147)
Q Consensus       108 ~~  109 (147)
                      ..
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            54

>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=93.23  E-value=0.91  Score=26.03  Aligned_cols=55  Identities=13%  Similarity=0.275  Sum_probs=42.0

Q ss_pred             CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           44 GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        44 ~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .++-++++.-|..|. ...|.  .++ +     --||.|.+..+|+++....++..+-...+.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~--~d~-t-----GfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIR--DDR-T-----GFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEE--ecC-C-----EEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            357789999999995 44443  332 2     4689999999999999999998887776654

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

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

Probab=93.19  E-value=0.019  Score=47.94  Aligned_cols=78  Identities=21%  Similarity=0.371  Sum_probs=61.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|++||+..+++.+|...|..+|.|..|.+....-.. ---|+||.|.+.+.+-.|...+.+..|..-.+++.+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~-esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKT-ESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCc-ccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            45789999999999999999999999999888775542211 2248999999999999998888888775444444444

>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=93.13  E-value=0.55  Score=32.61  Aligned_cols=61  Identities=26%  Similarity=0.383  Sum_probs=43.1

Q ss_pred             CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEEEeecC
Q 032111           46 DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD--GQELNGRNIRVSFAND  112 (147)
Q Consensus        46 ~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--~~~~~g~~l~v~~~~~  112 (147)
                      ..+.|+++|..++.+..+...+.-      .=..|.|.+.+.|.+|...|+  +..+.+..+++.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            447889999999987776555431      247899999999999999999  8999999999987743

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.

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=89.11  E-value=0.52  Score=35.77  Aligned_cols=8  Identities=50%  Similarity=1.074  Sum_probs=3.7

Q ss_pred             CCCCCCCC
Q 032111          140 YRGGDDGF  147 (147)
Q Consensus       140 ~~~~~~g~  147 (147)
                      ++||++||
T Consensus       377 G~GGGggy  384 (465)
T KOG3973|consen  377 GRGGGGGY  384 (465)
T ss_pred             CCCCCCCC
Confidence            33444555

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=88.51  E-value=0.31  Score=36.23  Aligned_cols=76  Identities=22%  Similarity=0.187  Sum_probs=57.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ..++.|++++.+.+.+.+...++..+|......+........+++++++.|...+.+..++.......+.+..+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~  162 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEK  162 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccC
Confidence            3567889999888888888888888887766656555556778899999999999999999954433444444333

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=83.64  E-value=4.4  Score=30.16  Aligned_cols=47  Identities=15%  Similarity=0.099  Sum_probs=35.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEEecCCCCccceEEEEEeCCH
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGD-ITEAKVITERESGKSRGFGFVTYDSN   85 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~afv~f~~~   85 (147)
                      ...|++.|||.++.-.+|+..+.+.+- ..++.|      ..+.+-||+.|.+.
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~  377 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNR  377 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCc
Confidence            456999999999999999999988653 344433      34456899999654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=83.23  E-value=0.31  Score=37.49  Aligned_cols=67  Identities=15%  Similarity=0.107  Sum_probs=51.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN  101 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~  101 (147)
                      +....+++|.+|+..+...++.++|..+|.+....|-.    +-...+|.++|........|+. +++..+.
T Consensus       148 eeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  148 EEIRRTREVQSLISAAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             HHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            33447899999999999999999999999887665533    2223478899998888888888 5666553

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=80.80  E-value=0.16  Score=39.41  Aligned_cols=74  Identities=15%  Similarity=0.335  Sum_probs=59.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEe-cCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVIT-ERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~-~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.+-|.|+|+...|+-+..++.+|+.+..+.... +..    .-..-|+|.+.+.+..+|.+|++..+...-+++.+-.
T Consensus        81 rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e----tavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   81 RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE----TAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH----HHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            4578899999999999999999999998875532 222    1245577889999999999999999988888887753

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=80.12  E-value=3.5  Score=23.82  Aligned_cols=61  Identities=15%  Similarity=0.250  Sum_probs=42.8

Q ss_pred             HHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           48 SSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        48 ~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      .+|++.|...| .+.++..+....+..+.-.-+|+.....+...   .|+=.+++++.+.|+...
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~   63 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPH   63 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCc
Confidence            46778888888 57788777776666677788888876544443   344457788888777654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	147
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-17
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-13
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		3e-13
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		5e-13
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		7e-13
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		7e-13
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		7e-13
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		8e-13
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		1e-12
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-12
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		7e-12
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-11
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-11
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-11
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		4e-11
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		6e-11
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		7e-11
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-10
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-10
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		3e-10
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		5e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-10
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-10
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-10
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-10
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		7e-10
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		8e-10
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-10
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-10
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-09
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		1e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-09
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-09
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-09
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		3e-09
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		3e-09
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		4e-09
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		4e-09
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		5e-09
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		6e-09
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		7e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		7e-09
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		2e-08
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-08
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-08
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-08
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-08
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-08
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		4e-08
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		4e-08
3q2s_C	229	Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX Lengt		4e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		7e-08
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		7e-08
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		8e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-07
3p5t_L	90	Cfim25-Cfim68 Complex Length = 90		1e-07
2khc_A	118	Bruno Rrm3+ Length = 118		1e-07
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		2e-07
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-07
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		2e-07
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-07
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		3e-07
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		3e-07
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		3e-07
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		4e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		4e-07
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-07
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		5e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-07
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		6e-07
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		9e-07
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		9e-07
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		9e-07
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-06
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-06
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-06
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		3e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		3e-06
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-06
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		6e-06
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		7e-06
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-05
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		1e-05
2lcw_A	116	Solution Structure Of FusTLS RRM DOMAIN Length = 11		1e-05
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		1e-05
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		1e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		1e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-05
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		2e-05
2la6_A	99	Solution Nmr Structure Of Rrm Domain Of Rna-Binding		2e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-05
3n9u_C	156	Crystal Structure Of The Complex Between The 25 Kda		2e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-05
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-05
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		2e-05
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-05
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		4e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		4e-05
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		4e-05
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		5e-05
2la4_A	101	Nmr Structure Of The C-Terminal Rrm Domain Of Poly(		5e-05
1x4h_A	111	Solution Structure Of Rrm Domain In Rna-Binding Pro		5e-05
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		6e-05
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		6e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		7e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		7e-05
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		8e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		8e-05
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		8e-05
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		8e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		8e-05
1why_A	97	Solution Structure Of The Rna Recognition Motif Fro		9e-05
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-04
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		1e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		1e-04
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		2e-04
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		2e-04
2fc9_A	101	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		2e-04
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		2e-04
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		2e-04
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		2e-04
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		3e-04
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		3e-04
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		3e-04
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		3e-04
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		4e-04
2cpe_A	113	Solution Structure Of The Rna Recognition Motif Of		4e-04

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 82.8 bits (203), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 39/82 (47%), Positives = 60/82 (73%)
Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M+  + KLFVGGLS+ T++ SL++ FS +G I+E  V+ +RE+ +SRGFGFVT+++ + A
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 89  SSAQSAMDGQELNGRNIRVSFA 110
             A  AM+G+ ++GR IRV  A
Sbjct: 68  KDAMMAMNGKSVDGRQIRVDQA 89

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/85 (43%), Positives = 55/85 (64%), Gaps = 7/85 (8%)
Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA-- 91
           TK+FVGGL + T D+SL++ F  FGDI EA VIT+R++GKSRG+GFVT     +A  A  
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 92  --QSAMDGQELNGRNIRVSFANDRP 114
                +DG++    N+ +++   +P
Sbjct: 78  DPNPIIDGRKA---NVNLAYLGAKP 99

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/82 (42%), Positives = 51/82 (62%)
Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M+ ++  L+VGGL+   DD  L  AF  FGDIT+ ++  + E+ K RGF FV ++  E A
Sbjct: 3   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 89  SSAQSAMDGQELNGRNIRVSFA 110
           ++A   M+  EL GR IRV+ A
Sbjct: 63  AAAIDNMNESELFGRTIRVNLA 84

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 69.7 bits (169), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 50/75 (66%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L+   DD +L+ AF +F       V+ + ++G SRG+GFV++ S + A +A  +M
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 96  DGQELNGRNIRVSFA 110
            GQ+LNGR +R+++A
Sbjct: 150 QGQDLNGRPLRINWA 164

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 69.3 bits (168), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/82 (42%), Positives = 51/82 (62%)
Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M+ ++  L+VGGL+   DD  L  AF  FGDIT+ ++  + E+ K RGF FV ++  E A
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 89  SSAQSAMDGQELNGRNIRVSFA 110
           ++A   M+  EL GR IRV+ A
Sbjct: 68  AAAIDNMNESELFGRTIRVNLA 89

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 69.3 bits (168), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 49/79 (62%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+  L+VGGL+   DD  L  AF  FGDIT+ ++  + E+ K RGF FV ++  E A++A
Sbjct: 1   SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 92  QSAMDGQELNGRNIRVSFA 110
              M+  EL GR IRV+ A
Sbjct: 61  IDNMNESELFGRTIRVNLA 79

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 69.3 bits (168), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 50/75 (66%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFVG L+   DD +L+ AF +F       V+ + ++G SRG+GFV++ S + A +A  +M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 96  DGQELNGRNIRVSFA 110
            GQ+LNGR +R+++A
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 69.3 bits (168), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 50/81 (61%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S ++  L+VGGL+   DD  L  AF  FGDIT+ ++  + E+ K RGF FV ++  E A+
Sbjct: 2   STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 90  SAQSAMDGQELNGRNIRVSFA 110
           +A   M+  EL GR IRV+ A
Sbjct: 62  AAIDNMNESELFGRTIRVNLA 82

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 68.6 bits (166), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 47/75 (62%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VGGL+   DD  L  AF  FGDIT+ ++  + E+ K RGF FV ++  E A++A   M
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 96  DGQELNGRNIRVSFA 110
           +  EL GR IRV+ A
Sbjct: 126 NESELFGRTIRVNLA 140

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 67.0 bits (162), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 51/80 (63%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS       +K AF+ FG I++A+V+ +  +GKS+G+GFV++ +   A +A   M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 96  DGQELNGRNIRVSFANDRPP 115
            GQ L GR IR ++A  +PP
Sbjct: 78  GGQWLGGRQIRTNWATRKPP 97

>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 = 66.2 bits (160), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 51/80 (63%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVG LS       +K AF+ FG I++A+V+ +  +GKS+G+GFV++ +   A +A   M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 96  DGQELNGRNIRVSFANDRPP 115
            GQ L GR IR ++A  +PP
Sbjct: 78  GGQWLGGRQIRTNWATRKPP 97

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 50/80 (62%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V GLS  T +  L+E FS +G I +  ++ +++S +SRGF FV +++ + A  A+   
Sbjct: 15  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +G EL+GR IRV F+  + P
Sbjct: 75  NGMELDGRRIRVDFSITKRP 94

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 50/80 (62%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V GLS  T +  L+E FS +G I +  ++ +++S +SRGF FV +++ + A  A+   
Sbjct: 49  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +G EL+GR IRV F+  + P
Sbjct: 109 NGMELDGRRIRVDFSITKRP 128

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 63.9 bits (154), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 53/84 (63%), Gaps = 3/84 (3%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           SQ    LFV GLS  T + +LKE+F        A+++T+RE+G S+GFGFV ++S E A 
Sbjct: 12  SQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 90  SAQSAMDGQELNGRNIRVSFANDR 113
           +A+ AM+  E++G  + + +A  +
Sbjct: 69  AAKEAMEDGEIDGNKVTLDWAKPK 92

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 63.5 bits (153), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 50/80 (62%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V GLS  T +  L+E FS +G I +  ++ +++S +SRGF FV +++ + A  A+   
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +G EL+GR IRV F+  + P
Sbjct: 78  NGMELDGRRIRVDFSITKRP 97

>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 = 62.8 bits (151), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 49/82 (59%)
Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           + +S   +FVG + +   +  LK+ FS  G +   +++ +RE+GK +G+GF  Y   E+A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 89  SSAQSAMDGQELNGRNIRVSFA 110
            SA   ++G+E +GR +RV  A
Sbjct: 64  LSAMRNLNGREFSGRALRVDNA 85

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 62.8 bits (151), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 52/90 (57%), Gaps = 10/90 (11%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGL+  T++  LK  F   G I+E  +I +R S KSRGF F+T+++   A +A   
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKD 67
Query: 95  MDGQELNGRNIRVSFAND---------RPP 115
           M+G+ L+G+ I+V  A           RPP
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSGGRRRPP 97

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

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VG L +      +KE FS FG +   K+I +RE+ K +GFGFV     ES S A + +
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 96  DGQELNGRNIRVSFANDR 113
           D  +  GR IRV+ AN +
Sbjct: 63  DNTDFMGRTIRVTEANPK 80

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 49/78 (62%), Gaps = 2/78 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V  L  G DD  L++AFS FG IT AKV+   E G+S+GFGFV + S E A+ A + M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 96  DGQELNGRNIRVSFANDR 113
           +G+ +  + + V+ A  +
Sbjct: 76  NGRIVATKPLYVALAQRK 93

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 60.8 bits (146), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 47/73 (64%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V GLS  T +  L+E FS +G I +  ++ +++S +SRGF FV +++ + A  A+   
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96  DGQELNGRNIRVS 108
           +G EL+GR IRVS
Sbjct: 78  NGMELDGRRIRVS 90

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           +  T L V  L++ T   +L+  F  +G + +  +  +R + +SRGF FV +     A  
Sbjct: 45  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 91  AQSAMDGQELNGRNIRVSFAN-DRPP 115
           A  AMDG  L+GR +RV  A   RPP
Sbjct: 105 AMDAMDGAVLDGRELRVQMARYGRPP 130

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 59.7 bits (143), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 48/84 (57%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S    +L+VG L +   +  L+  F  FG I   +++ + E+G+S+G+GF+T+  +E A 
Sbjct: 23  SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 90  SAQSAMDGQELNGRNIRVSFANDR 113
            A   ++G EL GR ++V    +R
Sbjct: 83  KALEQLNGFELAGRPMKVGHVTER 106

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 59.7 bits (143), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 51/99 (51%), Gaps = 10/99 (10%)
Query: 12  RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES 71
           R++ Q P A L         +  K+FVGG+   T++  L++ F  +G I   +++T+R S
Sbjct: 90  REDSQRPGAHL---------TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 140
Query: 72  GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           GK RGF FVT+D ++S            +NG N  V  A
Sbjct: 141 GKKRGFAFVTFDDHDSVDKI-VIQKYHTVNGHNCEVRKA 178

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 59.7 bits (143), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 51/99 (51%), Gaps = 10/99 (10%)
Query: 12  RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES 71
           R++ Q P A L         +  K+FVGG+   T++  L++ F  +G I   +++T+R S
Sbjct: 85  REDSQRPGAHL---------TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 135
Query: 72  GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           GK RGF FVT+D ++S            +NG N  V  A
Sbjct: 136 GKKRGFAFVTFDDHDSVDKI-VIQKYHTVNGHNCEVRKA 173

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 59.3 bits (142), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 51/99 (51%), Gaps = 10/99 (10%)
Query: 12  RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES 71
           R++ Q P A L         +  K+FVGG+   T++  L++ F  +G I   +++T+R S
Sbjct: 92  REDSQRPGAHL---------TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 142
Query: 72  GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           GK RGF FVT+D ++S            +NG N  V  A
Sbjct: 143 GKKRGFAFVTFDDHDSVDKI-VIQKYHTVNGHNCEVRKA 180

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 59.3 bits (142), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 51/96 (53%), Gaps = 3/96 (3%)
Query: 22  LINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVT 81
           L+     M  S  K+F+GGLSW T    L+E F  FG++ E  V+ +  + +SRGFGFVT
Sbjct: 14  LVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73
Query: 82  YDSNESASSAQSAMDGQELNGRNI--RVSFANDRPP 115
           +  +++      A    EL+ + I  +V+F     P
Sbjct: 74  F-MDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQP 108

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

Iteration: 1
 Score = 59.3 bits (142), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 48/76 (63%), Gaps = 3/76 (3%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           +   K+F+GGL+W T + +L+E F  +G +T+ K++ +  +G+SRGFGF++++   S   
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 91  A---QSAMDGQELNGR 103
               Q  +DG+ ++ +
Sbjct: 61  VVKTQHILDGKVIDPK 76

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 59.3 bits (142), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 51/99 (51%), Gaps = 10/99 (10%)
Query: 12  RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES 71
           R++ Q P A L         +  K+FVGG+   T++  L++ F  +G I   +++T+R S
Sbjct: 92  REDSQRPGAHL---------TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 142
Query: 72  GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           GK RGF FVT+D ++S            +NG N  V  A
Sbjct: 143 GKKRGFAFVTFDDHDSVDKI-VIQKYHTVNGHNCEVRKA 180

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 58.9 bits (141), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 51/99 (51%), Gaps = 10/99 (10%)
Query: 12  RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES 71
           R++ Q P A L         +  K+FVGG+   T++  L++ F  +G I   +++T+R S
Sbjct: 91  REDSQRPGAHL---------TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 141
Query: 72  GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           GK RGF FVT+D ++S            +NG N  V  A
Sbjct: 142 GKKRGFAFVTFDDHDSVDKI-VIQKYHTVNGHNCEVRKA 179

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           +  T L V  L++ T   +L+  F  +G + +  +  +R + +SRGF FV +     A  
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 91  AQSAMDGQELNGRNIRVSFAN-DRPP 115
           A  AMDG  L+GR +RV  A   RPP
Sbjct: 128 AMDAMDGAVLDGRELRVQMARYGRPP 153

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 46/73 (63%), Gaps = 5/73 (6%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K FVGGLSW T    LK+ F+ FG++ +  +  +  +G+SRGFGF+ +   + A+S +  
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKV 69
Query: 95  MDGQE--LNGRNI 105
           +D +E  L+GR I
Sbjct: 70  LDQKEHRLDGRVI 82

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 58.9 bits (141), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 51/99 (51%), Gaps = 10/99 (10%)
Query: 12  RQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES 71
           R++ Q P A L         +  K+FVGG+   T++  L++ F  +G I   +++T+R S
Sbjct: 93  REDSQRPGAHL---------TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 143
Query: 72  GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
           GK RGF FVT+D ++S            +NG N  V  A
Sbjct: 144 GKKRGFAFVTFDDHDSVDKI-VIQKYHTVNGHNCEVRKA 181

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 44/72 (61%), Gaps = 5/72 (6%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+GGLSW T    LK+ FS FG++ +  +  +  +G+SRGFGFV +  +ES       M
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD---KVM 58
Query: 96  DGQE--LNGRNI 105
           D +E  LNG+ I
Sbjct: 59  DQKEHKLNGKVI 70

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLFVGGL W T   +L+  FS +G++ +  ++ ++ + +SRGFGFV +       +  ++
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 95  MDGQELNGRNI 105
                L+GRNI
Sbjct: 78  RP-HTLDGRNI 87

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 41/78 (52%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  +++ T +S L+  F  +G I    ++  + SGK RG+ F+ Y+      SA    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96  DGQELNGRNIRVSFANDR 113
           DG++++GR + V     R
Sbjct: 165 DGKKIDGRRVLVDVERGR 182

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/82 (39%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 24  NAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYD 83
           + V        KLFVG +  G D+  LK  F  FG I E  V+ +R +G  +G  F+TY 
Sbjct: 6   SGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYC 65
Query: 84  SNESASSAQSAMDGQE-LNGRN 104
           + +SA  AQSA+  Q+ L G N
Sbjct: 66  ARDSALKAQSALHEQKTLPGMN 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 57.0 bits (136), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 40/76 (52%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  L++ T   SL+  F  +G + +  +  E  +   RGF FV +     A  A++AM
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 96  DGQELNGRNIRVSFAN 111
           DG EL+GR +RV  A 
Sbjct: 76  DGAELDGRELRVQVAR 91

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGG+     ++ L+E F  FG +TE  +I + E  + RGFGF+T++  +S   A + 
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70
Query: 95  MDGQELNGRNIRVSFANDR 113
           M   ++ G+ + V  A  R
Sbjct: 71  MHFHDIMGKKVEVKRAEPR 89

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 56.6 bits (135), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 46/78 (58%), Gaps = 3/78 (3%)
Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            K+F+GGLSW T    L+E F  FG++ E  V+ +  + +SRGFGFVT+  +++      
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF-MDQAGVDKVL 59
Query: 94  AMDGQELNGRNI--RVSF 109
           A    EL+ + I  +V+F
Sbjct: 60  AQSRHELDSKTIDPKVAF 77

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 56.2 bits (134), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 52/83 (62%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S   +FVG LS     +++  AF+ FG I++A+V+ +  +GKS+G+GFV++ +   A +A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64
Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
              M GQ L GR IR ++A  +P
Sbjct: 65  IQQMGGQWLGGRQIRTNWATRKP 87

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 56.2 bits (134), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 33/80 (41%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+G +    D+  LK  F  FG I E  V+ +R +G  +G  F+TY   ESA  AQSA
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 95  MDGQE-LNG--RNIRVSFAN 111
           +  Q+ L G  R I+V  A+
Sbjct: 75  LHEQKTLPGMNRPIQVKPAD 94

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 55.8 bits (133), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 47/84 (55%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S   + L+VG L +   +  L+  F  FG I    ++ + ++G+S+G+GF+T+  +E A 
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 90  SAQSAMDGQELNGRNIRVSFANDR 113
            A   ++G EL GR +RV    +R
Sbjct: 62  RALEQLNGFELAGRPMRVGHVTER 85

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 41/78 (52%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  +++ T +S L+  F  +G I    ++  + SGK RG+ F+ Y+      SA    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96  DGQELNGRNIRVSFANDR 113
           DG++++GR + V     R
Sbjct: 165 DGKKIDGRRVLVDVERGR 182

>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 = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +T L V  L        L+  FS+ G++  AK+I ++ +G S G+GFV Y + + A  A 
Sbjct: 4   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 93  SAMDGQELNGRNIRVSFANDRP 114
           + ++G  L  + I+VS+A  RP
Sbjct: 64  NTLNGLRLQSKTIKVSYA--RP 83

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  +    D+  L++ F  +G I   K++ +RE+ +SRG+GFV + S  SA  A + +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 96  DGQELNGRNIRVSFA---NDRP 114
           +G  +  + ++V+ A   + RP
Sbjct: 105 NGFNILNKRLKVALAASGHQRP 126

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L         K  F + GDI   K++ ++ +G+S G+GFV Y     A  A
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
            + ++G +L  + I+VS+A  RP
Sbjct: 63  INTLNGLKLQTKTIKVSYA--RP 83

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +T L V  L        L+  FS+ G++  AK+I ++ +G S G+GFV Y + + A  A 
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 93  SAMDGQELNGRNIRVSFANDRP 114
           + ++G  L  + I+VS+A  RP
Sbjct: 62  NTLNGLRLQSKTIKVSYA--RP 81

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +T L V  L        L+  FS+ G++  AK+I ++ +G S G+GFV Y + + A  A 
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 93  SAMDGQELNGRNIRVSFANDRP 114
           + ++G  L  + I+VS+A  RP
Sbjct: 62  NTLNGLRLQSKTIKVSYA--RP 81

>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 = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 2/81 (2%)
Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L V  L        L+  FS+ G++  AK+I ++ +G S G+GFV Y + + A  A +
Sbjct: 20  TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 94  AMDGQELNGRNIRVSFANDRP 114
            ++G  L  + I+VS+A  RP
Sbjct: 80  TLNGLRLQSKTIKVSYA--RP 98

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L         K  F + GDI   K++ ++ +G+S G+GFV Y     A  A
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
            + ++G +L  + I+VS+A  RP
Sbjct: 63  INTLNGLKLQTKTIKVSYA--RP 83

>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX Length = 229

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 47/95 (49%), Gaps = 2/95 (2%)
Query: 19  KASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRG 76
           K +  N V   +  +  L++G L+W T D  L EA  + G  DI E K    R +G+S+G
Sbjct: 54  KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113
Query: 77  FGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN 111
           F  V   S  S+      +  +EL+G+N  V+  N
Sbjct: 114 FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVN 148

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 44/71 (61%), Gaps = 1/71 (1%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGLS+ T + SL+  +  +G +T+  V+ +  S +SRGFGFVT+ S     +A +A
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 95  MDGQELNGRNI 105
                ++GR +
Sbjct: 89  RP-HSIDGRVV 98

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 52.8 bits (125), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEA-KVITERESGKSRGFGFVTYDSNESA 88
           S   + +F+G L    D+  L + FS FG I +  K++ + ++G S+G+ F+ + S +++
Sbjct: 2   SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 89  SSAQSAMDGQELNGRNIRVSFA 110
            +A  AM+GQ L  R I VS+A
Sbjct: 62  DAAIEAMNGQYLCNRPITVSYA 83

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 52.8 bits (125), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +LFV  LS+ + +  L++ FS +G ++E     +  + K +GF FVT+   E A  A + 
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 95  MDGQELNGRNIRV 107
           +DGQ   GR + V
Sbjct: 70  VDGQVFQGRMLHV 82

>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 = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  L    D+ +L + FS FG+I   KV+ + E+G S+G+GFV +++ E+A  A   M
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 158
Query: 96  DGQELNGRNIRV 107
           +G  LN R + V
Sbjct: 159 NGMLLNDRKVFV 170

>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex Length = 90

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           L++G L+W T D  L EA  + G  DI E K    R +G+S+GF  V   S  S+     
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 94  AMDGQELNGRNIRVSFAN 111
            +  +EL+G+N  V+ +N
Sbjct: 64  LLPKRELHGQNPVVTPSN 81

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 43/72 (59%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+  L     D+ L   F  FG++  AKV  ++++  S+ FGFV++D+ +SA  A  AM
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 96  DGQELNGRNIRV 107
           +G ++  + ++V
Sbjct: 103 NGFQVGTKRLKV 114

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S  + KLF+ GL +      L+E     G + + +++T R +GK +G  +V Y++   AS
Sbjct: 14  SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQAS 72
Query: 90  SAQSAMDGQELNGRNIRVSFANDRP 114
            A   MDG  +    I+V+ +N  P
Sbjct: 73  QAVMKMDGMTIKENIIKVAISNSGP 97

>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 = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  L    D+ +L + FS FG+I   KV+ + E+G S+G+GFV +++ E+A  A   M
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 163
Query: 96  DGQELNGRNIRV 107
           +G  LN R + V
Sbjct: 164 NGMLLNDRKVFV 175

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 47/80 (58%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  +     +  ++E F ++G+I    +  +R +G S+G+  V Y++++ A +A+ A+
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +G E+ G+ I+V +   + P
Sbjct: 89  NGAEIMGQTIQVDWCFVKGP 108

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  L    D+ +L + FS FG+I   KV+ + E+G S+G+GFV +++ E+A  A   M
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 96  DGQELNGRNIRV 107
           +G  LN R + V
Sbjct: 72  NGMLLNDRKVFV 83

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 3/78 (3%)
Query: 24 NAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFV--- 80
          + V+   Q  + L V GL W T +  LKE FS FG++   +V  + ++G S+GFGFV   
Sbjct: 6  SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
Query: 81 TYDSNESASSAQSAMDGQ 98
           Y++     S +  +DG+
Sbjct: 66 EYETQVKVMSQRHMIDGR 83

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           ++   +FVG L     +  L E F   G +T+  +  +RE GK + FGFV +   ES S 
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72
Query: 91  AQSAMDGQELNGRNIRVS 108
           A + ++G  L GR I VS
Sbjct: 73  AIALLNGIRLYGRPINVS 90

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  L    D+ +L + FS FG+I   KV+ + E+G S+G+GFV +++ E+A  A   M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 96  DGQELNGRNIRV 107
           +G  LN R + V
Sbjct: 66  NGMLLNDRKVFV 77

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 34/100 (34%), Positives = 54/100 (54%), Gaps = 6/100 (6%)
Query: 15  GQAPKASLINAVRFMSQSQTK-LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGK 73
           G  P+ S +N     ++SQ K L V  + +   D  L++ F  FG I + ++I   E G 
Sbjct: 13  GLVPRGSHMNT---ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG- 67
Query: 74  SRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR 113
           S+GFGFVT++++  A  A+  + G  + GR I V+ A  R
Sbjct: 68  SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 43/80 (53%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +++V  +     D  +K  F  FG I  A +  +  +GK +G+GF+ Y+  +S+  A S+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 95  MDGQELNGRNIRVSFANDRP 114
           M+  +L G+ +RV  A   P
Sbjct: 187 MNLFDLGGQYLRVGKAVTPP 206

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L         +  F + G+I   K++ ++ +G+S G+GFV Y   + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
            + ++G  L  + I+VS+A  RP
Sbjct: 61  INTLNGLRLQTKTIKVSYA--RP 81

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 21/75 (28%), Positives = 45/75 (60%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  +     +  ++E F ++G+I    +  +R +G S+G+  V Y++++ A +A+ A+
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 96  DGQELNGRNIRVSFA 110
           +G E+ G+ I+V + 
Sbjct: 135 NGAEIMGQTIQVDWC 149

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 42/73 (57%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +++VG + +   + ++++AF+ FG I    +  +  + K +GF FV Y+  E+A  A   
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 95  MDGQELNGRNIRV 107
           M+   L GRNI+V
Sbjct: 75  MNSVMLGGRNIKV 87

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 49.7 bits (117), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+V GL        +++ FS +G I  ++++ ++ +G SRG GF+ +D    A  A   +
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 96  DGQELNG--RNIRVSFAND 112
           +GQ+  G    I V FAN+
Sbjct: 64  NGQKPLGAAEPITVKFANN 82

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 44/78 (56%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LF+  L     D  L + F  FG++  AKV  ++++  S+ FGFV+YD+  SA +A  +M
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 96  DGQELNGRNIRVSFANDR 113
           +G ++  + ++V     +
Sbjct: 88  NGFQIGMKRLKVQLKRSK 105

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S     ++ GG++ G  D  +++ FS FG I E +V  E      +G+ FV + ++ESA+
Sbjct: 22  SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAA 75
Query: 90  SAQSAMDGQELNGRNIRVSFANDRP 114
            A  +++G  + G  ++  +  + P
Sbjct: 76  HAIVSVNGTTIEGHVVKCYWGKESP 100

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 48.9 bits (115), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +FVGGLS  T    +K  F  FG + +A ++ ++ + + RGFGFVT++S E        +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES-EDIVEKVCEI 60
Query: 96  DGQELNGRNIR 106
              E+N + + 
Sbjct: 61  HFHEINNKMVE 71

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VGGL     +  L E F   G +    +  +R +G+ +G+GFV + S E A  A   M
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 96  DGQELNGRNIRVSFA 110
           D  +L G+ IRV+ A
Sbjct: 78  DMIKLYGKPIRVNKA 92

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
            + +LFVG L     +   K  F  +G+ +E  +       + RGFGF+  +S   A  A
Sbjct: 21  QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIA 74
Query: 92  QSAMDGQELNGRNIRVSFAN 111
           ++ +DG  L  R +R+ FA 
Sbjct: 75  KAELDGTILKSRPLRIRFAT 94

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 43/80 (53%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV G+     +  + + F+ +G+I    +  +R +G  +G+  V Y++ + A +A   +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +GQ+L G+ I V +   R P
Sbjct: 70  NGQDLMGQPISVDWCFVRGP 89

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 43/80 (53%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV G+     +  + + F+ +G+I    +  +R +G  +G+  V Y++ + A +A   +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +GQ+L G+ I V +   R P
Sbjct: 70  NGQDLMGQPISVDWCFVRGP 89

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 43/80 (53%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV G+     +  + + F+ +G+I    +  +R +G  +G+  V Y++ + A +A   +
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +GQ+L G+ I V +   R P
Sbjct: 72  NGQDLMGQPISVDWCFVRGP 91

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 10/80 (12%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV  L+    +  L++AFS FG +   K        K + + F+ +D  + A  A   M
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 65
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +G++L G NI + FA  +PP
Sbjct: 66  NGKDLEGENIEIVFA--KPP 83

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 47.0 bits (110), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 43/80 (53%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV G+     +  + + F+ +G+I    +  +R +G  +G+  V Y++ + A +A   +
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 96  DGQELNGRNIRVSFANDRPP 115
           +GQ+L G+ I V +   R P
Sbjct: 86  NGQDLMGQPISVDWCFVRGP 105

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 40/73 (54%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +++VG + +   + ++++AF+ FG I       +  + K +GF FV Y+  E+A  A   
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 95  MDGQELNGRNIRV 107
            +   L GRNI+V
Sbjct: 74  XNSVXLGGRNIKV 86

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 47.0 bits (110), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +L V  + +   D  L++ F  FG I + ++I   E G S+GFGFVT++++  A  A+  
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERG-SKGFGFVTFENSADADRAREK 74
Query: 95  MDGQELNGRNIRVSFANDR 113
           + G  + GR I V+ A  R
Sbjct: 75  LHGTVVEGRKIEVNNATAR 93

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 34/60 (56%)
Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
          L++ GL  GT D  L +    +G I   K I ++ + K +G+GFV +DS  +A  A +A+
Sbjct: 8  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV G+     +  + + F+ +G+I    +  +R +G  +G+  V Y++ + A +A   +
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 96  DGQELNGRNIRVSFA 110
           +GQ+L G+ I V + 
Sbjct: 70  NGQDLMGQPISVDWC 84

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
            +++LFVG L     +  +++ F  +G   E  +       K +GFGF+  ++   A  A
Sbjct: 21  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIA 74
Query: 92  QSAMDGQELNGRNIRVSFA 110
           +  +D   L G+ +RV FA
Sbjct: 75  KVELDNMPLRGKQLRVRFA 93

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN---ESASSAQ 92
           +FVGG+    D++ ++  F+ +G + E K+IT+R +G S+G+GFV++ ++   +    +Q
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 93  SAMDGQEL 100
               G++L
Sbjct: 71  INFHGKKL 78

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           LFV G+     +  + + F+ +G+I    +  +R +G  +G+  V Y++ + A +A   +
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 96  DGQELNGRNIRVSFA 110
           +GQ+L G+ I V + 
Sbjct: 85  NGQDLMGQPISVDWC 99

>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/86 (34%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAK--------VITERESGKSRGFGFVTYDSNES 87
           +FV GL       S+ + F   G I   K        + T+RE+GK +G   V++D   S
Sbjct: 10  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 88  ASSAQSAMDGQELNGRNIRVSFANDR 113
           A +A    DG+E +G  I+VSFA  R
Sbjct: 70  AKAAIDWFDGKEFSGNPIKVSFATRR 95

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 19/56 (33%), Positives = 32/56 (57%)
Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
          K+FVGGLS  T +  ++E F  FG++   ++  + ++ K RGF F+T+   E    
Sbjct: 3  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 58

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 40/79 (50%)
Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           +  S  KLF+GGL    +D  +KE  ++FG +    ++ +  +G S+G+ F  Y      
Sbjct: 110 VPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 169
Query: 89  SSAQSAMDGQELNGRNIRV 107
             A + ++G +L  + + V
Sbjct: 170 DQAIAGLNGMQLGDKKLLV 188

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 8/96 (8%)
Query: 15  GQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKS 74
           G  P+ S ++  +    S T+LFV        +S L E F  FG + E K++        
Sbjct: 13  GLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN------- 65
Query: 75  RGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA 110
            GF FV ++  ESA+ A   + G+    + + V ++
Sbjct: 66  -GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 43/69 (62%), Gaps = 4/69 (5%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN---ESASSAQ 92
           +FVGG+    D++ ++  F+ +G + E K+IT+R +G S+G+GFV++ ++   +    +Q
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 93  SAMDGQELN 101
               G++L 
Sbjct: 71  INFHGKKLK 79

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITER-ESGKSRGFGFVTYDSNESA 88
           S   TK+ +G L+       + E FS +G I    +  ER     S+G+ +V +++ + A
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 89  SSAQSAMDGQELNGRNI 105
             A   MDG +++G+ I
Sbjct: 61  EKALKHMDGGQIDGQEI 77

>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding Protein Fus From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6430a Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 8/83 (9%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAK--------VITERESGKSRGFGFVTYDSNES 87
           +FV GL       S+ + F   G I   K        + T+RE+GK +G   V++D   S
Sbjct: 16  IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 88  ASSAQSAMDGQELNGRNIRVSFA 110
           A +A    DG+E +G  I+VSFA
Sbjct: 76  AKAAIDWFDGKEFSGNPIKVSFA 98

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 39/76 (51%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGL    +D  +KE  ++FG +    ++ +  +G S+G+ F  Y        A + 
Sbjct: 98  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 95  MDGQELNGRNIRVSFA 110
           ++G +L  + + V  A
Sbjct: 158 LNGMQLGDKKLLVQRA 173

>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda Subunit And The 59 Kda Subunit (Rrm Domain) Of Human Cleavage Factor Im Length = 156

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           ++VG  SW T D  L +   + G  D+ E K    R +G+S+G+  V   S  S      
Sbjct: 58  VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 94  AMDGQELNGRNIRVSFA 110
            + G+ LNG  + V  A
Sbjct: 118 LLPGKVLNGEKVDVRPA 134

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN---ESASSAQ 92
           +FVGG+    D++ ++  F+ +G + E K+IT+R +G S+G+GFV++ ++   +    +Q
Sbjct: 13  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 93  SAMDGQEL 100
               G++L
Sbjct: 72  INFHGKKL 79

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 38/73 (52%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGL    +D  +KE  ++FG +    ++ +  +G S+G+ F  Y        A + 
Sbjct: 96  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 95  MDGQELNGRNIRV 107
           ++G +L  + + V
Sbjct: 156 LNGMQLGDKKLLV 168

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +++LFVG L     +  +++ F  +G   E  +       K +GFGF+  ++   A  A+
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAK 68
Query: 93  SAMDGQELNGRNIRVSFA 110
             +D   L G+ +RV FA
Sbjct: 69  VELDNMPLRGKQLRVRFA 86

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 38/73 (52%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGL    +D  +KE  ++FG +    ++ +  +G S+G+ F  Y        A + 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 95  MDGQELNGRNIRV 107
           ++G +L  + + V
Sbjct: 63  LNGMQLGDKKLLV 75

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
          +FVGGLS  T +  ++E F  FG++   ++  + ++ K RGF F+T+   E    
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK 56

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 16/77 (20%), Positives = 46/77 (59%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++G + +   +  + +  SN G +   K++ + ++G+S+G+ F+ +   ES++SA   +
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 96  DGQELNGRNIRVSFAND 112
           +G +L  R ++  ++++
Sbjct: 67  NGYQLGSRFLKCGYSSN 83

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 43.5 bits (101), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S    ++FV  L +      LK+ F+  G +  A +  + E+GKS+G G V ++S E A 
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAE 62
Query: 90  SAQSAMDGQELNGRNIRV 107
            A   M+G +L+GR I V
Sbjct: 63  RACRMMNGMKLSGREIDV 80

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KL V  L +G  D+ ++E F+ FG + +A V  +R SG+S G   V ++    A  A   
Sbjct: 30  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 95  MDGQELNGRNIRVSFA 110
            +G  L+GR + +   
Sbjct: 89  YNGVPLDGRPMNIQLV 104

>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U) Binding 1 Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/107 (25%), Positives = 48/107 (44%), Gaps = 10/107 (9%)
Query: 7   LGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVI 66
           +G+  + N QA    + + +R      T  ++G +     ++ L   F NFG I + K  
Sbjct: 5   IGLPPQVNPQA----VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY 60
Query: 67  TERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR 113
            E+      G  F+ YD++E A+    A+      GRN+R  +  +R
Sbjct: 61  PEK------GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101

>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28 Length = 111

Iteration: 1
 Score = 43.1 bits (100), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 6/84 (7%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +F+  LS+ +++ +L E    FGD+   +V+   ++  S+G  F  + + E+A    +A 
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77
Query: 96  D------GQELNGRNIRVSFANDR 113
                  G +L+GR ++V  A  R
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVTR 101

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           + +FV  L +      LKE FS  G +  A ++ +++ GKSRG G VT++ +  A  A S
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
Query: 94  AMDGQELNGRNIRV 107
             +GQ L  R + V
Sbjct: 75  MFNGQLLFDRPMHV 88

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S T+LFV        +S L E F  FG + E K++         GF FV ++  ESA+ A
Sbjct: 3   SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKA 54
Query: 92  QSAMDGQELNGRNIRVSFA 110
              + G+    + + V ++
Sbjct: 55  IEEVHGKSFANQPLEVVYS 73

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 16/77 (20%), Positives = 46/77 (59%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++G + +   +  + +  SN G +   K++ + ++G+S+G+ F+ +   ES++SA   +
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 96  DGQELNGRNIRVSFAND 112
           +G +L  R ++  ++++
Sbjct: 65  NGYQLGSRFLKCGYSSN 81

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 42.7 bits (99), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+G +S    ++ ++  FS+FG I E +++     G SRG  FVT+ +   A +A  A
Sbjct: 97  KLFIGMISKKCTENDIRVMFSSFGQIEECRIL-RGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 95  MD-GQELNG 102
           M   Q + G
Sbjct: 156 MHQAQTMEG 164

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VG + +G+    L+  FS+ G I    ++ ++ SG  +G+ ++ +    S  +A  AM
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-VAM 97
Query: 96  DGQELNGRNIRV 107
           D     GR I+V
Sbjct: 98  DETVFRGRTIKV 109

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 16/77 (20%), Positives = 46/77 (59%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           +++G + +   +  + +  SN G +   K++ + ++G+S+G+ F+ +   ES++SA   +
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 96  DGQELNGRNIRVSFAND 112
           +G +L  R ++  ++++
Sbjct: 66  NGYQLGSRFLKCGYSSN 82

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+G +S    ++ ++  FS+FG I E +++     G SRG  FVT+ +   A +A  A
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRIL-RGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 95  MD-GQELNG 102
           M   Q + G
Sbjct: 168 MHQAQTMEG 176

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 42.7 bits (99), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 27  RFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSR-GFGFVTYDSN 85
           + + +S T L+VG LS+ T +  + E FS  GDI   K+I   +  K+  GF FV Y S 
Sbjct: 13  KLLKKSCT-LYVGNLSFYTTEEQIYELFSKSGDI--KKIIMGLDKMKTACGFCFVEYYSR 69
Query: 86  ESASSAQSAMDGQELNGRNIRVSF 109
             A +A   ++G  L+ R IR  +
Sbjct: 70  ADAENAMRYINGTRLDDRIIRTDW 93

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S   + +FV  L +      LK+ F+  G +  A +  + E+GKS+G G V ++S E A 
Sbjct: 2   SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAE 59
Query: 90  SAQSAMDGQELNGRNIRV 107
            A   M+G +L+GR I V
Sbjct: 60  RACRMMNGMKLSGREIDV 77

>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From Hypothetical Rna Binding Protein Bc052180 Length = 97

Iteration: 1
 Score = 42.4 bits (98), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T+L+VGGL   T  ++L   F  FG I     +      K   F ++ Y+S ++A +A +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71
Query: 94  AMDGQELNG--RNIRVSFANDRP 114
            M G  L G  R +RV FA   P
Sbjct: 72  KMRGFPLGGPDRRLRVDFAKSGP 94

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 39/74 (52%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L+VG LS+ T +  + E FS  GDI +  +  ++    + GF FV Y S   A +A   +
Sbjct: 42  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 96  DGQELNGRNIRVSF 109
           +G  L+ R IR  +
Sbjct: 102 NGTRLDDRIIRTDW 115

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           ++  KL V  L +G  D+ ++E F+ FG + +A V  +R SG+S G   V ++    A  
Sbjct: 86  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 144
Query: 91  AQSAMDGQELNGRNIRVSF 109
           A     G  L+GR + +  
Sbjct: 145 AMKQYKGVPLDGRPMDIQL 163

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGK---SRGFGFVTYDSNESASSAQ 92
           LF+  L++ T + +LK  FS  G I    +  ++       S GFGFV Y   E A  A 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 93  SAMDGQELNGRN--IRVSFANDRP 114
             + G  ++G    +R+S    +P
Sbjct: 68  KQLQGHTVDGHKLEVRISERATKP 91

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KL V  L +G  D+ ++E F+ FG + +A V  +R SG+S G   V ++    A  A   
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 95  MDGQELNGR--NIRV 107
            +G  L+GR  NI++
Sbjct: 90  YNGVPLDGRPXNIQL 104

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 13/89 (14%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K++VG L  G     L+ AFS +G +    +     +    GF FV ++    A  A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 95  MDGQELNGRNIRVSFAN--------DRPP 115
           +DG+ + G  +RV  +         DRPP
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPP 85

>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 101

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L +  LS+   + +L+E F     I     + + ++GKS+G+ F+ + S E A  A ++ 
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 96  DGQELNGRNIRVSFANDR 113
           + +E+ GR IR+     R
Sbjct: 74  NKREIEGRAIRLELQGPR 91

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M      ++VG + +G     L+  F   G +    ++ ++ SG  +GF ++ +   ES 
Sbjct: 1   MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 89  SSAQSAMDGQELNGRNIRV 107
            ++  A+D     GR I+V
Sbjct: 61  RTSL-ALDESLFRGRQIKV 78

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 36/76 (47%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  L         +E    FG +    ++    +G+S+G+GF  Y   +SA+ A+S +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96  DGQELNGRNIRVSFAN 111
            G+ L  R + V + +
Sbjct: 158 LGKPLGPRTLYVHWTD 173

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 36/76 (47%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  L         +E    FG +    ++    +G+S+G+GF  Y   +SA+ A+S +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96  DGQELNGRNIRVSFAN 111
            G+ L  R + V + +
Sbjct: 158 LGKPLGPRTLYVHWTD 173

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 36/76 (47%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L V  L         +E    FG +    ++    +G+S+G+GF  Y   +SA+ A+S +
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 96  DGQELNGRNIRVSFAN 111
            G+ L  R + V + +
Sbjct: 156 LGKPLGPRTLYVHWTD 171

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 50/100 (50%), Gaps = 12/100 (12%)
Query: 14  NGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE-SG 72
           +GQ PK           Q+ +K+ V  + +  +   ++E FS FG++   ++  +   +G
Sbjct: 6   SGQVPK----------KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTG 55
Query: 73  KSRGFGFVTYDSNESASSAQSAM-DGQELNGRNIRVSFAN 111
             RGFGFV + + + A  A +A+     L GR + + +A+
Sbjct: 56  AHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWAD 95

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           ++  KL V  L +G  D+ ++E F+ FG + +A V  +R SG+S G   V ++    A  
Sbjct: 33  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 91
Query: 91  AQSAMDGQELNGRNIRVSF 109
           A     G  L+GR + +  
Sbjct: 92  AMKQYKGVPLDGRPMDIQL 110

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
          S  KLFVG L+    +  ++  F  FG+I E  ++   + G S+G  FV Y S+  A +A
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPD-GNSKGCAFVKYSSHAEAQAA 72
Query: 92 QSAMDGQE 99
           +A+ G +
Sbjct: 73 INALHGSQ 80

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

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           ++VG + +G     L+  F   G +    ++ ++ SG  +GF ++ +   ES  ++  A+
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 96  DGQELNGRNIRV 107
           D     GR I+V
Sbjct: 68  DESLFRGRQIKV 79

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           ++  KL V  L +G  D+ ++E F+ FG + +A V  +R SG+S G   V ++    A  
Sbjct: 33  ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 91
Query: 91  AQSAMDGQELNGRNIRVSF 109
           A     G  L+GR + +  
Sbjct: 92  AMKQYKGVPLDGRPMDIQL 110

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESG--KSRGFGFVTYDSNESASSAQ 92
           K+FVG +     +  L+E F  +G + E  V+ +R     +S+G  FVT+ + ++A  AQ
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 93  SAMDGQEL 100
           +A+   ++
Sbjct: 65  NALHNMKV 72

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+G +S    ++ ++  FS+FG I E +++     G SRG  FVT+ +   A +A  A
Sbjct: 97  KLFIGXISKKCTENDIRVXFSSFGQIEECRIL-RGPDGLSRGCAFVTFTTRAXAQTAIKA 155

>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing Sarcoma(Ews) Protein Length = 113

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 30/51 (58%)
Query: 65  VITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPP 115
           +  ++E+GK +G   V+Y+   +A +A    DG++  G  ++VS A  +PP
Sbjct: 55  IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	147
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.93
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.88
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.88
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.88
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.87
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.87
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.86
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.85
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.85
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.85
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.85
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.85
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.84
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.84
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.84
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.84
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.83
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.83
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.83
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.83
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.83
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.83
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.83
2div_A	99	TRNA selenocysteine associated protein; structural	99.83
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.83
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.83
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.83
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.82
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.82
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.82
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.82
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.82
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.82
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.82
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.82
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.82
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.81
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.81
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.81
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.81
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.81
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.81
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.81
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.8
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.8
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.8
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.8
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.8
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.8
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.68
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.8
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.8
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.79
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.79
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.79
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.79
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.79
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.79
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.79
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.78
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.78
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.78
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.78
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.78
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.78
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.78
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.78
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.78
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.78
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.77
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.77
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.77
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.77
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.77
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.77
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.77
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.76
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.76
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.76
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.75
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.75
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.75
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.75
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.75
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.75
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.75
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.75
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.75
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.74
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.74
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.74
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.74
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
1x5p_A	97	Negative elongation factor E; structure genomics,	99.74
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.73
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.73
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.73
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.72
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.7
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.7
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.69
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.69
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.69
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.69
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.68
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.67
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.67
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.67
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.66
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.66
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.66
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.63
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.63
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.62
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.62
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.61
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.59
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.59
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.57
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.56
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.55
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.55
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.55
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.55
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.54
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.53
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.52
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.5
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.5
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.49
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.45
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.41
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.36
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.23
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.21
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.03
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.93
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.83
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.2
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.93
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.83
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.73
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.53
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.29
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.7
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.53
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.93
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.69
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.2
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.99
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	83.38

>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=99.93  E-value=6.9e-25  Score=146.96  Aligned_cols=89  Identities=28%  Similarity=0.425  Sum_probs=82.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++||..|++..|.++.|.|+
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 032111          109 FANDRPPRS  117 (147)
Q Consensus       109 ~~~~~~~~~  117 (147)
                      ++++..+..
T Consensus       115 ~a~~~~~~~  123 (156)
T 1h2v_Z          115 WDAGFKEGR  123 (156)
T ss_dssp             EESCCCTTC
T ss_pred             ECCCCCCcC
Confidence            998765543

>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=99.89  E-value=1.6e-22  Score=125.94  Aligned_cols=85  Identities=31%  Similarity=0.540  Sum_probs=79.1

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .....+++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..+.|++|.|
T Consensus        14 n~~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V   93 (99)
T 4fxv_A           14 NLYFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV   93 (99)
T ss_dssp             --CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecC
Q 032111          108 SFAND  112 (147)
Q Consensus       108 ~~~~~  112 (147)
                      +++++
T Consensus        94 ~~AkP   98 (99)
T 4fxv_A           94 SYARP   98 (99)
T ss_dssp             EECCB
T ss_pred             EEeeC
Confidence            99864

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.88  E-value=1.2e-21  Score=128.79  Aligned_cols=88  Identities=27%  Similarity=0.536  Sum_probs=81.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+|||.++++++|+++|..||.|..|.++.++.++++++||||+|.+.++|++|++.|++..+.++.|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34556899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++++...+
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            99876544

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.88  E-value=2.4e-22  Score=130.05  Aligned_cols=88  Identities=26%  Similarity=0.510  Sum_probs=81.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++++++||||+|.+.++|++|++.|++..|.++.|.|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++.++.+.
T Consensus        98 ~a~~~~~~  105 (126)
T 3ex7_B           98 WCFVRGPP  105 (126)
T ss_dssp             ESEESSSC
T ss_pred             EecCCCCC
Confidence            99876554

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=1.4e-21  Score=120.37  Aligned_cols=86  Identities=30%  Similarity=0.655  Sum_probs=80.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||.|||..+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..+.++.|+|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            45689999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876553

>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=99.87  E-value=3.8e-21  Score=147.50  Aligned_cols=84  Identities=29%  Similarity=0.601  Sum_probs=79.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||.|||+.+++++|+++|.+||.|..|.|+.++.+++++|||||+|.+.++|++||..||+..|.|+.|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      +...
T Consensus       181 ~~~~  184 (437)
T 3pgw_S          181 GRTV  184 (437)
T ss_pred             CCCC
Confidence            7644

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.87  E-value=4.6e-21  Score=121.43  Aligned_cols=83  Identities=14%  Similarity=0.242  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|.|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=1.7e-20  Score=119.44  Aligned_cols=89  Identities=37%  Similarity=0.675  Sum_probs=82.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++||+.|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 032111          110 ANDRPPRSD  118 (147)
Q Consensus       110 ~~~~~~~~~  118 (147)
                      +.++.....
T Consensus        92 a~~~~~~~~  100 (115)
T 2dgo_A           92 ATRKPPAPK  100 (115)
T ss_dssp             SSCCCCCSC
T ss_pred             ccCCCCCCc
Confidence            987765443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=2.9e-21  Score=119.21  Aligned_cols=86  Identities=31%  Similarity=0.607  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEE-EEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEA-KVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+.++|||.|||+.+++++|+++|.+||.|..+ .++.++.++.+++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            356899999999999999999999999999999 9999888899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++..+
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.6e-21  Score=120.09  Aligned_cols=88  Identities=44%  Similarity=0.809  Sum_probs=81.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.++.|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34566899999999999999999999999999999999988889999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++++....
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=3.7e-21  Score=120.03  Aligned_cols=88  Identities=40%  Similarity=0.639  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..+.++.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++.++..+
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99876554

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.86  E-value=7.1e-21  Score=118.10  Aligned_cols=86  Identities=29%  Similarity=0.476  Sum_probs=80.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.++.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45689999999999999999999999999999999998888999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      .++...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            887554

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.86  E-value=8.1e-21  Score=115.08  Aligned_cols=83  Identities=37%  Similarity=0.647  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||..+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.|+.|.|+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            35579999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            865

>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=99.86  E-value=9.7e-21  Score=120.61  Aligned_cols=87  Identities=28%  Similarity=0.502  Sum_probs=81.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+++++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..|.++.|.|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      ++++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=9.6e-21  Score=117.56  Aligned_cols=85  Identities=32%  Similarity=0.644  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++ |++..+.++.|.|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            455899999999999999999999999999999999998889999999999999999999999 9999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      .++...
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876554

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=6.8e-21  Score=119.40  Aligned_cols=87  Identities=30%  Similarity=0.479  Sum_probs=81.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34568999999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.+....
T Consensus        92 a~~~~~~   98 (105)
T 1x5u_A           92 ASAHNKN   98 (105)
T ss_dssp             TTTTSCC
T ss_pred             CCCCCcC
Confidence            9876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.1e-20  Score=118.08  Aligned_cols=87  Identities=24%  Similarity=0.462  Sum_probs=81.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++..+
T Consensus        92 a~~~~~~   98 (103)
T 2cq0_A           92 AKPSTNS   98 (103)
T ss_dssp             SSCCCCS
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.85  E-value=1.7e-20  Score=112.65  Aligned_cols=81  Identities=38%  Similarity=0.726  Sum_probs=77.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      .+|||+|||+++++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.|+.|.|+++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999889999999999999999999999999999999999999999876


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=2e-20  Score=119.35  Aligned_cols=84  Identities=44%  Similarity=0.697  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++++++||||+|.+.++|++||+.+++ .+.++.|.|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999998 89999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +....
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            97643

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.2e-20  Score=118.20  Aligned_cols=84  Identities=24%  Similarity=0.505  Sum_probs=78.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCC-CccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES-GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+.++|||.|||+.+++++|+++|.+|| |..|.++.++.+ +.+++||||+|.+.++|++|| .|++..+.++.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4558999999999999999999999999 999999998877 899999999999999999999 8999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++..+
T Consensus        91 a~~~~~~   97 (104)
T 1wi8_A           91 ADQAQDK   97 (104)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9887654

>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=99.85  E-value=1.9e-20  Score=119.62  Aligned_cols=84  Identities=37%  Similarity=0.670  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+++++++|+++|.+||.|..|.++.+. ++++++||||+|.+.++|++|++.|++..+.|+.|.|+++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            455899999999999999999999999999999999987 8899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      +++..
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=1.7e-20  Score=116.18  Aligned_cols=86  Identities=27%  Similarity=0.517  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCC---CCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE---SGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .+.++|||.|||+++++++|+++|.+||.|..+.++.++.   ++.+++||||+|.+.++|++|+..|++..+.++.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4568999999999999999999999999999999988765   5588999999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q 032111          108 SFANDRPPR  116 (147)
Q Consensus       108 ~~~~~~~~~  116 (147)
                      +++++....
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=1.6e-21  Score=119.54  Aligned_cols=82  Identities=18%  Similarity=0.451  Sum_probs=75.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc-CCeeCCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD-GQELNGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~-~~~~~g~~l~v~~~~  111 (147)
                      ++|||+|||+++++++|+++|++|| .|..|++++++.++.++|||||+|.+.++|++||+.++ +..+.|++|.|+++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 79999999999999999999999999999999999774 567999999999998


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      +++.
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=8.3e-21  Score=119.19  Aligned_cols=86  Identities=27%  Similarity=0.531  Sum_probs=80.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.|+.|.|++
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +.++++
T Consensus       100 a~~~~~  105 (106)
T 1p27_B          100 CFVRGP  105 (106)
T ss_dssp             SEESSC
T ss_pred             ecCCCC
Confidence            987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=2.2e-20  Score=116.07  Aligned_cols=86  Identities=30%  Similarity=0.606  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.++.++ ++++++||||+|.+.++|++|++.|++..+.++.|.|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999987 899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +++++.+
T Consensus        93 a~~~~~~   99 (100)
T 2do4_A           93 SNSGPSS   99 (100)
T ss_dssp             CCCCSCC
T ss_pred             CCCCCCC
Confidence            9876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=8.1e-21  Score=118.71  Aligned_cols=87  Identities=31%  Similarity=0.546  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      ++...+.
T Consensus        90 a~~~~~~   96 (103)
T 2dnm_A           90 ARYGRRD   96 (103)
T ss_dssp             CSSCCSC
T ss_pred             CCcCCCC
Confidence            9875443

>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=99.85  E-value=1.6e-20  Score=113.27  Aligned_cols=82  Identities=41%  Similarity=0.682  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.|+.|.|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.85  E-value=2.5e-20  Score=116.48  Aligned_cols=85  Identities=25%  Similarity=0.530  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+|+ |..|.++.++.++++++||||+|.+.++|++|+ .|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            34568999999999999999999999996 999999999889999999999999999999999 7999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2dng_A           90 AEGRKQD   96 (103)
T ss_dssp             CCCCCCC
T ss_pred             ecCCCCC
Confidence            9876543

>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=99.85  E-value=2e-21  Score=137.65  Aligned_cols=80  Identities=35%  Similarity=0.590  Sum_probs=75.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..++|||+|||+.+++++|+++|.+||  .|..|.|+.++.+++++|||||+|.+.++|++||+.|++..|.++.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            557899999999999999999999999  999999999999999999999999999999999999999999999999998


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus       147 a~  148 (229)
T 3q2s_C          147 VN  148 (229)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.3e-20  Score=116.60  Aligned_cols=85  Identities=40%  Similarity=0.667  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.++.+  ++.+++||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345689999999999999999999999999999999887  788999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++..+
T Consensus        90 a~~~~~~   96 (103)
T 2d9p_A           90 AQRKEER   96 (103)
T ss_dssp             CSSCCCC
T ss_pred             ecccccC
Confidence            9887654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.84  E-value=4.7e-21  Score=118.29  Aligned_cols=79  Identities=23%  Similarity=0.444  Sum_probs=74.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCC--eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC----eeCCeEEEE
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGD--ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ----ELNGRNIRV  107 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~--i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~----~~~g~~l~v  107 (147)
                      .+|||+|||+.+|+++|+++|++||.  +..|++++++.+++++|||||+|.+.++|++|++.|++.    .+.|++|.|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V   89 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV   89 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEE
Confidence            68999999999999999999999995  678999999999999999999999999999999999987    589999999


Q ss_pred             EeecC
Q 032111          108 SFAND  112 (147)
Q Consensus       108 ~~~~~  112 (147)
                      +++++
T Consensus        90 ~~Aks   94 (95)
T 2lkz_A           90 DFAKS   94 (95)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99875

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.84  E-value=1.6e-20  Score=117.87  Aligned_cols=88  Identities=35%  Similarity=0.522  Sum_probs=80.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee---CCeEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL---NGRNI  105 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~---~g~~l  105 (147)
                      ...+.++|||.|||..+++++|+++|.+||.|..|.++.++.++++++||||+|.+.++|++|++.|++..+   .++.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            344568999999999999999999999999999999999988899999999999999999999999999988   89999


Q ss_pred             EEEeecCCCCC
Q 032111          106 RVSFANDRPPR  116 (147)
Q Consensus       106 ~v~~~~~~~~~  116 (147)
                      .|.++.+...+
T Consensus        89 ~v~~a~~~~~~   99 (106)
T 2dgp_A           89 QVKPADSESRG   99 (106)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEECCccccc
Confidence            99999876543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=2.9e-20  Score=116.85  Aligned_cols=87  Identities=25%  Similarity=0.559  Sum_probs=80.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEec-CCCCccceEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITE-RESGKSRGFGFVTYDSNESASSAQSAM-DGQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~ai~~l-~~~~~~g~~l~v  107 (147)
                      ....++|||.|||+.+++++|+++|.+||.|..|.++.+ +.++.+++||||+|.+.++|++|+..| ++..+.++.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            345689999999999999999999999999999999988 678999999999999999999999999 999999999999


Q ss_pred             EeecCCCCC
Q 032111          108 SFANDRPPR  116 (147)
Q Consensus       108 ~~~~~~~~~  116 (147)
                      .++.+....
T Consensus        92 ~~a~~~~~~  100 (107)
T 2cph_A           92 EWADSEVTV  100 (107)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999876554

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.7e-19  Score=114.58  Aligned_cols=86  Identities=31%  Similarity=0.501  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||.|||+.+++++|+++|.+||.|..+.++.++ ++++++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3456899999999999999999999999999999999886 588999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      ++...++
T Consensus        91 a~~~~~~   97 (114)
T 2do0_A           91 DERALPK   97 (114)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            9865444

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.6e-20  Score=118.23  Aligned_cols=87  Identities=25%  Similarity=0.515  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDIT--------EAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN  101 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~  101 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|.        .+.++.++.++++++||||+|.+.++|++||+.|++..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            34568999999999999999999999999998        6999998888999999999999999999999999999999


Q ss_pred             CeEEEEEeecCCCCC
Q 032111          102 GRNIRVSFANDRPPR  116 (147)
Q Consensus       102 g~~l~v~~~~~~~~~  116 (147)
                      ++.|.|.+++++...
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999876554

>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=99.84  E-value=3.6e-20  Score=117.10  Aligned_cols=87  Identities=25%  Similarity=0.531  Sum_probs=80.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc------CCeeCCe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD------GQELNGR  103 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~------~~~~~g~  103 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++||..|+      +..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            3456899999999999999999999999999999999998889999999999999999999999999      9999999


Q ss_pred             EEEEEeecCCCCC
Q 032111          104 NIRVSFANDRPPR  116 (147)
Q Consensus       104 ~l~v~~~~~~~~~  116 (147)
                      .|.|.++.++...
T Consensus        92 ~l~v~~a~~~~~~  104 (111)
T 1x4h_A           92 QLKVDLAVTRDEA  104 (111)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCccC
Confidence            9999999876543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=2.5e-20  Score=116.62  Aligned_cols=86  Identities=30%  Similarity=0.515  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhc-cCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCe-eCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSN-FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQE-LNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~-~~g~~l~v  107 (147)
                      ..+.++|||+|||+.+++++|+++|.+ ||.|..+.++.+. ++.+++||||+|.+.++|++|++.|++.. +.|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            345689999999999999999999999 9999999999997 89999999999999999999999999999 99999999


Q ss_pred             EeecCCCCC
Q 032111          108 SFANDRPPR  116 (147)
Q Consensus       108 ~~~~~~~~~  116 (147)
                      .++.++..+
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999876544

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=3.4e-20  Score=114.06  Aligned_cols=83  Identities=36%  Similarity=0.593  Sum_probs=78.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +.+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.+++|.|++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44568999999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            864

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.84  E-value=3.5e-20  Score=112.41  Aligned_cols=84  Identities=26%  Similarity=0.493  Sum_probs=77.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCc-cceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGK-SRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~-~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ..++|||+|||+++++++|+++|.+||.|..+.++.+..++. +++||||+|.+.++|++|+..|++..+.|+.|.|+++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            457999999999999999999999999999999988876655 8899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      .++.+
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87554

>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=99.84  E-value=1e-19  Score=113.68  Aligned_cols=85  Identities=27%  Similarity=0.504  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||.|||+.+++++|+++|.+||.|..|.++.+..+  +++||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            345689999999999999999999999999999999887443  688999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++..+
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9876554

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.84  E-value=5.5e-21  Score=116.78  Aligned_cols=82  Identities=34%  Similarity=0.560  Sum_probs=72.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      .+|||+|||+++++++|+++|.+||  .|..+.++.++.+++++|||||+|.+.++|++|++.|++..+.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999998899999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      +.++
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7654

>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=99.84  E-value=2.8e-20  Score=117.57  Aligned_cols=87  Identities=26%  Similarity=0.555  Sum_probs=81.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.|+.|.|.+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34568999999999999999999999999999999999888899999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.+++++
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9876543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=3.7e-20  Score=113.76  Aligned_cols=82  Identities=24%  Similarity=0.554  Sum_probs=77.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.++.|.|++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            44568999999999999999999999999999999999988899999999999999999999999999999999999998


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>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=99.83  E-value=9e-20  Score=114.23  Aligned_cols=85  Identities=29%  Similarity=0.467  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC---eEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG---RNIRV  107 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g---~~l~v  107 (147)
                      ...++|||+|||+.+++++|+++|.+||.|..+.++.++ ++++++||||+|.+.++|++|++.|++..+.+   +.|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456899999999999999999999999999999999986 78999999999999999999999999999988   99999


Q ss_pred             EeecCCCCC
Q 032111          108 SFANDRPPR  116 (147)
Q Consensus       108 ~~~~~~~~~  116 (147)
                      .++.+...+
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999876654

>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=99.83  E-value=1.3e-19  Score=114.26  Aligned_cols=83  Identities=20%  Similarity=0.449  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.+..+   +.+++||||+|.+.++|++|++.|++..+.++.|.|++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            445689999999999999999999999999999988543   45789999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +++...
T Consensus        96 a~~~~~  101 (109)
T 1x4a_A           96 PRSGRG  101 (109)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            987543

>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=99.83  E-value=5.9e-20  Score=113.40  Aligned_cols=82  Identities=20%  Similarity=0.537  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||..+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.|+.|.|.++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            47999999999999999999999999999999999988899999999999999999999999999999999999999986


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=99.83  E-value=2e-19  Score=112.30  Aligned_cols=85  Identities=29%  Similarity=0.586  Sum_probs=77.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.+..  .+++||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999988753  3789999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++...
T Consensus        90 a~~~~~~   96 (103)
T 2cq3_A           90 ATARVMT   96 (103)
T ss_dssp             CCSSCCC
T ss_pred             cccCCCC
Confidence            9877554

>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=99.83  E-value=7.8e-20  Score=116.55  Aligned_cols=81  Identities=32%  Similarity=0.587  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ..+|||+|||+.+++++|+++|.+||.|..+.++.+.  +.++|||||+|.+.++|++||+.|++..+.|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999885  45789999999999999999999999999999999999887


Q ss_pred             CCC
Q 032111          113 RPP  115 (147)
Q Consensus       113 ~~~  115 (147)
                      +..
T Consensus        83 ~~~   85 (115)
T 4f25_A           83 RKE   85 (115)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            554

>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=99.83  E-value=5e-20  Score=116.24  Aligned_cols=86  Identities=31%  Similarity=0.671  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||+|||+.+++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|.|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34456899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998653

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=3.8e-20  Score=116.00  Aligned_cols=86  Identities=30%  Similarity=0.659  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++||.. ++..|.++.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            44568999999999999999999999999999999999988999999999999999999999998 99999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++...
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9876543

>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=99.83  E-value=6.9e-20  Score=123.69  Aligned_cols=87  Identities=26%  Similarity=0.555  Sum_probs=79.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++||..|++..|.|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34557899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.+..++
T Consensus       149 a~~~~~~  155 (165)
T 1rk8_A          149 CFVKGPK  155 (165)
T ss_dssp             SEECC--
T ss_pred             ecCCCCC
Confidence            9876554

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.83  E-value=1.3e-19  Score=113.85  Aligned_cols=83  Identities=29%  Similarity=0.529  Sum_probs=77.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..+.++.++ ++++++||||+|.+.++|++|++.|++..+.|+.|.|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34566899999999999999999999999999999999987 89999999999999999999999999999999999999


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      ++++
T Consensus       104 ~a~s  107 (107)
T 3ulh_A          104 LVTS  107 (107)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9863

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.83  E-value=8.9e-20  Score=113.19  Aligned_cols=83  Identities=34%  Similarity=0.521  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITE--------AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      .+...++|||+|||+.+++++|+++|.+||.|..        +.++.++.++.++|||||+|.+.++|++|++.|++..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4456689999999999999999999999999999        99999988999999999999999999999999999999


Q ss_pred             CCeEEEEEeec
Q 032111          101 NGRNIRVSFAN  111 (147)
Q Consensus       101 ~g~~l~v~~~~  111 (147)
                      .|+.|+|++++
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999874

>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=99.83  E-value=1e-19  Score=111.96  Aligned_cols=83  Identities=34%  Similarity=0.535  Sum_probs=76.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..+.++.++. +++++||||+|.+.++|++|++.|++..+.++.|.|+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            344568999999999999999999999999999999999865 8899999999999999999999999999999999999


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      ++++
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=8.7e-20  Score=113.15  Aligned_cols=84  Identities=24%  Similarity=0.469  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCee-EEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE----
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDIT-EAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN----  104 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~-~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~----  104 (147)
                      ....++|||+|||+.+++++|+++|.+||.|. .+.++.++.++.+++||||+|.+.++|++|++.|++..+.++.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34568999999999999999999999999999 9999999889999999999999999999999999999999999    


Q ss_pred             EEEEeecCC
Q 032111          105 IRVSFANDR  113 (147)
Q Consensus       105 l~v~~~~~~  113 (147)
                      |+|.++++.
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998764

>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=99.83  E-value=2.2e-19  Score=113.22  Aligned_cols=79  Identities=27%  Similarity=0.417  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC-----eEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG-----RNI  105 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g-----~~l  105 (147)
                      ...++|||.|||+.+++++|+++|.+||.|..+.++.+       +||||+|.+.++|++||+.||+..|.+     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45689999999999999999999999999999988775       699999999999999999999999999     999


Q ss_pred             EEEeecCCCCC
Q 032111          106 RVSFANDRPPR  116 (147)
Q Consensus       106 ~v~~~~~~~~~  116 (147)
                      .|+++.++.+.
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99999986543

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.83  E-value=1.2e-19  Score=110.30  Aligned_cols=80  Identities=23%  Similarity=0.561  Sum_probs=76.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|+ .|++..+.|+.|.|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            479999999999999999999999999999999999889999999999999999999999 8999999999999999876


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.83  E-value=2.6e-19  Score=111.83  Aligned_cols=79  Identities=29%  Similarity=0.567  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||.|||+.+++++|+++|.+||.|..+.+++        +||||+|.+.++|++|+..|++..+.++.|.|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            4558999999999999999999999999999998763        49999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 032111          111 NDRPPRS  117 (147)
Q Consensus       111 ~~~~~~~  117 (147)
                      +++....
T Consensus        81 ~~~~~~~   87 (103)
T 2dgu_A           81 KPPDQKR   87 (103)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccc
Confidence            8765543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=1.2e-19  Score=113.11  Aligned_cols=85  Identities=39%  Similarity=0.693  Sum_probs=76.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.++   ..+.++.++.++++++||||+|.+.++|++||..|++..|.++.|.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34566899999999999999999999977   367788887889999999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      +++++..+
T Consensus        88 ~a~~~~~~   95 (102)
T 2fc8_A           88 WAKPKGEG   95 (102)
T ss_dssp             ECCCCCSS
T ss_pred             EecCCCCC
Confidence            99876543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=9.4e-20  Score=116.18  Aligned_cols=83  Identities=35%  Similarity=0.613  Sum_probs=78.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||.|||+.+++++|+++|.+||.|..|.++.++.++++++||||+|.+.++|++||.. ++..|.|+.|.|.++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            37999999999999999999999999999999999988899999999999999999999997 99999999999999987


Q ss_pred             CCCC
Q 032111          113 RPPR  116 (147)
Q Consensus       113 ~~~~  116 (147)
                      +...
T Consensus       106 ~~~~  109 (116)
T 1x4b_A          106 REES  109 (116)
T ss_dssp             CCCC
T ss_pred             CccC
Confidence            6543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.82  E-value=4.7e-20  Score=117.87  Aligned_cols=83  Identities=29%  Similarity=0.525  Sum_probs=77.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||+|||+++++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.||+..+.|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eec
Q 032111          109 FAN  111 (147)
Q Consensus       109 ~~~  111 (147)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>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=99.82  E-value=3.5e-20  Score=120.48  Aligned_cols=87  Identities=36%  Similarity=0.620  Sum_probs=81.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .+.+.++|||.|||+.+++++|+++|.+||.|..|.++.++.+++.++||||+|.+.++|++||+.|++..|.|+.|.|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44566899999999999999999999999999999999998889999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 032111          109 FANDRPP  115 (147)
Q Consensus       109 ~~~~~~~  115 (147)
                      ++.++.+
T Consensus       122 ~a~~~~p  128 (129)
T 2kxn_B          122 FSITKRP  128 (129)
T ss_dssp             CCSSSSC
T ss_pred             EecCCCC
Confidence            9987654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.82  E-value=1.4e-19  Score=110.78  Aligned_cols=84  Identities=32%  Similarity=0.515  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.++.+  ++++++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   82 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRI   82 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345689999999999999999999999999999988873  688999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +++...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            987654

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.5e-19  Score=111.68  Aligned_cols=82  Identities=16%  Similarity=0.268  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLK----EAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      .+.++|||+|||+.+++++|+    ++|.+||.|..+.++.++.+   ++||||+|.+.++|++|++.||+..+.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            456799999999999999999    99999999999999987655   78999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 032111          107 VSFANDRPP  115 (147)
Q Consensus       107 v~~~~~~~~  115 (147)
                      |+++++...
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999987654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=2.7e-19  Score=109.32  Aligned_cols=83  Identities=16%  Similarity=0.340  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||+|||+.+++++|+++|.+| .|..+.++.+ .+++++|||||+|.+.++|++|+. |++..+.++.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3456899999999999999999999999 9999999998 789999999999999999999999 999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +++++.
T Consensus        84 a~~~~~   89 (91)
T 2dgw_A           84 EKSGPS   89 (91)
T ss_dssp             ESSCCC
T ss_pred             CCcCCC
Confidence            987643

>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=99.82  E-value=4.2e-19  Score=110.82  Aligned_cols=86  Identities=31%  Similarity=0.586  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||.|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++||.  ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            34456899999999999999999999999999999999998899999999999999999999999  4678999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99876543

>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=99.82  E-value=1.1e-19  Score=113.47  Aligned_cols=82  Identities=16%  Similarity=0.274  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +...++|||.|||+++++++|+++|.+||. ..|.++.++ +++++|||||+|.+.++|++||+ +++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            445689999999999999999999999995 599999986 89999999999999999999996 799999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +...+
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.82  E-value=1.4e-19  Score=114.31  Aligned_cols=88  Identities=34%  Similarity=0.629  Sum_probs=76.8

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ....+.++|||+|||+++++++|+++|.+||.|..|.++.++.++.++|||||+|.+.++|++|+..+ +..+.|+.|.|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V   98 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDP   98 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEE
Confidence            34556789999999999999999999999999999999999888999999999999999999999976 59999999999


Q ss_pred             EeecCCCCC
Q 032111          108 SFANDRPPR  116 (147)
Q Consensus       108 ~~~~~~~~~  116 (147)
                      .++.++..+
T Consensus        99 ~~a~~~~~~  107 (109)
T 2rs2_A           99 KVAFPRRAQ  107 (109)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.82  E-value=8.3e-20  Score=113.04  Aligned_cols=84  Identities=14%  Similarity=0.305  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||.|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..+.++.|.|+++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            34578999999999999999999999999988888888888999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      ..+.
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            7543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.82  E-value=3.5e-19  Score=107.87  Aligned_cols=80  Identities=34%  Similarity=0.704  Sum_probs=74.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++ +++..+.|+.|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4466899999999999999999999999999999999998899999999999999999999997 588899999999987


Q ss_pred             e
Q 032111          110 A  110 (147)
Q Consensus       110 ~  110 (147)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.82  E-value=8.5e-20  Score=117.63  Aligned_cols=83  Identities=25%  Similarity=0.572  Sum_probs=77.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||+|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+ .|++..+.|+.|.|.+++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999999999999999889999999999999999999999 799999999999999998


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      +..+
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>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=99.81  E-value=7e-20  Score=112.70  Aligned_cols=81  Identities=16%  Similarity=0.305  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||.|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..+.++.|.|+++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            34899999999999999999999999999888888888889999999999999999999999999999999999999876


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            4

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.81  E-value=3e-20  Score=115.69  Aligned_cols=81  Identities=21%  Similarity=0.321  Sum_probs=77.3

Q ss_pred             CCeEEEcCCCC------CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC-eEE
Q 032111           33 QTKLFVGGLSW------GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG-RNI  105 (147)
Q Consensus        33 ~~~i~v~nlp~------~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g-~~l  105 (147)
                      .++|||+|||+      ++++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.+ +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            47999999999      99999999999999999999999999999999999999999999999999999999999 999


Q ss_pred             EEEeecCC
Q 032111          106 RVSFANDR  113 (147)
Q Consensus       106 ~v~~~~~~  113 (147)
                      .|.++.++
T Consensus        86 ~V~~a~~~   93 (100)
T 3ns6_A           86 FLYTMKDV   93 (100)
T ss_dssp             EEEESHHH
T ss_pred             EEEECchh
Confidence            99998753

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.81  E-value=2.5e-19  Score=120.02  Aligned_cols=81  Identities=30%  Similarity=0.525  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFG--DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..++|||+|||+.+++++|+++|.+||  .|..+.++.++.+++++|||||+|.+.++|++||+.|++..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            864

>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=99.81  E-value=1.9e-19  Score=114.08  Aligned_cols=83  Identities=24%  Similarity=0.377  Sum_probs=76.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHH---HHhhccCCeeEEEEEecCCCC---ccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLK---EAFSNFGDITEAKVITERESG---KSRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~---~~f~~~g~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      ..++|||.|||+.+++++|+   ++|.+||.|..+.++.+..++   .++|||||+|.+.++|++||+.||+..+.|+.|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            45899999999999999999   999999999999998876643   456999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q 032111          106 RVSFANDRP  114 (147)
Q Consensus       106 ~v~~~~~~~  114 (147)
                      .|.++.+++
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999998765

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=5.4e-19  Score=107.78  Aligned_cols=79  Identities=25%  Similarity=0.544  Sum_probs=72.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+++++++|+++|.+||.|..+.++        ++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   76 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA   76 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEE
Confidence            3456899999999999999999999999999999887        46999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++...
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.81  E-value=1.3e-20  Score=119.81  Aligned_cols=81  Identities=25%  Similarity=0.411  Sum_probs=76.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||.|||+.+++++|+++|.+||.|..|.++.++.++.+++||||+|.+.++|++|| .|++..|.|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            479999999999999999999999999999999999888999999999999999999999 8999999999999999876


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      +.
T Consensus       104 ~~  105 (114)
T 2cq4_A          104 EK  105 (114)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=4.3e-19  Score=110.40  Aligned_cols=82  Identities=30%  Similarity=0.534  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|   .++.+ .++++++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4456899999999999999999999999876   45555 6788999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      ++++..
T Consensus        88 a~~~~~   93 (101)
T 2fc9_A           88 QGPRGS   93 (101)
T ss_dssp             CSSCCC
T ss_pred             cCCCCC
Confidence            987643

>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=99.81  E-value=1.4e-18  Score=109.59  Aligned_cols=85  Identities=28%  Similarity=0.616  Sum_probs=76.4

Q ss_pred             hhhCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           26 VRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        26 ~~~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      ........++|||+|||..+++++|+++|.+||.|..+.++.+      ++||||+|.+.++|++|+..|++..+.|+.|
T Consensus        18 ~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   91 (109)
T 1x4g_A           18 VNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV   91 (109)
T ss_dssp             HHHSCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             ccCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            3345566789999999999999999999999999999988875      5799999999999999999999999999999


Q ss_pred             EEEeecCCCCC
Q 032111          106 RVSFANDRPPR  116 (147)
Q Consensus       106 ~v~~~~~~~~~  116 (147)
                      .|.++++.+..
T Consensus        92 ~v~~a~~~~~~  102 (109)
T 1x4g_A           92 KCYWGKESPDM  102 (109)
T ss_dssp             EEECCCCCCSS
T ss_pred             EEEecCCCCCC
Confidence            99999876543

>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=99.80  E-value=2.6e-19  Score=111.91  Aligned_cols=83  Identities=33%  Similarity=0.679  Sum_probs=78.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.|++..+.|+.|.|.++.+
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            47999999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          113 RPP  115 (147)
Q Consensus       113 ~~~  115 (147)
                      ...
T Consensus        88 ~~~   90 (104)
T 1p1t_A           88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             ccc
Confidence            643

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.80  E-value=7.1e-20  Score=119.25  Aligned_cols=84  Identities=18%  Similarity=0.395  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC----eeCCe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITE--AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ----ELNGR  103 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~--~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~----~~~g~  103 (147)
                      ....++|||+|||+++++++|+++|.+||.|..  |+++.++.+++++|||||+|.+. +|++|+..|++.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            355689999999999999999999999999966  99999988999999999999999 999999999999    99999


Q ss_pred             EEEEEeecCCC
Q 032111          104 NIRVSFANDRP  114 (147)
Q Consensus       104 ~l~v~~~~~~~  114 (147)
                      .|.|+++.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999998754

>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=99.80  E-value=3.5e-19  Score=119.20  Aligned_cols=86  Identities=33%  Similarity=0.592  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ....+|||+|||+.+++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|+..|++..+.|+.|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            44689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      ++..++
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            876443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.2e-20  Score=112.04  Aligned_cols=81  Identities=27%  Similarity=0.505  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++.||+..+.++.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45689999999999999999999999999999999999888999999999999999999999999999999988776654


Q ss_pred             c
Q 032111          111 N  111 (147)
Q Consensus       111 ~  111 (147)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.80  E-value=5.9e-19  Score=111.19  Aligned_cols=85  Identities=25%  Similarity=0.446  Sum_probs=77.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEE-ecCCCCccceEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGD-ITEAKVI-TERESGKSRGFGFVTYDSNESASSAQSAMD--GQELNGRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~-~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--~~~~~g~~l~  106 (147)
                      .+.++|||+|||+.+++++|+++|.+||. |..+.++ .+..++.+++||||+|.+.++|++|+..|+  +..+.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35689999999999999999999999998 9999888 677788999999999999999999999996  5899999999


Q ss_pred             EEeecCCCC
Q 032111          107 VSFANDRPP  115 (147)
Q Consensus       107 v~~~~~~~~  115 (147)
                      |.+++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999987654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.8e-19  Score=111.23  Aligned_cols=82  Identities=15%  Similarity=0.281  Sum_probs=73.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG--QELNGRNIR  106 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~--~~~~g~~l~  106 (147)
                      .+.+.++|||+|||+++++++|+++|++||.|..+.++.+      +|||||+|.+.++|++|++.|++  ..+.|++|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4556789999999999999999999999999999998865      58999999999999999998864  789999999


Q ss_pred             EEeecCCCCC
Q 032111          107 VSFANDRPPR  116 (147)
Q Consensus       107 v~~~~~~~~~  116 (147)
                      |.++++++..
T Consensus        86 V~~A~~~~~~   95 (105)
T 1sjq_A           86 IQFSNHKELK   95 (105)
T ss_dssp             BCCCSSSSCC
T ss_pred             EEEcCCCCCC
Confidence            9999876544

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.80  E-value=4.3e-19  Score=110.41  Aligned_cols=78  Identities=29%  Similarity=0.602  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ++|||+|||+++++++|+++|.+||.|..+.++.+     +++||||+|.+.++|++|++.|++..+.|+.|.|+++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999998876     5789999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          114 PPR  116 (147)
Q Consensus       114 ~~~  116 (147)
                      +..
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            644

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.80  E-value=9.3e-20  Score=113.41  Aligned_cols=84  Identities=25%  Similarity=0.497  Sum_probs=74.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecC-CCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITER-ESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .....++|||+|||+++++++|+++|.+|| |..+.++.++ .+++++|||||+|.+.++|++|+ .|++..+.|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            445668999999999999999999999999 9999999887 58999999999999999999999 79999999999999


Q ss_pred             EeecCCC
Q 032111          108 SFANDRP  114 (147)
Q Consensus       108 ~~~~~~~  114 (147)
                      ++++++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9988653

>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=99.80  E-value=7.7e-20  Score=116.33  Aligned_cols=87  Identities=22%  Similarity=0.400  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.+..+..++++++||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34568999999999999999999999999884332222223678899999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.++..+
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9876554

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

Probab=99.68  E-value=3.1e-21  Score=123.12  Aligned_cols=86  Identities=34%  Similarity=0.512  Sum_probs=79.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITE--------AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      .+.++|||+|||+.+++++|+++|.+||.|..        +.++.++.++.+++||||+|.+.++|++|+..|++..+.+
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            45589999999999999999999999999988        8888888889999999999999999999999999999999


Q ss_pred             eEEEEEeecCCCCC
Q 032111          103 RNIRVSFANDRPPR  116 (147)
Q Consensus       103 ~~l~v~~~~~~~~~  116 (147)
                      +.|.|+++.+++.+
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999876544

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.4e-18  Score=106.33  Aligned_cols=78  Identities=26%  Similarity=0.539  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||+|||+.+++++|+++|.+||.|..+.++++        ||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            445689999999999999999999999999999988743        999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      ++++..
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            987654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=5.4e-19  Score=111.60  Aligned_cols=83  Identities=30%  Similarity=0.598  Sum_probs=76.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+|||.++++++|+++|.+||.|..+.++.++  +.+++||||+|.+.++|++|++.|++..+.|+.|.|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999998874  3488999999999999999999999999999999999


Q ss_pred             eecCC
Q 032111          109 FANDR  113 (147)
Q Consensus       109 ~~~~~  113 (147)
                      +++++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            98865

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.1e-19  Score=111.71  Aligned_cols=79  Identities=20%  Similarity=0.323  Sum_probs=74.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+++++++|+++|.+||.|..|.++.++. +.++|||||+|.+.++|++|+. +++..+.|+.|.|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            347999999999999999999999999999999999876 8999999999999999999999 89999999999999865


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.79  E-value=1.4e-19  Score=118.42  Aligned_cols=85  Identities=33%  Similarity=0.593  Sum_probs=79.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||+|||+.+++++|+++|.+||.|..|.++.++.++++++||||+|.+.++|++|+..|++..+.++.|.|++++
T Consensus        46 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~  125 (135)
T 2lea_A           46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR  125 (135)
T ss_dssp             GCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45789999999999999999999999999999999988889999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 032111          112 DRPPR  116 (147)
Q Consensus       112 ~~~~~  116 (147)
                      +..+.
T Consensus       126 ~~~~~  130 (135)
T 2lea_A          126 YGRPP  130 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.79  E-value=1e-18  Score=107.97  Aligned_cols=80  Identities=33%  Similarity=0.593  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC--CeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN--GRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~--g~~l~v  107 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.+..+      ++||||+|.+.++|++|++.||+..+.  ++.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345589999999999999999999999999999988653      579999999999999999999999999  999999


Q ss_pred             EeecCCCC
Q 032111          108 SFANDRPP  115 (147)
Q Consensus       108 ~~~~~~~~  115 (147)
                      .+++++++
T Consensus        88 ~~a~~~~~   95 (97)
T 1why_A           88 DFAKSGPS   95 (97)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99998654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.79  E-value=1.9e-19  Score=106.18  Aligned_cols=75  Identities=32%  Similarity=0.615  Sum_probs=71.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++ +++..+.|+.|.|+++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999988889999999999999999999998 9999999999999875

>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=99.79  E-value=3.3e-19  Score=113.46  Aligned_cols=83  Identities=12%  Similarity=0.251  Sum_probs=76.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCe-eEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDI-TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +.+.++|||.|||+++++++|+++|.+||.| ..|.++.++ +++++|||||+|.+.++|++||+. ++..|.++.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4456899999999999999999999999999 889999987 899999999999999999999996 9999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++...+
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.79  E-value=1.2e-18  Score=112.21  Aligned_cols=85  Identities=28%  Similarity=0.499  Sum_probs=78.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+|||+.+++++|+++|.+||.|..+.++.+. ++++++||||+|.+.++|++|+..|++..+.|+.|.|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34556899999999999999999999999999999999987 88999999999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++....
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            998653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.79  E-value=4.9e-19  Score=112.13  Aligned_cols=83  Identities=22%  Similarity=0.285  Sum_probs=71.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .+...++|||+|||+++++++|+++|.+|| .|..+.+..+    .++|||||+|.+.++|++||+.|++..+.|+.|.|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            445668999999999999999999999999 8998877532    46799999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 032111          108 SFANDRPP  115 (147)
Q Consensus       108 ~~~~~~~~  115 (147)
                      +++..+++
T Consensus       100 ~~a~~~p~  107 (111)
T 2jvr_A          100 ERDDNPPP  107 (111)
T ss_dssp             EESCC---
T ss_pred             EECCCCCC
Confidence            99986544

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=2.4e-18  Score=104.89  Aligned_cols=78  Identities=26%  Similarity=0.513  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++++        ||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            445689999999999999999999999999999988743        999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +++...
T Consensus        78 a~~~~~   83 (90)
T 2dnp_A           78 STKGQK   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            987644

>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=99.79  E-value=2.7e-18  Score=106.95  Aligned_cols=81  Identities=14%  Similarity=0.240  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD--GQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--~~~~~g~~l~v  107 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++.+      ++||||+|.+.++|++|++.|+  +..+.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345689999999999999999999999999999988764      6799999999999999999774  67899999999


Q ss_pred             EeecCCCCC
Q 032111          108 SFANDRPPR  116 (147)
Q Consensus       108 ~~~~~~~~~  116 (147)
                      .+++++...
T Consensus        86 ~~a~~~~~~   94 (101)
T 2cq1_A           86 QYSNHKELK   94 (101)
T ss_dssp             EECSCSSCC
T ss_pred             EEcCcccCc
Confidence            999876554

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.79  E-value=1.7e-18  Score=107.35  Aligned_cols=79  Identities=19%  Similarity=0.336  Sum_probs=70.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCe--eCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQE--LNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~--~~g~~l~v  107 (147)
                      ..+.++|||+|||+++++++|+++|.+||.|..+.+++.      +++|||+|.+.++|.+|++.|++..  +.|++|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            345689999999999999999999999999999988753      5799999999999999999999875  78999999


Q ss_pred             EeecCCC
Q 032111          108 SFANDRP  114 (147)
Q Consensus       108 ~~~~~~~  114 (147)
                      .++++++
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9998753

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=2.4e-19  Score=106.12  Aligned_cols=76  Identities=36%  Similarity=0.697  Sum_probs=72.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|++.++ ..+.|+.|.|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998889999999999999999999999988 9999999999886

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

Probab=99.78  E-value=1.1e-18  Score=114.49  Aligned_cols=82  Identities=41%  Similarity=0.673  Sum_probs=76.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ...+.++|||+|||+.+++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..+.|+.|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34566899999999999999999999999999999999998889999999999999999999999999999999999998


Q ss_pred             ee
Q 032111          109 FA  110 (147)
Q Consensus       109 ~~  110 (147)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.3e-18  Score=108.92  Aligned_cols=83  Identities=19%  Similarity=0.305  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITE-AKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ....++|||+|||+.+++++|+++|.+||.|.. +.++.+ .+++++|||||+|.+.++|++||.. ++..+.++.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            345689999999999999999999999999987 778777 7899999999999999999999997 9999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++...+
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.78  E-value=1.7e-18  Score=109.20  Aligned_cols=80  Identities=29%  Similarity=0.518  Sum_probs=72.0

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ......++|||+|||+.+++++|+++|.+||.|..+.++        ++||||+|.+.++|++|+..|++..+.|+.|.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   97 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV   97 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345567899999999999999999999999999999887        579999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 032111          108 SFANDRPP  115 (147)
Q Consensus       108 ~~~~~~~~  115 (147)
                      .++++...
T Consensus        98 ~~a~~~~~  105 (108)
T 2jvo_A           98 VYSKLPAK  105 (108)
T ss_dssp             ESCSCCC-
T ss_pred             EEecCCCC
Confidence            99987654

>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=99.78  E-value=8e-19  Score=111.83  Aligned_cols=76  Identities=26%  Similarity=0.410  Sum_probs=66.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE-----EE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN-----IR  106 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~-----l~  106 (147)
                      ..++|||.|||+++++++|+++|.+||.|..+.++.+       +||||+|.+.++|++||+.||+..|.|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4589999999999999999999999999999988765       79999999999999999999999999988     67


Q ss_pred             EEeecCCC
Q 032111          107 VSFANDRP  114 (147)
Q Consensus       107 v~~~~~~~  114 (147)
                      |..+.++.
T Consensus        88 v~~~~~~~   95 (115)
T 3beg_B           88 VKVDGPRS   95 (115)
T ss_dssp             EEECC---
T ss_pred             eccCCCCC
Confidence            77666543

>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=99.78  E-value=1.6e-18  Score=106.27  Aligned_cols=79  Identities=24%  Similarity=0.458  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcC-CeeCCeEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGD-ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG-QELNGRNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~-~~~~g~~l~v~  108 (147)
                      ...++|||+|||+++++++|+++|.+||. |..+.+.       .++||||+|.+.++|++|+..||+ ..+.++.|.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45589999999999999999999999998 6655552       357999999999999999999999 99999999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      ++.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876543

>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=99.78  E-value=9.1e-20  Score=119.80  Aligned_cols=83  Identities=17%  Similarity=0.274  Sum_probs=73.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .+...++|||.|||+++++++|+++|.+|| +..|.++.++. ++++|||||+|.+.++|++|| .+++..+.++.|.|.
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELF  118 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEE
Confidence            345568999999999999999999999999 67999988865 899999999999999999999 689999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++...+
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            988654

>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=99.78  E-value=2.2e-18  Score=109.39  Aligned_cols=82  Identities=23%  Similarity=0.517  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee--------CC
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL--------NG  102 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~--------~g  102 (147)
                      .+.++|||.|||+.+++++|+++|.+||.|..+.++.++ ++.+++||||+|.+.++|++|+..||+..+        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            456899999999999999999999999999999999987 899999999999999999999999999999        57


Q ss_pred             eEEEEEeecCC
Q 032111          103 RNIRVSFANDR  113 (147)
Q Consensus       103 ~~l~v~~~~~~  113 (147)
                      ++|.|.++.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999998843

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.78  E-value=1.2e-18  Score=111.59  Aligned_cols=82  Identities=21%  Similarity=0.315  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCC---eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGD---ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ....++|||+|||+++++++|+++|..||.   |..|.++.++. ++++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            345689999999999999999999999998   89999998866 8999999999999999999999 999999999999


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      |.++...
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9998643

>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=99.78  E-value=3.7e-18  Score=109.12  Aligned_cols=82  Identities=15%  Similarity=0.278  Sum_probs=73.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD--GQELNGRNIR  106 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--~~~~~g~~l~  106 (147)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.+      ++||||+|.+.++|++|++.|+  +..+.|++|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            4456689999999999999999999999999999998865      5899999999999999999887  4689999999


Q ss_pred             EEeecCCCCC
Q 032111          107 VSFANDRPPR  116 (147)
Q Consensus       107 v~~~~~~~~~  116 (147)
                      |.++++++..
T Consensus       101 V~~a~~k~~~  110 (119)
T 2ad9_A          101 IQFSNHKELK  110 (119)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCCCCC
Confidence            9999876554

>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=99.78  E-value=3.4e-18  Score=107.97  Aligned_cols=77  Identities=25%  Similarity=0.583  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ...++|||.|||+. +++++|+++|.+||.|..+.+        +++||||+|.+.++|++|+..|++..+.++.|.|++
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34589999999999 999999999999999999988        357999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +..+.+
T Consensus        97 a~~~~~  102 (110)
T 1wf1_A           97 AGEPKP  102 (110)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            985443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=2.2e-18  Score=103.79  Aligned_cols=73  Identities=19%  Similarity=0.276  Sum_probs=68.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...|||+||++.+++++|+++|.+||.|..+.+..      ++|||||+|.+.++|++|++.||+..+.++.|+|+.+.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46899999999999999999999999999998865      47999999999999999999999999999999999884

>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=99.78  E-value=3.1e-18  Score=106.15  Aligned_cols=80  Identities=26%  Similarity=0.555  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|||+.+++++|+++|.+||.|..+.+.++      ++||||+|.+.++|++|++.|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345689999999999999999999999999999988754      57999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2cpj_A           86 ACHSAS   91 (99)
T ss_dssp             SSCCSC
T ss_pred             cCCCCC
Confidence            987654

>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=99.77  E-value=1.5e-18  Score=108.25  Aligned_cols=79  Identities=14%  Similarity=0.212  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC--eeCCeEEE
Q 032111           30 SQSQTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ--ELNGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~--~~~g~~l~  106 (147)
                      ..+.++|||+|||+ .+++++|+++|.+||.|..+.++++      ++||||+|.+.++|++|++.|++.  .+.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34568999999999 9999999999999999999988765      369999999999999999998854  59999999


Q ss_pred             EEeecCCC
Q 032111          107 VSFANDRP  114 (147)
Q Consensus       107 v~~~~~~~  114 (147)
                      |.+++...
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99998654

>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=99.77  E-value=1.6e-19  Score=110.03  Aligned_cols=80  Identities=36%  Similarity=0.674  Sum_probs=73.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ++|||+|||.++++++|+++|.+||.|..+.++.++.++.+++||||+|.+.+ |++|+..|++..+.|+.|.|+++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999999888999999999999999 99999999999999999999998865


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=4e-19  Score=114.61  Aligned_cols=83  Identities=18%  Similarity=0.312  Sum_probs=75.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+|||+.+++++|+++|..||.|..+.++.+..+++++|||||+|.+.++|++||. |++..|.++.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34556899999999999999999999999999886666666789999999999999999999999 99999999999999


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      ++..
T Consensus       100 ~a~~  103 (124)
T 1wel_A          100 PITK  103 (124)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9864

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.77  E-value=1.2e-18  Score=114.12  Aligned_cols=81  Identities=21%  Similarity=0.298  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCC---eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGD---ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ....++|||+|||+++++++|+++|.+||.   |..|.++.++. ++++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            345689999999999999999999999998   88999999876 9999999999999999999999 999999999999


Q ss_pred             EEeecC
Q 032111          107 VSFAND  112 (147)
Q Consensus       107 v~~~~~  112 (147)
                      |.++..
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            998764

>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=99.77  E-value=6.6e-18  Score=104.47  Aligned_cols=78  Identities=22%  Similarity=0.428  Sum_probs=70.6

Q ss_pred             hCCCCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           28 FMSQSQTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ....+.++|||+|||+ .+++++|+++|.+||.|..+.+.        ++||||+|.+.++|++|+..|++..+.|+.|.
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3455678999999998 99999999999999999999883        57999999999999999999999999999999


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      |+++++.
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.77  E-value=3.4e-18  Score=106.32  Aligned_cols=79  Identities=25%  Similarity=0.462  Sum_probs=71.9

Q ss_pred             hCCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           28 FMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        28 ~~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ..+...++|||+|||.++++++|+++|.+||.|..+.+..      .++||||+|.+.++|++|+..|++..+.|+.|+|
T Consensus        22 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   95 (101)
T 2la4_A           22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT   95 (101)
T ss_dssp             TSCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCC
T ss_pred             cCCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3445568999999999999999999999999999998873      4689999999999999999999999999999999


Q ss_pred             EeecC
Q 032111          108 SFAND  112 (147)
Q Consensus       108 ~~~~~  112 (147)
                      .++++
T Consensus        96 ~~a~~  100 (101)
T 2la4_A           96 GWGKE  100 (101)
T ss_dssp             CBCCC
T ss_pred             EeccC
Confidence            99875

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-17  Score=103.71  Aligned_cols=78  Identities=29%  Similarity=0.512  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNF--GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ..+.++|||.|||+.+++++|+++|.+|  |.|..+.+.        ++||||+|.+.++|++|+..|++..+.++.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            4456899999999999999999999999  889888764        469999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 032111          108 SFANDRPP  115 (147)
Q Consensus       108 ~~~~~~~~  115 (147)
                      .+++++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987543

>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=99.77  E-value=4.3e-18  Score=106.61  Aligned_cols=80  Identities=16%  Similarity=0.255  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC--eeCCeEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ--ELNGRNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~--~~~g~~l~v~  108 (147)
                      .+.++|||+|||+++++++|+++|.+||.|..+.++.+      ++||||+|.+.++|++|++.|++.  .+.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45589999999999999999999999999999988753      579999999999999999988754  5899999999


Q ss_pred             eecCCCCC
Q 032111          109 FANDRPPR  116 (147)
Q Consensus       109 ~~~~~~~~  116 (147)
                      +++.+...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-19  Score=112.03  Aligned_cols=83  Identities=24%  Similarity=0.423  Sum_probs=74.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||+|||+.+++++|+++|.+||.|.. .++.+..++.+++||||+|.+.++|++|++ |++..+.++.|.|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            34679999999999999999999999998876 555665678889999999999999999999 9999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      .++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.76  E-value=1.7e-18  Score=108.60  Aligned_cols=82  Identities=27%  Similarity=0.400  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCC------CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCe-
Q 032111           31 QSQTKLFVGGLSWGT------DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGR-  103 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~-  103 (147)
                      ...++|||+|||+.+      ++++|+++|.+||.|..+.++  ..+++++|||||+|.+.++|++|+..|++..+.|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            345799999999999      779999999999999999887  36789999999999999999999999999999998 


Q ss_pred             EEEEEeecCCC
Q 032111          104 NIRVSFANDRP  114 (147)
Q Consensus       104 ~l~v~~~~~~~  114 (147)
                      .|.|.++....
T Consensus        91 ~l~V~~a~~~~  101 (105)
T 2nlw_A           91 TFRVNLFTDFD  101 (105)
T ss_dssp             EEEEECSCCCC
T ss_pred             eEEEEEcchHh
Confidence            99999987643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.76  E-value=3.7e-18  Score=105.29  Aligned_cols=77  Identities=21%  Similarity=0.457  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+.++|||+|||+ .+++++|+++|.+||.|..+.+.        ++||||+|.+.++|++|+..|++..+.|+.|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4568999999998 99999999999999999999884        57999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +.+...
T Consensus        80 a~~~~~   85 (96)
T 2kvi_A           80 SSSNAR   85 (96)
T ss_dssp             EECCCC
T ss_pred             cCcCCC
Confidence            987543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=4.2e-18  Score=105.25  Aligned_cols=81  Identities=23%  Similarity=0.416  Sum_probs=71.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||+|||+.+++++|+++|.+||.|. +.++.+    .+++||||+|.+.++|++|+..|++..+.|+.|.|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34468999999999999999999999999986 555543    4678999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      ++++.+
T Consensus        91 a~~~~~   96 (97)
T 2e5j_A           91 ARQQRD   96 (97)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987643

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.76  E-value=6.8e-18  Score=107.29  Aligned_cols=82  Identities=20%  Similarity=0.389  Sum_probs=74.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ++...++|||+|||+.+++++|+++|.+||.|..+.++.+   +..++||||+|.+.++|++|+..||+..+.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   80 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVL   80 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            4456689999999999999999999999999999998865   3458999999999999999999999999999999999


Q ss_pred             eecCC
Q 032111          109 FANDR  113 (147)
Q Consensus       109 ~~~~~  113 (147)
                      ++.+.
T Consensus        81 ~a~~~   85 (115)
T 3lqv_A           81 YYNAN   85 (115)
T ss_dssp             ECCHH
T ss_pred             EecCC
Confidence            98753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.75  E-value=1.4e-17  Score=116.43  Aligned_cols=83  Identities=23%  Similarity=0.412  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+++++++|+++|++||.|..|.+++++.+++++|||||+|.+.++|++||..+++..+.++.|.+.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ...
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=5.9e-18  Score=109.58  Aligned_cols=81  Identities=19%  Similarity=0.322  Sum_probs=72.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLK----EAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|.+.   .+++++|||||+|.+.++|++|+..||+..+.|++|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~---~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            456899999999999999876    689999999988764   3577899999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 032111          107 VSFANDRP  114 (147)
Q Consensus       107 v~~~~~~~  114 (147)
                      |.+++.+.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99998654

>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=99.75  E-value=1.1e-18  Score=102.79  Aligned_cols=75  Identities=27%  Similarity=0.520  Sum_probs=70.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +|||+|||+++++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|++ +++..+.|+.|.|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999988889999999999999999999999 5889999999998874

>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=99.75  E-value=4.8e-18  Score=104.80  Aligned_cols=81  Identities=27%  Similarity=0.455  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLK----EAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      .+.++|||+|||+.+++++|+    ++|.+||.|..+.++.   ++.+++||||+|.+.++|++|+..|++..+.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            456899999999999999999    9999999999988763   466789999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 032111          107 VSFANDRP  114 (147)
Q Consensus       107 v~~~~~~~  114 (147)
                      |.++++..
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99998754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.75  E-value=4.2e-18  Score=104.93  Aligned_cols=80  Identities=23%  Similarity=0.497  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+.+++++|+++|.+||.|..+     ..++.++|||||+|.+.++|++|+..|++..+.|+.|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            355899999999999999999999999877655     256788999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      .++..
T Consensus        89 ~~~~~   93 (96)
T 1fjc_A           89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            87643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=9.4e-18  Score=105.90  Aligned_cols=77  Identities=17%  Similarity=0.329  Sum_probs=71.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ..+|||+|||+++++++|+++|.+| .|..|.++.++. ++++|||||+|.+.++|++|| .+++..+.++.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            3689999999999999999999999 899999998865 899999999999999999999 5899999999999988764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.75  E-value=2.5e-17  Score=110.15  Aligned_cols=82  Identities=28%  Similarity=0.552  Sum_probs=77.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+++++++|+++|.+||.|..+.++.++.++.++++|||+|.+.++|++|++.|++..+.++.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            47999999999999999999999999999999999988999999999999999999999999999999999999999875


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            43

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.75  E-value=7.4e-18  Score=114.99  Aligned_cols=83  Identities=29%  Similarity=0.535  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||.|||+.+++++|+++|.+||.|..|.++.+. ++.+++||||+|.+.++|++|++.|++..+.++.|.|++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999887 889999999999999999999999999999999999999


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      +...
T Consensus       164 a~~~  167 (177)
T 2f3j_A          164 VASQ  167 (177)
T ss_dssp             ESSG
T ss_pred             ecCC
Confidence            8753

>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=99.75  E-value=1.6e-17  Score=114.05  Aligned_cols=86  Identities=33%  Similarity=0.582  Sum_probs=75.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||.|||+.+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            3458999999999999999999999999999999999988899999999999999999999995 789999999999999


Q ss_pred             cCCCCCC
Q 032111          111 NDRPPRS  117 (147)
Q Consensus       111 ~~~~~~~  117 (147)
                      .++....
T Consensus       181 ~~k~~~~  187 (196)
T 1l3k_A          181 LSKQEMA  187 (196)
T ss_dssp             C------
T ss_pred             CChhHhc
Confidence            8876543

>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=99.74  E-value=5.7e-18  Score=107.14  Aligned_cols=81  Identities=14%  Similarity=0.222  Sum_probs=71.1

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcC--CeeCCeEE
Q 032111           29 MSQSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG--QELNGRNI  105 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~--~~~~g~~l  105 (147)
                      ...+.++|||+|||++ +++++|+++|.+||.|..+.+++.      ++||||+|.+.++|++|++.|++  ..+.|+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3456789999999998 999999999999999999988643      57999999999999999998864  56899999


Q ss_pred             EEEeecCCCC
Q 032111          106 RVSFANDRPP  115 (147)
Q Consensus       106 ~v~~~~~~~~  115 (147)
                      .|.+++.+..
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999986543

>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=99.74  E-value=1.7e-17  Score=99.86  Aligned_cols=75  Identities=25%  Similarity=0.522  Sum_probs=69.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM-DGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l-~~~~~~g~~l~v~~  109 (147)
                      ...++|||+|||+.+++++|+++|.+||.|..+.++.+      ++||||+|.+.++|++|+..| ++..+.|++|.|++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            44589999999999999999999999999999988864      579999999999999999998 99999999999998


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=2.7e-17  Score=101.03  Aligned_cols=78  Identities=23%  Similarity=0.447  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+.+++++|+++|.+||.|..|  +.++.+++   ||||+|.+.++|++|+. |++..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            34799999999999999999999999999987  55545554   99999999999999999 99999999999999887


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      ++..
T Consensus        81 ~~~~   84 (94)
T 2e5g_A           81 QKEF   84 (94)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            5543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.74  E-value=2.2e-18  Score=103.13  Aligned_cols=72  Identities=29%  Similarity=0.455  Sum_probs=66.4

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCe-EEE
Q 032111           34 TKLFVGGLSWGT------DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGR-NIR  106 (147)
Q Consensus        34 ~~i~v~nlp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~-~l~  106 (147)
                      ++|||+|||+.+      ++++|+++|.+||.|..+.++  +.+++++|||||+|.+.++|++|+..||+..+.|+ +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      679999999999999999877  36788999999999999999999999999999998 876


Q ss_pred             E
Q 032111          107 V  107 (147)
Q Consensus       107 v  107 (147)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            5

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.74  E-value=3.5e-17  Score=109.36  Aligned_cols=82  Identities=39%  Similarity=0.741  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+..+|||.|||..+++++|+++|.+||.|..+.++.+..++.++|+|||+|.+.++|.+|+..|++..+.|+.|.|.+
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            86

>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=99.74  E-value=2.1e-18  Score=108.51  Aligned_cols=81  Identities=19%  Similarity=0.265  Sum_probs=74.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCC---eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGD---ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ....++|||+|||+++++++|+++|..+|.   |..|.++.++. ++++|||||+|.+.++|++||. +++..+.++.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            345689999999999999999999999887   89999998866 9999999999999999999999 999999999999


Q ss_pred             EEeecC
Q 032111          107 VSFAND  112 (147)
Q Consensus       107 v~~~~~  112 (147)
                      |.++..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            998864

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.74  E-value=2.6e-17  Score=110.42  Aligned_cols=83  Identities=25%  Similarity=0.460  Sum_probs=78.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.++.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            45899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=4.3e-17  Score=113.51  Aligned_cols=87  Identities=28%  Similarity=0.553  Sum_probs=81.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||.|||..+++++|+++|.+||.|..+.++.+..++++++||||+|.+.++|.+|+..||+..|.|+.|.|.+
T Consensus       122 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~  201 (216)
T 2qfj_A          122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK  201 (216)
T ss_dssp             HTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEE
T ss_pred             cCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.+++..
T Consensus       202 a~~~~~~  208 (216)
T 2qfj_A          202 AVTPPMP  208 (216)
T ss_dssp             CSSCSST
T ss_pred             ecCCCCC
Confidence            9876543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.1e-17  Score=100.28  Aligned_cols=79  Identities=29%  Similarity=0.497  Sum_probs=70.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ..+.++|||.|+  .+++++|+++|.+||.|..|.+.      ..++||||+|.+.++|++|+..|++..+.++.|.|.+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            445689999996  89999999999999999999884      3468999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +.+++..
T Consensus        84 a~~~~~~   90 (97)
T 1x5p_A           84 ARKQPML   90 (97)
T ss_dssp             CSSCCCC
T ss_pred             CCCCCCC
Confidence            9876544

>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=99.73  E-value=4.1e-18  Score=112.32  Aligned_cols=87  Identities=22%  Similarity=0.414  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEE-----EEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAK-----VITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN  104 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~-----~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~  104 (147)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.     -+....++.++|||||+|.+.++|.+|+..||+..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            34568999999999999999999999999887631     0111246788999999999999999999999999999999


Q ss_pred             EEEEeecCCCCC
Q 032111          105 IRVSFANDRPPR  116 (147)
Q Consensus       105 l~v~~~~~~~~~  116 (147)
                      |.|.++++..++
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999876544

>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=99.73  E-value=1.9e-17  Score=109.98  Aligned_cols=81  Identities=27%  Similarity=0.524  Sum_probs=74.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+|||+.+++++|+++|.+||.|..+.++.+     ++|||||+|.+.++|++|+..|++..+.|++|.|+
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  143 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE  143 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3445689999999999999999999999999999998876     46899999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++.++.
T Consensus       144 ~a~~~~  149 (150)
T 2i2y_A          144 LSNGEK  149 (150)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998753

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.73  E-value=5.5e-17  Score=111.55  Aligned_cols=85  Identities=26%  Similarity=0.495  Sum_probs=80.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||.|||+.+++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++|+..|++..+.|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            55689999999999999999999999999999999999888999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      .++..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.73  E-value=3.2e-17  Score=99.48  Aligned_cols=75  Identities=16%  Similarity=0.297  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+.+++++|+++|.+| .|..+.+.      ++++||||+|.+.++|++|++.|++..+.|++|+|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            45899999999999999999999999 99998874      567899999999999999999999999999999999986


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1e-17  Score=107.85  Aligned_cols=81  Identities=20%  Similarity=0.252  Sum_probs=73.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCe----eEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDI----TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i----~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      ..+..+|||+|||+++++++|+++|.+||.|    ..|.++.+ .+++++|||||+|.+.++|++||.. ++..+.++.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            4556899999999999999999999999875    68888888 5899999999999999999999995 9999999999


Q ss_pred             EEEeecC
Q 032111          106 RVSFAND  112 (147)
Q Consensus       106 ~v~~~~~  112 (147)
                      .|..+..
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9988753

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.72  E-value=2e-17  Score=103.01  Aligned_cols=80  Identities=25%  Similarity=0.605  Sum_probs=74.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+.+++++|+++|.+||.|..+.++.++ +++++|||||+|.+.++|++|+.  ++..+.|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            34799999999999999999999999999999999997 89999999999999999999999  8999999999999987


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      ++.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            654

>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=99.72  E-value=2.4e-17  Score=104.30  Aligned_cols=76  Identities=18%  Similarity=0.201  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+.+++++|+++|.+||.|..|.++.      .++||||+|.+.++|++|+..||+..+.++.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            357999999999999999999999999999988764      45799999999999999999999999999999999987


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.72  E-value=7.1e-17  Score=108.72  Aligned_cols=80  Identities=26%  Similarity=0.532  Sum_probs=76.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...+|||.|||+.+++++|+++|.+||.|..+.++.++.++.++|+|||+|.+.++|++|+..|++..+.|+.|.|+++.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            45899999999999999999999999999999999998889999999999999999999999999999999999999873

>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=99.72  E-value=1.4e-17  Score=107.60  Aligned_cols=80  Identities=25%  Similarity=0.362  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCee--EEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDIT--EAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~--~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .....+|||+|||+++++++|+++|.+| .|.  .|.++.++. ++++|||||+|.+.++|++||+ +++..|.++.|.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            3456899999999999999999999999 676  888888866 9999999999999999999999 4779999999999


Q ss_pred             EeecC
Q 032111          108 SFAND  112 (147)
Q Consensus       108 ~~~~~  112 (147)
                      ..+..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            88764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=4.3e-17  Score=100.32  Aligned_cols=79  Identities=22%  Similarity=0.306  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEE-EEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEA-KVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ..++|||+|||+.+++++|+++|.+||.|..+ .++.++.++    .|||+|.+.++|++|+..|++..+.|+.|.|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45799999999999999999999999999999 477765443    3999999999999999999999999999999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      .++.
T Consensus        90 ~~~~   93 (96)
T 2e44_A           90 PDEM   93 (96)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            8763

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.71  E-value=1.1e-16  Score=109.81  Aligned_cols=84  Identities=37%  Similarity=0.660  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +.+.++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++||.. ++..+.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            34558999999999999999999999999999999999988999999999999999999999985 88999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +....
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
T ss_pred             ccCcc
Confidence            87653

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.70  E-value=2.5e-16  Score=101.91  Aligned_cols=79  Identities=23%  Similarity=0.414  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceE-EEEEeCCHHHHHHHHHHhcCCeeCC--eEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGF-GFVTYDSNESASSAQSAMDGQELNG--RNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~ai~~l~~~~~~g--~~l~  106 (147)
                      +...-.|||+||++.+++++|+++|.+||.|.+|.+..+.     +++ |||+|.+.++|++|++.|++..|.+  ..|+
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~Lr   99 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   99 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEE
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEE
Confidence            3444578899999999999999999999999999887642     467 9999999999999999999999988  8899


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      |++++..
T Consensus       100 I~~ak~~  106 (130)
T 3zzy_A          100 IDFSKLT  106 (130)
T ss_dssp             EEECSCS
T ss_pred             EEecCCC
Confidence            9999865

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.70  E-value=3.6e-17  Score=109.67  Aligned_cols=80  Identities=34%  Similarity=0.633  Sum_probs=76.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ..+|||.|||+.+++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++|++ +++..+.|++|.|.++.+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCC
Confidence            4689999999999999999999999999999999988889999999999999999999998 899999999999999987


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.70  E-value=1.4e-16  Score=106.78  Aligned_cols=78  Identities=22%  Similarity=0.368  Sum_probs=69.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEee
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVSFA  110 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~~  110 (147)
                      ..+|||+||++.+++++|+++|++||.|.+|.+..+.    .++||||+|.+.++|++|++.|++..|.+  +.|+|+++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            4578999999999999999999999999999886432    46899999999999999999999999966  99999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      +++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=2e-16  Score=110.62  Aligned_cols=80  Identities=33%  Similarity=0.589  Sum_probs=74.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ..+|||.|||+.+++++|+++|.+||.|..+.++.+.  +.++|||||+|.+.++|++||+.||+..|.|++|.|.++.+
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999999874  44789999999999999999999999999999999999876


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      +.
T Consensus       181 ~~  182 (213)
T 4f02_A          181 RK  182 (213)
T ss_dssp             HH
T ss_pred             Cc
Confidence            43

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.69  E-value=1.1e-16  Score=102.56  Aligned_cols=78  Identities=21%  Similarity=0.255  Sum_probs=71.1

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCC----HHH----HHHHHH--HhcCCe
Q 032111           34 TKLFVGGL----SWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDS----NES----ASSAQS--AMDGQE   99 (147)
Q Consensus        34 ~~i~v~nl----p~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~----~~~----a~~ai~--~l~~~~   99 (147)
                      ..|||+||    |+.+++.+|+++|.+||.|.++.++.|+.|+.++||+||+|.+    .++    |.+|+.  .+++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    9999999999999999999999999999999999999999995    322    788888  789999


Q ss_pred             eCCeEEEEEeec
Q 032111          100 LNGRNIRVSFAN  111 (147)
Q Consensus       100 ~~g~~l~v~~~~  111 (147)
                      |.|+.|+|.+..
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999865

>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=99.69  E-value=1.5e-16  Score=100.82  Aligned_cols=80  Identities=20%  Similarity=0.389  Sum_probs=69.9

Q ss_pred             CCCCCCeEEE--cCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee-----C
Q 032111           29 MSQSQTKLFV--GGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL-----N  101 (147)
Q Consensus        29 ~~~~~~~i~v--~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~-----~  101 (147)
                      ...+..+|||  +||++.+++++|+++|++||.|..+.++.+      ++||||+|.+.++|++|++.||+..+     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3445678999  679999999999999999999999877532      68999999999999999999999998     6


Q ss_pred             CeEEEEEeecCCC
Q 032111          102 GRNIRVSFANDRP  114 (147)
Q Consensus       102 g~~l~v~~~~~~~  114 (147)
                      +++|.|.++...+
T Consensus        95 g~~l~v~~a~~~p  107 (114)
T 2cq2_A           95 KITLYLNFVEKVQ  107 (114)
T ss_dssp             EEECEEEEESCCC
T ss_pred             CcEEEEEecccCc
Confidence            8899999987543

>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=99.69  E-value=3.2e-16  Score=105.03  Aligned_cols=80  Identities=29%  Similarity=0.549  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~  108 (147)
                      ...++|||.|||..+++++|+++|++||.|..+.++.++.++.++++|||+|.+.++|.+|+..|++..+.|  ++|.|+
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            356899999999999999999999999999999999998889999999999999999999999999999977  999998


Q ss_pred             ee
Q 032111          109 FA  110 (147)
Q Consensus       109 ~~  110 (147)
                      ++
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=6.4e-17  Score=98.09  Aligned_cols=77  Identities=25%  Similarity=0.432  Sum_probs=65.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+++++++|+++|.+||.|..+.++.+     +++||||+|.+.++|++++..  ...+.++.|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            4589999999999999999999999999999988754     578999999999999865331  345589999999988


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      ++..
T Consensus        77 ~~~~   80 (88)
T 1wf0_A           77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.69  E-value=3e-16  Score=104.78  Aligned_cols=80  Identities=23%  Similarity=0.473  Sum_probs=73.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ++|||+|||+++++++|+++|.+||.|..+.++.++ ++++++||||+|.+.++|++|+..|++..+.++.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999998885 4778999999999999999999999999999999999998765


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.68  E-value=1.8e-16  Score=110.33  Aligned_cols=82  Identities=28%  Similarity=0.533  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||+|||.++++++|+++|.+||.|..+.++.++.++++++||||+|.+.++|++|++.|++..+.++.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            34799999999999999999999999999999999988889999999999999999999999999999999999998876


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus       107 ~~  108 (216)
T 2qfj_A          107 NI  108 (216)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.68  E-value=1.9e-16  Score=95.58  Aligned_cols=71  Identities=21%  Similarity=0.556  Sum_probs=65.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF----G-------DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      +.++|||+|||+.+++++|+++|.+|    |       .|..+.+..+      ++||||+|.+.++|++|+ .|++..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            45899999999999999999999999    8       8888887654      589999999999999999 8999999


Q ss_pred             CCeEEEEEe
Q 032111          101 NGRNIRVSF  109 (147)
Q Consensus       101 ~g~~l~v~~  109 (147)
                      .|+.|+|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999874

>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=99.67  E-value=4e-16  Score=108.68  Aligned_cols=77  Identities=16%  Similarity=0.298  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLS-WGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +.++|||+||| +.+++++|+++|.+||.|..|+++.++     +|||||+|.+.++|++||+.||+..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            45899999999 899999999999999999999987652     689999999999999999999999999999999998


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      +..
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.5e-16  Score=101.09  Aligned_cols=77  Identities=23%  Similarity=0.395  Sum_probs=65.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCC---CccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERES---GKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ...++|||+|||+++++++|+++|.+||.|. +.++.+..+   ++++|||||+|.+.++|++||+.|+  .++|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3458999999999999999999999999999 777777666   6899999999999999999999884  366666655


Q ss_pred             Eee
Q 032111          108 SFA  110 (147)
Q Consensus       108 ~~~  110 (147)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>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=99.67  E-value=3.8e-16  Score=95.03  Aligned_cols=78  Identities=23%  Similarity=0.471  Sum_probs=62.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCe--eCCeEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQE--LNGRNIR  106 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~--~~g~~l~  106 (147)
                      ...+..+|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++    +++..  +.++.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            3456689999999999999999999999999999988764     67999999999999884    45554  4599999


Q ss_pred             EEeecCCCC
Q 032111          107 VSFANDRPP  115 (147)
Q Consensus       107 v~~~~~~~~  115 (147)
                      |.++.++..
T Consensus        78 v~~a~~k~~   86 (89)
T 3d2w_A           78 ISNAEPKHN   86 (89)
T ss_dssp             EEECC----
T ss_pred             EEEcCCCCc
Confidence            999886543

>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=99.67  E-value=7.3e-16  Score=103.00  Aligned_cols=79  Identities=32%  Similarity=0.632  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE--EEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN--IRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~--l~v~~  109 (147)
                      ...+|||.|||..+++++|+++|.+||.|..+.++.++.++.++++|||+|.+.++|.+|+..||+..+.|+.  |.|.+
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4578999999999999999999999999999999998888999999999999999999999999999999965  77776


Q ss_pred             e
Q 032111          110 A  110 (147)
Q Consensus       110 ~  110 (147)
                      +
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.67  E-value=6.9e-16  Score=103.94  Aligned_cols=82  Identities=27%  Similarity=0.477  Sum_probs=73.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCC--ccceEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESG--KSRGFGFVTYDSNESASSAQSAMDGQELN---GRNIR  106 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~ai~~l~~~~~~---g~~l~  106 (147)
                      +.++|||+|||+.+++++|+++|.+||.|..+.++.++.++  ++++||||+|.+.++|++|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            45799999999999999999999999999999999987776  89999999999999999999999998775   57777


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      +.++...
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8777654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.67  E-value=8.8e-16  Score=98.78  Aligned_cols=75  Identities=15%  Similarity=0.294  Sum_probs=66.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceE-EEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEee
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGF-GFVTYDSNESASSAQSAMDGQELNG--RNIRVSFA  110 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~~  110 (147)
                      ..|||.||++.+++++|+++|++||.|..|.+...      .|| |||+|.+.++|++|++.||+..|.+  +.|+|.++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            45789999999999999999999999999988642      276 9999999999999999999999987  68999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      +++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8653

>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=99.66  E-value=7e-16  Score=103.91  Aligned_cols=81  Identities=31%  Similarity=0.525  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC---CeEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN---GRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~---g~~l~  106 (147)
                      .....+|||.|||+.+++++|+++|.+||.|..+.++.++ ++.++|||||+|.+.++|.+|+..||+..+.   +++|.
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeE
Confidence            3356799999999999999999999999999999998884 5889999999999999999999999998776   48999


Q ss_pred             EEeec
Q 032111          107 VSFAN  111 (147)
Q Consensus       107 v~~~~  111 (147)
                      |.++.
T Consensus       171 V~~ad  175 (175)
T 3nmr_A          171 VKFAD  175 (175)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99874

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.66  E-value=2.1e-15  Score=94.44  Aligned_cols=83  Identities=16%  Similarity=0.238  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCC-----CCCHHHHHHHhhccCCeeEEEEEecCCC-CccceEEEEEeCCHHHHHHHHHHhcCCeeCCe
Q 032111           30 SQSQTKLFVGGLSW-----GTDDSSLKEAFSNFGDITEAKVITERES-GKSRGFGFVTYDSNESASSAQSAMDGQELNGR  103 (147)
Q Consensus        30 ~~~~~~i~v~nlp~-----~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~  103 (147)
                      ..+.++|+|.||..     +.++++|++.|++||.|..+.++.++.+ +.++|++||+|.+.++|.+|+..||+..+.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            34568999999863     2367899999999999999999987543 57899999999999999999999999999999


Q ss_pred             EEEEEeecC
Q 032111          104 NIRVSFAND  112 (147)
Q Consensus       104 ~l~v~~~~~  112 (147)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999999863

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=7e-16  Score=93.75  Aligned_cols=71  Identities=28%  Similarity=0.402  Sum_probs=63.4

Q ss_pred             CeEEEcCCCCCCCHHH----HHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           34 TKLFVGGLSWGTDDSS----LKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~----l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +.|||.|||+.+++++    |+++|.+|| .|..|       ++   |+|||+|.+.++|++|++.|++..+.|++|+|.
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~   79 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVS   79 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEE
Confidence            3499999999999987    558999994 99887       22   899999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      +++...
T Consensus        80 ~A~~~s   85 (96)
T 2diu_A           80 FTPKNR   85 (96)
T ss_dssp             SSCCSC
T ss_pred             ecCCCc
Confidence            998654

>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=99.64  E-value=8.6e-16  Score=103.78  Aligned_cols=78  Identities=23%  Similarity=0.510  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||.|||+.+++++|+++|.+||.|..+     ..++.+++||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            45799999999999999999999999977655     4678889999999999999999999999999999999999998


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      +++
T Consensus       173 ~k~  175 (175)
T 1fje_B          173 EKG  175 (175)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            753

>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=99.64  E-value=2.2e-15  Score=103.98  Aligned_cols=79  Identities=20%  Similarity=0.311  Sum_probs=72.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+++++++|+++|.+||.|..|.++++. ++.++|||||+|.+.++|++|+..+ +..+.|+.|.|.+...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            3789999999999999999999999999999999875 4889999999999999999999865 4699999999998775


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      .
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            4

>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=99.63  E-value=1.3e-15  Score=110.89  Aligned_cols=84  Identities=25%  Similarity=0.465  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCC-CCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERE-SGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ....++|||.|||+. +++++|+++|.+||.|..+.++.+.. ++.+++||||+|.+.++|.+|+ .||+..+.|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            445689999999999 99999999999999999999988765 5889999999999999999999 99999999999999


Q ss_pred             EeecCCC
Q 032111          108 SFANDRP  114 (147)
Q Consensus       108 ~~~~~~~  114 (147)
                      .++.+++
T Consensus       286 ~~a~~k~  292 (292)
T 2ghp_A          286 SLADKKP  292 (292)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9998763

>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=99.63  E-value=1e-15  Score=102.52  Aligned_cols=79  Identities=32%  Similarity=0.705  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..  ...+.|+.|.+.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            357999999999999999999999999999999999988999999999999999999999994  568899998888765


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.63  E-value=3.3e-15  Score=108.16  Aligned_cols=81  Identities=27%  Similarity=0.457  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLK----EAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      .+.++|||+|||+++++++|+    ++|.+||.|..|.+++   +++++|||||+|.+.++|++|++.|++..+.|+.|.
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            446899999999999999976    8999999999998775   577899999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 032111          107 VSFANDRP  114 (147)
Q Consensus       107 v~~~~~~~  114 (147)
                      |.+++...
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99987543

>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=99.62  E-value=6.7e-15  Score=106.64  Aligned_cols=85  Identities=24%  Similarity=0.449  Sum_probs=79.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .....+|||+|||+.+++++|+++|.+||.|..+.++.+..++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +.+..
T Consensus       172 a~~~~  176 (284)
T 3smz_A          172 TDAGQ  176 (284)
T ss_dssp             CCGGG
T ss_pred             CCCCC
Confidence            87643

>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=99.62  E-value=4.2e-15  Score=107.70  Aligned_cols=84  Identities=32%  Similarity=0.463  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCC-CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGT-DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....+|||.|||+.+ ++++|+++|..||.|..+.++.+. ++.++++|||+|.+.++|.+|+..|++..+.|+.|.|.+
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            456899999999995 999999999999999999998875 788999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +.+...
T Consensus       261 a~~~~~  266 (284)
T 3smz_A          261 CAPGPP  266 (284)
T ss_dssp             CCSSSC
T ss_pred             ecCCCc
Confidence            987654

>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=99.61  E-value=3.4e-15  Score=105.40  Aligned_cols=80  Identities=23%  Similarity=0.417  Sum_probs=73.4

Q ss_pred             CCCCCCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           29 MSQSQTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      ...+.++|||+|||+ .+++++|+++|.+||.|..|.++.++     ++||||+|.+.++|++|++.|++..+.|+.|.|
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v  104 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            345668999999999 99999999999999999999998764     679999999999999999999999999999999


Q ss_pred             EeecCC
Q 032111          108 SFANDR  113 (147)
Q Consensus       108 ~~~~~~  113 (147)
                      .++...
T Consensus       105 ~~a~~~  110 (229)
T 2adc_A          105 TLSKHQ  110 (229)
T ss_dssp             ECCSCC
T ss_pred             EEecCc
Confidence            998754

>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=99.61  E-value=1.5e-14  Score=91.42  Aligned_cols=83  Identities=19%  Similarity=0.321  Sum_probs=69.6

Q ss_pred             CCCCCCeEEEcCCCCCCC-----------HHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcC
Q 032111           29 MSQSQTKLFVGGLSWGTD-----------DSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDG   97 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~-----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~   97 (147)
                      .+.+.++|+|.||.....           +++|+++|.+||.|..+.+ .++   .++|||||+|.+.++|++|+..||+
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            344568999999944332           5799999999999999955 443   2689999999999999999999999


Q ss_pred             CeeCCeEEEEEeecCCCC
Q 032111           98 QELNGRNIRVSFANDRPP  115 (147)
Q Consensus        98 ~~~~g~~l~v~~~~~~~~  115 (147)
                      ..+.+++|.|.++.++..
T Consensus        87 ~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             CEECCcEEEEEEeCCCCC
Confidence            999999999999987543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.59  E-value=4.4e-15  Score=105.37  Aligned_cols=79  Identities=30%  Similarity=0.569  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCCC---------CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           30 SQSQTKLFVGGLSWGT---------DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      ....++|||+||+..+         ++++|+++|.+||.|..|.++..      ++||||+|.+.++|+.|++.|++..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4456899999999998         79999999999999999998853      68999999999999999999999999


Q ss_pred             ------------CCeEEEEEeecCCC
Q 032111          101 ------------NGRNIRVSFANDRP  114 (147)
Q Consensus       101 ------------~g~~l~v~~~~~~~  114 (147)
                                  .|+.|.|.|++..+
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             eccccccccccCCCCEEEEEEccCCC
Confidence                        89999999998654

>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=99.59  E-value=1.2e-14  Score=105.16  Aligned_cols=76  Identities=25%  Similarity=0.490  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l~v~~  109 (147)
                      ...++|||.|||..+++++|+++|.+||.|..+.++.++     ++||||+|.+.++|++|+..||+..+. |+.|+|.|
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            356789999999999999999999999999999988653     479999999999999999999999999 99999999


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            86

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.57  E-value=4.8e-15  Score=102.09  Aligned_cols=76  Identities=24%  Similarity=0.440  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           33 QTKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        33 ~~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      .++|||+|||+ .+++++|+++|.+||.|..+.++.++     ++||||+|.+.++|++|+..|++..+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            47999999999 99999999999999999999888764     5799999999999999999999999999999999987


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.57  E-value=1.4e-15  Score=102.70  Aligned_cols=83  Identities=25%  Similarity=0.442  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +.+.++|||+|||+.+++++|+++|.++|.+..+ ++.+..++.++|||||+|.+.++|++|++ |++..+.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            4456899999999999999999999999866542 23333567788999999999999999995 999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +.+..
T Consensus        88 ~~~~~   92 (175)
T 1fje_B           88 PKGRD   92 (175)
T ss_dssp             CCCSS
T ss_pred             CCCcc
Confidence            87654

>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=99.56  E-value=1.2e-14  Score=101.28  Aligned_cols=78  Identities=13%  Similarity=0.213  Sum_probs=67.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCe--eEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCe----E
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDI--TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGR----N  104 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i--~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~----~  104 (147)
                      .+..+|||.|||+.+++++|+++|++||.|  ..++++.+.  +..+++|||+|.+.++|.+||..||+..+.+.    +
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            456789999999999999999999999998  888887764  45569999999999999999999999999775    5


Q ss_pred             EEEEee
Q 032111          105 IRVSFA  110 (147)
Q Consensus       105 l~v~~~  110 (147)
                      +.|+++
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            666554

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.55  E-value=1.7e-14  Score=99.26  Aligned_cols=78  Identities=22%  Similarity=0.349  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l~v~  108 (147)
                      .+.++|||.|||..+++++|+++|.+|| .|..+.+..+.     +++|||+|.+.++|.+|+..|++..+. ++.|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4468999999999999999999999999 99999886542     579999999999999999999999999 9999999


Q ss_pred             eecCC
Q 032111          109 FANDR  113 (147)
Q Consensus       109 ~~~~~  113 (147)
                      +++++
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            98764

>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=99.55  E-value=5.1e-14  Score=99.31  Aligned_cols=79  Identities=22%  Similarity=0.336  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l~v  107 (147)
                      ..+.++|||.|||+.+++++|+++|.+|| .|..+.++.+     .+++|||+|.+.++|.+|+..|++..+. ++.|.|
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEE
Confidence            34568999999999999999999999999 9999988653     2579999999999999999999999999 999999


Q ss_pred             EeecCC
Q 032111          108 SFANDR  113 (147)
Q Consensus       108 ~~~~~~  113 (147)
                      .+++++
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            998864

>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=99.55  E-value=2.2e-14  Score=103.08  Aligned_cols=77  Identities=31%  Similarity=0.608  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||+|||+++++++|+++|..||.|..|.+.++      +|||||+|.+.++|.+|+..|++..+.++.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            345579999999999999999999999999999988643      57999999999999999999999999999999998


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      +.+
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            864

>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=99.55  E-value=3.4e-14  Score=102.11  Aligned_cols=82  Identities=27%  Similarity=0.353  Sum_probs=73.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC-eeC---CeEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ-ELN---GRNIR  106 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~-~~~---g~~l~  106 (147)
                      .+..+|||.|||+.+++++|+++|..||.|..+.++.+ .+++++|||||+|.+.++|.+|+..|++. .+.   +++|.
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            45679999999999999999999999999999999998 68999999999999999999999999554 443   89999


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      |.++.+.
T Consensus       173 v~~~~~~  179 (261)
T 3sde_A          173 VEPMEQF  179 (261)
T ss_dssp             EEECCCE
T ss_pred             Eeecccc
Confidence            9998754

>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=99.54  E-value=3.4e-14  Score=103.27  Aligned_cols=83  Identities=13%  Similarity=0.266  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFG-DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ...++|||+|||+.+++++|+++|.+|| .|..+.++.+.. +.+++||||+|.+.++|.+|+..|++..+.|+.|.|.+
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3568999999999999999999999999 999999988754 77899999999999999999999999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +.+..
T Consensus       194 a~~~~  198 (292)
T 2ghp_A          194 SNPLE  198 (292)
T ss_dssp             CCCC-
T ss_pred             CCCCc
Confidence            87654

>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=99.53  E-value=6.1e-14  Score=87.76  Aligned_cols=80  Identities=13%  Similarity=0.196  Sum_probs=67.9

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHhhccCCeeEEEEEecCCC--CccceEEEEEeCCHHHHHHHHHHhcCCe
Q 032111           32 SQTKLFVGGL--SWGTD--------DSSLKEAFSNFGDITEAKVITERES--GKSRGFGFVTYDSNESASSAQSAMDGQE   99 (147)
Q Consensus        32 ~~~~i~v~nl--p~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~ai~~l~~~~   99 (147)
                      +.+.|.|.|+  |.+..        .++|++.|++||.|.++.++++..+  ..++|++||+|.+.++|.+|+..||+..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4577888887  33333        3689999999999999999887544  3578999999999999999999999999


Q ss_pred             eCCeEEEEEeec
Q 032111          100 LNGRNIRVSFAN  111 (147)
Q Consensus       100 ~~g~~l~v~~~~  111 (147)
                      +.|+.|.|.+..
T Consensus        84 f~GR~i~v~~~~   95 (105)
T 3v4m_A           84 FANRVVVTKYCD   95 (105)
T ss_dssp             ETTEECEEEEEC
T ss_pred             eCCCEEEEEEeC
Confidence            999999999875

>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=99.52  E-value=8.2e-14  Score=93.57  Aligned_cols=76  Identities=21%  Similarity=0.528  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF----G-------DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      +.++|||+|||+++++++|+++|.+|    |       .|..+.+..      .++||||+|.+.++|++|+ .|++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            35799999999999999999999999    6       566665543      3689999999999999999 7999999


Q ss_pred             CCeEEEEEeecCCC
Q 032111          101 NGRNIRVSFANDRP  114 (147)
Q Consensus       101 ~g~~l~v~~~~~~~  114 (147)
                      .|+.|.|.++....
T Consensus        76 ~g~~i~v~~~~~~~   89 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQ   89 (172)
T ss_dssp             TTEECEEECCSSCC
T ss_pred             cCceeeecCCcccC
Confidence            99999999877543

>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=99.50  E-value=2e-13  Score=87.13  Aligned_cols=80  Identities=15%  Similarity=0.263  Sum_probs=69.0

Q ss_pred             CCCeEEEcCCC--CCC---CHHHHHHHhhccCCeeEEEEEecCC----CCccceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           32 SQTKLFVGGLS--WGT---DDSSLKEAFSNFGDITEAKVITERE----SGKSRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        32 ~~~~i~v~nlp--~~~---~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      +.++|+|.|+-  .++   .+++|++.|.+||.|..|.++.+..    ++..+|++||+|.+.++|.+|+..||+..+.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            45889999983  222   3579999999999999999988754    35678999999999999999999999999999


Q ss_pred             eEEEEEeec
Q 032111          103 RNIRVSFAN  111 (147)
Q Consensus       103 ~~l~v~~~~  111 (147)
                      +.|.|.+..
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.50  E-value=1.2e-13  Score=94.74  Aligned_cols=76  Identities=20%  Similarity=0.519  Sum_probs=65.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF----G-------DITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      ..++|||+|||+++++++|+++|.+|    +       .|..+.+.      ..++||||+|.+.++|++|+ .|++..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            45899999999999999999999999    4       45555443      34689999999999999999 7999999


Q ss_pred             CCeEEEEEeecCCC
Q 032111          101 NGRNIRVSFANDRP  114 (147)
Q Consensus       101 ~g~~l~v~~~~~~~  114 (147)
                      .|+.|.|.++....
T Consensus        76 ~g~~i~v~~~~~~~   89 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQ   89 (198)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             cCceEEEeCCCCCC
Confidence            99999999987653

>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=99.49  E-value=1.7e-14  Score=90.13  Aligned_cols=72  Identities=21%  Similarity=0.409  Sum_probs=60.4

Q ss_pred             EcCCCCCCCHHHHHHHh------------hccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           38 VGGLSWGTDDSSLKEAF------------SNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        38 v~nlp~~~~~~~l~~~f------------~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      +.+||+.+++++|++.|            ++||.|..+.++.+. +++++|||||+|.+.++|++|+..||+..+.|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            34555556666665555            999999999998874 47889999999999999999999999999999999


Q ss_pred             EEEee
Q 032111          106 RVSFA  110 (147)
Q Consensus       106 ~v~~~  110 (147)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.45  E-value=9.5e-13  Score=81.55  Aligned_cols=66  Identities=17%  Similarity=0.289  Sum_probs=57.3

Q ss_pred             CCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCCCC
Q 032111           43 WGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPP  115 (147)
Q Consensus        43 ~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~~~  115 (147)
                      ..+++++|+++|.+||.|..|.++     ++++|||||+|.+.++|++|+..++  .+.+++|.|.|++.++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEEEEccCCCC
Confidence            468999999999999999999887     3568999999999999999999744  46789999999887654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.41  E-value=7.9e-13  Score=98.31  Aligned_cols=77  Identities=19%  Similarity=0.383  Sum_probs=64.5

Q ss_pred             hCCCCCCeEEEcC--CCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC---C
Q 032111           28 FMSQSQTKLFVGG--LSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN---G  102 (147)
Q Consensus        28 ~~~~~~~~i~v~n--lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~---g  102 (147)
                      ..+.+..+|||+|  |++.+++++|+++|++||.|..|.+..      .++||||+|.+.++|++||+.||+..+.   |
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g   86 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccC
Confidence            3456678999999  578999999999999999999886643      3689999999999999999999999883   3


Q ss_pred             e--EEEEEee
Q 032111          103 R--NIRVSFA  110 (147)
Q Consensus       103 ~--~l~v~~~  110 (147)
                      +  .|.+.+.
T Consensus        87 ~~~~ly~~~~   96 (345)
T 3tht_A           87 QKITLYLNFV   96 (345)
T ss_dssp             CEEECEEEEC
T ss_pred             CceEEEEEEe
Confidence            4  5666655

>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=99.36  E-value=9.6e-12  Score=78.77  Aligned_cols=77  Identities=16%  Similarity=0.193  Sum_probs=63.3

Q ss_pred             CCCCeEEEcCCCCCC----------CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           31 QSQTKLFVGGLSWGT----------DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~----------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      .+.+.|.|.|+=...          .+++|++.|++||.|..+.+.++.    .+|++||+|.+.++|++|+..||+..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            345678888863211          124789999999999999886553    479999999999999999999999999


Q ss_pred             CCeEEEEEeec
Q 032111          101 NGRNIRVSFAN  111 (147)
Q Consensus       101 ~g~~l~v~~~~  111 (147)
                      .|+.|.|.++.
T Consensus        81 ~GR~i~v~~~~   91 (114)
T 3s6e_A           81 AGKMITAAYVP   91 (114)
T ss_dssp             TTEECEEEEEC
T ss_pred             CCEEEEEEEEc
Confidence            99999999874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.23  E-value=5.6e-11  Score=75.68  Aligned_cols=77  Identities=16%  Similarity=0.170  Sum_probs=67.5

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCC-HHHHHHHHHHhc--CCeeCCeE
Q 032111           29 MSQSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDS-NESASSAQSAMD--GQELNGRN  104 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~-~~~a~~ai~~l~--~~~~~g~~  104 (147)
                      ....+..|+|.||++. ++.++|+++|.+||.|..|.+..+..      .|||.|.+ ..+|.+|+..|+  +.+|.+..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            4567889999999999 99999999999999999999988754      59999999 899999999995  66888888


Q ss_pred             EEEEeec
Q 032111          105 IRVSFAN  111 (147)
Q Consensus       105 l~v~~~~  111 (147)
                      +.++...
T Consensus        88 ~~~evL~   94 (121)
T 1owx_A           88 VTWEVLE   94 (121)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            8887643

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.21  E-value=1e-10  Score=70.43  Aligned_cols=76  Identities=25%  Similarity=0.391  Sum_probs=63.1

Q ss_pred             CCCCeEEEcCCC----CCCCH----HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           31 QSQTKLFVGGLS----WGTDD----SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        31 ~~~~~i~v~nlp----~~~~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      ++..+|+|.-++    .++..    .+|.+.|.+||.|..+++..+.        +||+|.+.++|.+||+ |++..+.|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            345678787655    23333    5789999999999999998863        8999999999999999 99999999


Q ss_pred             eEEEEEeecCCCC
Q 032111          103 RNIRVSFANDRPP  115 (147)
Q Consensus       103 ~~l~v~~~~~~~~  115 (147)
                      +.|+|+++++...
T Consensus        76 r~LkV~lkt~dW~   88 (91)
T 2dnr_A           76 RTITIALKSPSGP   88 (91)
T ss_dssp             EEEEEEECCCSSC
T ss_pred             eEEEEEeCCCCcc
Confidence            9999999987654

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.03  E-value=5.9e-10  Score=67.42  Aligned_cols=74  Identities=20%  Similarity=0.291  Sum_probs=61.7

Q ss_pred             CCCCCCeEEEcCCCCC-----CCH----HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCe
Q 032111           29 MSQSQTKLFVGGLSWG-----TDD----SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQE   99 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~-----~~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~   99 (147)
                      .-++..+|+|.-++..     +..    .+|.+.|.+||.|..+++..++        +||+|.+.++|.+||+ |++..
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            4456678989877632     222    4688999999999999998873        9999999999999999 99999


Q ss_pred             eCCeEEEEEeec
Q 032111          100 LNGRNIRVSFAN  111 (147)
Q Consensus       100 ~~g~~l~v~~~~  111 (147)
                      +.|+.|+|++..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998754

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.93  E-value=4e-09  Score=73.77  Aligned_cols=67  Identities=16%  Similarity=0.299  Sum_probs=59.3

Q ss_pred             CCHHHHHHHhhccCCeeEEEEEecCC----CCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           45 TDDSSLKEAFSNFGDITEAKVITERE----SGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        45 ~~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      -.+++|.+.|.+||.|..+.++.+..    ++..+|++||+|.+.++|.+|+..|++..+.|+.|.+.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            34578999999999999999886543    34789999999999999999999999999999999999875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.83  E-value=5e-08  Score=60.30  Aligned_cols=72  Identities=15%  Similarity=0.183  Sum_probs=65.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhcc-----CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNF-----GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~-----g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ..++|-|.|||..++...|+.+++++     +.+..+.+..+.      +-|+|+|.+...|-+|.-.|++.+|.+++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            45889999999999999999999999     999999887764      4899999999999999988999999999999


Q ss_pred             EEe
Q 032111          107 VSF  109 (147)
Q Consensus       107 v~~  109 (147)
                      |.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            863

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.20  E-value=3.8e-05  Score=46.94  Aligned_cols=76  Identities=22%  Similarity=0.269  Sum_probs=60.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhcc-----CCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNF-----GDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~-----g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      ....+|.|.|||+.+.++.|.-+|+.-     |.|..+....        .-|+|+|.+.+.++++++. ....|++..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            456799999999999999999999872     4677776643        2699999999999999983 3678888888


Q ss_pred             EEEeecCCCC
Q 032111          106 RVSFANDRPP  115 (147)
Q Consensus       106 ~v~~~~~~~~  115 (147)
                      .|.-.-++.+
T Consensus        77 sV~P~~~~~~   86 (104)
T 2dhx_A           77 SLRPAPPRAP   86 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEcCCCCCc
Confidence            8876555443

>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=97.93  E-value=9.2e-05  Score=45.38  Aligned_cols=77  Identities=13%  Similarity=0.152  Sum_probs=61.9

Q ss_pred             CCCeEEEcCCCCCCCH-----HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           32 SQTKLFVGGLSWGTDD-----SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~-----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      -.++++|.||+.++-.     +.++++|..|+.+....+.+.-.      =..|.|.+.++|.+|-..||+..+.|+.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            3478999999876522     46788999999887766654321      368999999999999999999999999999


Q ss_pred             EEeecCCC
Q 032111          107 VSFANDRP  114 (147)
Q Consensus       107 v~~~~~~~  114 (147)
                      |-.+.+.+
T Consensus        78 ~YFgq~~~   85 (104)
T 1wey_A           78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EEecCCCC
Confidence            99987543

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.83  E-value=9.4e-05  Score=44.73  Aligned_cols=56  Identities=20%  Similarity=0.251  Sum_probs=46.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   96 (147)
                      +..||.-..|.++...||.++|+.||. ..|+++.|.       .|||.|.+.+.|..|+..+.
T Consensus        15 r~HVf~l~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEEeCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            344444499999999999999999984 467787763       79999999999999999663

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.73  E-value=0.00038  Score=41.78  Aligned_cols=69  Identities=12%  Similarity=0.138  Sum_probs=55.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCc--cceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGK--SRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      +.|-|++||+.++++++.+.+.....+....+...+.+.+  ...-|+|.|.+.+++....+.+++..+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            4678999999999999999999887666666655443332  23579999999999999999999998843

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.53  E-value=0.00017  Score=43.74  Aligned_cols=55  Identities=20%  Similarity=0.216  Sum_probs=46.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   96 (147)
                      ..||.-+.|.++...||.++|+.|| -..|.++.|.       .|||.|.+.+.|..|+..+.
T Consensus         6 ~HV~~l~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHVTFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEEECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEEeCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3455559999999999999999998 4567788763       79999999999999999764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.29  E-value=0.0022  Score=40.29  Aligned_cols=72  Identities=22%  Similarity=0.239  Sum_probs=56.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC-eEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG-RNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g-~~l~v~~~  110 (147)
                      ..+-|.|-+.|+.. ...+...|.++|.|.+......      ..+-.|.|.+..+|++||. .|+..+.+ ..|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            34678888998875 5678889999999988765221      2389999999999999999 69999974 66777774


Q ss_pred             c
Q 032111          111 N  111 (147)
Q Consensus       111 ~  111 (147)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.70  E-value=0.0022  Score=38.81  Aligned_cols=68  Identities=10%  Similarity=0.085  Sum_probs=48.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCc--cceEEEEEeCCHHHHHHHHHHhcCCeeC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGK--SRGFGFVTYDSNESASSAQSAMDGQELN  101 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~ai~~l~~~~~~  101 (147)
                      -.|.|+.||+.+|++++.+.+...-.+....+...+.+.+  .-.-|||.|.+.++.....+.+++..+-
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4688999999999999888777653332222222222211  1246899999999999999999998874

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.53  E-value=0.0016  Score=50.20  Aligned_cols=55  Identities=18%  Similarity=0.221  Sum_probs=41.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHH
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS   93 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~   93 (147)
                      .++|+|. .|..+++.+|.++|.+||.|..+.+..++.     .|++|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHh
Confidence            3789997 799999999999999999999987765432     699999999999887755

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.93  E-value=0.012  Score=37.54  Aligned_cols=76  Identities=24%  Similarity=0.253  Sum_probs=53.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEEe------------cCCCC-ccceEEEEEeCCHHHHHHHHHHhcCCe
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITE-AKVIT------------ERESG-KSRGFGFVTYDSNESASSAQSAMDGQE   99 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~------------~~~~~-~~~g~afv~f~~~~~a~~ai~~l~~~~   99 (147)
                      ..|.|-+.|+... ..+.+.|+++|.|.. .....            .+... .......|.|.+..+|++||. .|+..
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTCE
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCeE
Confidence            4677778876554 567788999998755 21111            00000 123577999999999999999 69999


Q ss_pred             eCCeEEEEEeec
Q 032111          100 LNGRNIRVSFAN  111 (147)
Q Consensus       100 ~~g~~l~v~~~~  111 (147)
                      +.|..|-|....
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988887764

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=95.69  E-value=0.016  Score=37.69  Aligned_cols=33  Identities=12%  Similarity=0.035  Sum_probs=26.8

Q ss_pred             EEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcC
Q 032111           63 AKVITERESGKSRGFGFVTYDSNESASSAQSAMDG   97 (147)
Q Consensus        63 ~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~   97 (147)
                      +.++++..  +++||+||+|.+.++|++|+..+++
T Consensus         3 ~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            3 YKLILNGK--TLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             EEEEecCc--cccchhHHHHHHHHhHHHHHHhhcc
Confidence            45555533  5889999999999999999988774

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.20  E-value=0.0079  Score=38.89  Aligned_cols=41  Identities=10%  Similarity=0.050  Sum_probs=36.3

Q ss_pred             CCccceEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEeecC
Q 032111           71 SGKSRGFGFVTYDSNESASSAQSAM-DGQELNGRNIRVSFAND  112 (147)
Q Consensus        71 ~~~~~g~afv~f~~~~~a~~ai~~l-~~~~~~g~~l~v~~~~~  112 (147)
                      ..+.+|+++++|.+.++|++|++.+ ++..+.| .+.+.++..
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            3467899999999999999999999 9999999 888887764

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=91.99  E-value=0.57  Score=36.51  Aligned_cols=55  Identities=20%  Similarity=0.247  Sum_probs=43.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   96 (147)
                      ..+++-.+|..+...+|.++|+.+|. ..|.++.+.       .|||.|.+.+.|..++..+.
T Consensus       440 ~~vl~v~f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEECCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEeCCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            33444458889999999999999984 456665542       69999999999999999875

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=83.38  E-value=3.5  Score=22.95  Aligned_cols=60  Identities=12%  Similarity=0.198  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHhhccCC-----eeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           43 WGTDDSSLKEAFSNFGD-----ITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        43 ~~~~~~~l~~~f~~~g~-----i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..+...+|..++..-+.     |-.|.+..        .|.||+... +.+..+++.|.+..+.++.+.++.++
T Consensus        11 ~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d--------~~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           11 KKIRAVDFVGTIAKIDGVSADDIGIITIMD--------NASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             ----CHHHHHHHHTSTTCCGGGEEEEEECS--------SCEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC
T ss_pred             cCCCHHHHHHHHHHccCCChhhccEEEEeC--------CcEEEEECH-HHHHHHHHHhccccCcCceEEEEECC
Confidence            34566677777765443     44454432        278888874 56778889999999999998887653

---

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	147
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-23
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-22
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-22
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-22
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-21
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-21
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-21
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-21
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-20
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-20
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-20
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-20
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-20
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	7e-20
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-19
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-19
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-19
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-19
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-19
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-19
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-19
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-19
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-18
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-18
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-18
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-18
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-18
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-18
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-18
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-18
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-18
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-17
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-17
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-17
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-16
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-16
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-16
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-16
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-12
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-16
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-16
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-16
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-16
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-16
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	8e-16
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-16
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-15
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-15
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-15
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-15
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-15
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-15
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-14
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-14
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-14
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-14
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	8e-13
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-13
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-12
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-12
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:) 6e-12
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-12
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	9e-12
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	9e-12
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-11
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-11
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-11
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-11
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-10
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-10
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	7e-10
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-09
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-09
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	1e-07
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	3e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-07
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	1e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	1e-06
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	0.004

>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 = 84.6 bits (209), Expect = 5e-23
 Identities = 22/87 (25%), Positives = 45/87 (51%), Gaps = 2/87 (2%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE-SGKSRGFGFVTYDSNESA 88
            Q+ +K+ V  + +  +   ++E FS FG++   ++  +   +G  RGFGFV + + + A
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 89  SSAQSAM-DGQELNGRNIRVSFANDRP 114
             A +A+     L GR + + +A+   
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 83.0 bits (205), Expect = 1e-22
 Identities = 19/77 (24%), Positives = 36/77 (46%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
            L+VG L     ++ L E FS  G I   +V  +  + +S G+ +V +     A  A   
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 95  MDGQELNGRNIRVSFAN 111
           M+   + G+ +R+ ++ 
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 82.8 bits (204), Expect = 2e-22
 Identities = 35/88 (39%), Positives = 52/88 (59%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M+ ++  L+VGGL+   DD  L  AF  FGDIT+ ++  + E+ K RGF FV ++  E A
Sbjct: 1   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPR 116
           ++A   M+  EL GR IRV+ A     +
Sbjct: 61  AAAIDNMNESELFGRTIRVNLAKPMRIK 88

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 81.2 bits (200), Expect = 7e-22
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+F+GGLSW T    L+E F  FG++ E  V+ +  + +SRGFGFVT+           A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 95  MDGQELNGRNIRVSFA 110
               EL+ + I    A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>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 = 81.2 bits (200), Expect = 1e-21
 Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 6/88 (6%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S     ++ GG++ G  D  +++ FS FG I E +V         +G+ FV + ++ESA+
Sbjct: 15  SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAA 68

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRS 117
            A  +++G  + G  ++  +  + P  +
Sbjct: 69  HAIVSVNGTTIEGHVVKCYWGKESPDMT 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 = 79.7 bits (196), Expect = 4e-21
 Identities = 21/83 (25%), Positives = 41/83 (49%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGL    +D  +KE  ++FG +    ++ +  +G S+G+ F  Y        A + 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 95  MDGQELNGRNIRVSFANDRPPRS 117
           ++G +L  + + V  A+     +
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKNA 85

>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 = 79.6 bits (196), Expect = 4e-21
 Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 2/91 (2%)

Query: 26  VRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN 85
           V+   Q  + L V GL W T +  LKE FS FG++   +V  + ++G S+GFGFV +   
Sbjct: 1   VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 60

Query: 86  ESASSAQSAMDGQELNGRNIRVSFANDRPPR 116
           E+     S      ++GR       N +  +
Sbjct: 61  ETQVKVMSQR--HMIDGRWCDCKLPNSKQSQ 89

>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 = 79.3 bits (195), Expect = 7e-21
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 1/101 (0%)

Query: 16  QAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSR 75
           ++P    ++ +    +    +F   L+       L++ FS  G + + ++I++R S +S+
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 76  GFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPR 116
           G  +V +   +S       + GQ L G  I V  +     R
Sbjct: 61  GIAYVEFCEIQSV-PLAIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 78.5 bits (193), Expect = 1e-20
 Identities = 26/91 (28%), Positives = 43/91 (47%), Gaps = 3/91 (3%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           + +    L+VG LS+ T +  + E FS  GDI +  +  ++    + GF FV Y S   A
Sbjct: 3   LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 62

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPRSDG 119
            +A   ++G  L+ R IR  +        +G
Sbjct: 63  ENAMRYINGTRLDDRIIRTDWD---AGFKEG 90

>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 = 78.6 bits (193), Expect = 2e-20
 Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            KLF+GGLS+ T + SL+  +  +G +T+  V+ +  S +SRGFGFVT+ S     +A  
Sbjct: 21  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM- 79

Query: 94  AMDGQELNGRNIRVSFANDRPPR 116
           A     ++GR +    A  R   
Sbjct: 80  AARPHSIDGRVVEPKRAVAREES 102

>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 = 78.5 bits (193), Expect = 2e-20
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 3/91 (3%)

Query: 27  RFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
           R   +    L++  L +      + + F  +G I +   I    + ++RG  +V Y+   
Sbjct: 1   RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIF 57

Query: 87  SASSAQSAMDGQELNGRNIRVSFANDRPPRS 117
            A +A   + G  +  R + V + N      
Sbjct: 58  DAKNACDHLSGFNVCNRYLVVLYYNANRAFQ 88

>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 = 76.9 bits (189), Expect = 4e-20
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 2/79 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T L+V  L     D  L   F  +G I +  ++ ++ +G+ RG  FV Y+  E A  A S
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 94  AMDGQELNG--RNIRVSFA 110
           A++     G  + + V  A
Sbjct: 67  ALNNVIPEGGSQPLSVRLA 85

>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 = 76.6 bits (188), Expect = 6e-20
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERE---SGKSRGFGFVTYDSNESASSAQ 92
           LF+  L++ T + +LK  FS  G I    +  ++       S GFGFV Y   E A  A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 93  SAMDGQELNGRNIRVSFANDRP 114
             + G  ++G  + V  +    
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 82

>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 = 76.2 bits (187), Expect = 7e-20
 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGGLS  T +  ++E F  FG++   ++  + ++ K RGF F+T+   E        
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-E 59

Query: 95  MDGQELNGRNIRVSFA 110
                +      +  A
Sbjct: 60  KKYHNVGLSKCEIKVA 75

>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 = 76.4 bits (187), Expect = 1e-19
 Identities = 23/92 (25%), Positives = 43/92 (46%), Gaps = 8/92 (8%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVI--------TERESGKSRGFGFVTYDSN 85
           + ++V GL+       L + F   G +   K           ++E+GK +G   V+Y+  
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 86  ESASSAQSAMDGQELNGRNIRVSFANDRPPRS 117
            +A +A    DG++  G  ++VS A  +PP +
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 100

>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 = 75.8 bits (186), Expect = 1e-19
 Identities = 21/79 (26%), Positives = 37/79 (46%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S T L V  L     D  L   F   G I   +++ + ++G S G+ FV + S   +  A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 92  QSAMDGQELNGRNIRVSFA 110
              ++G  +  + ++VS+A
Sbjct: 61  IKVLNGITVRNKRLKVSYA 79

>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 = 75.1 bits (184), Expect = 2e-19
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L+V GL        L++ FS +G I  ++++ ++ +G SRG GF+ +D    A  A  
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 94  AMDGQELNGRN--IRVSFA 110
            ++GQ+ +G    I V FA
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 74.6 bits (183), Expect = 3e-19
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KL V  L +G  D+ ++E F+ FG + +A V  +R SG+S G   V ++    A  A   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 95  MDGQELNGRNIRVSFAN 111
            +G  L+GR + +    
Sbjct: 61  YNGVPLDGRPMNIQLVT 77

>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 = 74.7 bits (183), Expect = 3e-19
 Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KLF+GGLS+ T D SL+  F  +G +T+  V+ +  + +SRGFGFVTY + E   +A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-N 66

Query: 95  MDGQELNGRNIRVSFA 110
               +++GR +    A
Sbjct: 67  ARPHKVDGRVVEPKRA 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 = 74.4 bits (182), Expect = 4e-19
 Identities = 27/82 (32%), Positives = 49/82 (59%), Gaps = 1/82 (1%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEA-KVITERESGKSRGFGFVTYDSNESASSAQSA 94
           +F+G L    D+  L + FS FG I +  K++ + ++G S+G+ F+ + S +++ +A  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 95  MDGQELNGRNIRVSFANDRPPR 116
           M+GQ L  R I VS+A  +  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 74.0 bits (181), Expect = 5e-19
 Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
           S+T L V  L         +  F + G+I   K++ ++ +G+S G+GFV Y   + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
            + ++G  L  + I+VS+A  RP
Sbjct: 61  INTLNGLRLQTKTIKVSYA--RP 81

>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 = 73.1 bits (179), Expect = 9e-19
 Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+F+GGLSW T    LK+ FS FG++ +  +  +  +G+SRGFGFV +  +ES       
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-D 59

Query: 95  MDGQELNGRNIRV 107
               +LNG+ I  
Sbjct: 60  QKEHKLNGKVIDP 72

>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 = 73.5 bits (180), Expect = 1e-18
 Identities = 26/80 (32%), Positives = 41/80 (51%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             ++VGGL     +  L E F   G +    +  +R +G+ +G+GFV + S E A  A  
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 94  AMDGQELNGRNIRVSFANDR 113
            MD  +L G+ IRV+ A+  
Sbjct: 70  IMDMIKLYGKPIRVNKASAH 89

>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 = 73.1 bits (179), Expect = 1e-18
 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 7/89 (7%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           MS  +  L+V  L   T +  +++ F+N       +V       K R + FV + + E A
Sbjct: 5   MSSVKI-LYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDA 57

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPRS 117
             A  A++G+ L+G  I V+ A      S
Sbjct: 58  VEAMKALNGKVLDGSPIEVTLAKPVDKDS 86

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 72.0 bits (176), Expect = 4e-18
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEA--KVITERESGKSRGFGFVTYDSNESASSA 91
            +LF+GG+        + E  +   +         +  +  K+RGF FV Y+S+ +A+ A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 92  QSAMDGQ--ELNGRNIRVSFANDRPPRSD 118
           +  +     +L G  I V +A       +
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDE 90

>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 = 72.1 bits (176), Expect = 4e-18
 Identities = 14/87 (16%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKV-----ITERESGKSRGFGFVTYDSNESAS 89
           +L+VG + +G  + ++ + F+    +          +   +  + + F F+ + S +  +
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPR 116
            A +  DG    G+++++   +D  P 
Sbjct: 63  QAMA-FDGIIFQGQSLKIRRPHDYQPL 88

>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 = 71.6 bits (175), Expect = 5e-18
 Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             + V  LS  T ++ L+E F  FG I+   +  ++ +G+S+GF F+++   E A+ A +
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 94  AMDGQELNGRNIRVSFANDRPPRSD 118
            + G   +   + V +A    P ++
Sbjct: 69  GVSGFGYDHLILNVEWAK---PSTN 90

>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 = 72.1 bits (176), Expect = 5e-18
 Identities = 40/96 (41%), Positives = 57/96 (59%), Gaps = 3/96 (3%)

Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
            + TK+FVGGL + T D+SL++ F  FGDI EA VIT+R++GKSRG+GFVT     +A  
Sbjct: 8   TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 67

Query: 91  AQSAMDGQELNGRNIRVSFA--NDRPPRSDGGYGGG 124
           A    +   ++GR   V+ A    +P     G+  G
Sbjct: 68  ACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAIG 102

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.3 bits (174), Expect = 5e-18
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGGLS  T    +K  F  FG + +A ++ ++ + + RGFGFVT++S +        
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 95  MDGQELNGRNIRVSFA 110
           +   E+N + +    A
Sbjct: 60  IHFHEINNKMVECKKA 75

>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 = 71.2 bits (174), Expect = 7e-18
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             +F+  L    D+ +L + FS FG+I   KV+ +     S+G+GFV +++ E+A  A  
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIE 66

Query: 94  AMDGQELNGRNIRVSFANDRPPR 116
            M+G  LN R + V     R  R
Sbjct: 67  KMNGMLLNDRKVFVGRFKSRKER 89

>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 = 70.9 bits (173), Expect = 9e-18
 Identities = 39/88 (44%), Positives = 60/88 (68%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           M+  + KLFVGGLS+ T++ SL++ FS +G I+E  V+ +RE+ +SRGFGFVT+++ + A
Sbjct: 1   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPR 116
             A  AM+G+ ++GR IRV  A      
Sbjct: 61  KDAMMAMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 70.9 bits (173), Expect = 1e-17
 Identities = 29/95 (30%), Positives = 47/95 (49%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S    +LFV  LS+ + +  L++ FS +G ++E     +  + K +GF FVT+   E A 
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGGG 124
            A + +DGQ   GR + V  +  +   S  G   G
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 69.1 bits (168), Expect = 4e-17
 Identities = 10/78 (12%), Positives = 28/78 (35%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L++          ++++   +   +  +  +       SR F ++   S E A     
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 94  AMDGQELNGRNIRVSFAN 111
            ++G ++ G  +    +N
Sbjct: 62  KLNGLKIEGYTLVTKVSN 79

>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 = 69.5 bits (170), Expect = 4e-17
 Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 9/91 (9%)

Query: 34  TKLFVGGLS-WGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           +++F+G L+      S ++  FS +G I    V         +GF FV Y +  +A +A 
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAV 67

Query: 93  SAMDGQELNGRNIRVSFANDRPPRSDGGYGG 123
           +  DG+ + G+ + ++ A +      G   G
Sbjct: 68  AGEDGRMIAGQVLDINLAAEPKVNRSGPSSG 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 = 68.2 bits (166), Expect = 1e-16
 Identities = 12/79 (15%), Positives = 32/79 (40%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
             T + V  + +      + + F  +  I  +  +   E G   G   V ++S + A++A
Sbjct: 8   GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 67

Query: 92  QSAMDGQELNGRNIRVSFA 110
              ++ + +  R +++   
Sbjct: 68  VIDLNDRPIGSRKVKLVLG 86

>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 = 68.6 bits (167), Expect = 1e-16
 Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
             +  +L V  + +   D  L++ F  FG I + ++I       S+GFGFVT++++  A 
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADAD 65

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRS 117
            A+  + G  + GR I V+ A  R   +
Sbjct: 66  RAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 68.2 bits (166), Expect = 1e-16
 Identities = 29/74 (39%), Positives = 46/74 (62%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L V GLS  T +  L+E FS +G I +  ++ +++S +SRGF FV +++ + A  A+ 
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 94  AMDGQELNGRNIRV 107
             +G EL+GR IRV
Sbjct: 70  RANGMELDGRRIRV 83

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.8 bits (172), Expect = 1e-16
 Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 1/117 (0%)

Query: 1   MAFCGKLGMLVRQNGQAPKASLINAVRFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDI 60
           M              +   +   +       +  K+FVGG+   T++  L++ F  +G I
Sbjct: 65  MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 124

Query: 61  TEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRPPRS 117
              +++T+R SGK RGF FVT+D ++S            +NG N  V  A  +   +
Sbjct: 125 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMA 180

>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 = 58.1 bits (139), Expect = 6e-12
 Identities = 27/64 (42%), Positives = 41/64 (64%)

Query: 35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
          KLF+GGLS+ T D SL+  F  +G +T+  V+ +  + +SRGFGFVTY + E   +A +A
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 95 MDGQ 98
             +
Sbjct: 68 RPHK 71

>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 = 69.5 bits (169), Expect = 1e-16
 Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 2/98 (2%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
                 L V  +    D+  L++ F  +G I   K++ +RE+ +SRG+GFV + S  SA 
Sbjct: 39  PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSD--GGYGGGN 125
            A + ++G  +  + ++V+ A     R    G  G GN
Sbjct: 99  QAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>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 = 67.4 bits (164), Expect = 2e-16
 Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           K+FVGG+   T++  L++ F  +G I   +++T+R SGK RGF FVT+D ++S       
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-I 62

Query: 95  MDGQELNGRNIRVSFA 110
                +NG N  V  A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>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 = 67.8 bits (165), Expect = 2e-16
 Identities = 24/83 (28%), Positives = 44/83 (53%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             LF+  L     D  L + F  FG++  AKV  ++++  S+ FGFV+YD+  SA +A  
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 94  AMDGQELNGRNIRVSFANDRPPR 116
           +M+G ++  + ++V     +   
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 67.4 bits (164), Expect = 2e-16
 Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L+VG LS    +  + + FS  G     K+ITE     +  + FV +  +  A++A +
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALA 66

Query: 94  AMDGQELNGRNIRVSFANDRPPR 116
           AM+G+++ G+ ++V++A     +
Sbjct: 67  AMNGRKILGKEVKVNWATTPSSQ 89

>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 = 66.6 bits (162), Expect = 5e-16
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 5/84 (5%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L    LS+   +  LKE F +  +I         + GKS+G  ++ + S   A     
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 94  AMDGQELNGRNIRVSFANDRPPRS 117
              G E++GR++ + +  ++    
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKGGTR 95

>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 = 66.3 bits (161), Expect = 8e-16
 Identities = 20/84 (23%), Positives = 39/84 (46%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L++  LS    +  L   F+ F +     +     +G+ RG  F+T+ + E A  A  
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 94  AMDGQELNGRNIRVSFANDRPPRS 117
            ++G +L G+ + + F  ++  RS
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQRS 102

>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 = 65.9 bits (160), Expect = 9e-16
 Identities = 22/84 (26%), Positives = 47/84 (55%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S     LFV  +     +  ++E F ++G+I    +  +R +G S+G+  V Y++++ A 
Sbjct: 4   SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 63

Query: 90  SAQSAMDGQELNGRNIRVSFANDR 113
           +A+ A++G E+ G+ I+V +   +
Sbjct: 64  AAKEALNGAEIMGQTIQVDWCFVK 87

>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 = 65.9 bits (160), Expect = 1e-15
 Identities = 30/97 (30%), Positives = 53/97 (54%), Gaps = 1/97 (1%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           + +S   +FVG + +   +  LK+ FS  G +   +++ +RE+GK +G+GF  Y   E+A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPRSDG-GYGGG 124
            SA   ++G+E +GR +RV  A     + +    G G
Sbjct: 64  LSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 65.5 bits (159), Expect = 1e-15
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSN-FGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
             +++  L+       LK++    F    +   I    S K RG  FV +    SA++A 
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 93  SAMDGQELNGRNIRVSFANDR 113
            +M G     + +R+ +A   
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTD 84

>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 = 64.3 bits (156), Expect = 2e-15
 Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 7/84 (8%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           KL++G LS       L++ F +       +V          G+ FV Y     A  A   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIET 56

Query: 95  MDGQ-ELNGRNIRVSFANDRPPRS 117
           + G+ EL+G+ + V ++  +  RS
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLRS 80

>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 = 64.4 bits (156), Expect = 4e-15
 Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 6/90 (6%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             +F+  LS+ +++ +L E    FGD+   +V+   ++  S+G  F  + + E+A    +
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 94  AM------DGQELNGRNIRVSFANDRPPRS 117
           A        G +L+GR ++V  A  R   +
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>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 = 64.2 bits (156), Expect = 4e-15
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           ++LFVG L     +  +++ F  +G   E  +  ++       FGF+  ++   A  A+ 
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKV 62

Query: 94  AMDGQELNGRNIRVSFAN 111
            +D   L G+ +RV FA 
Sbjct: 63  ELDNMPLRGKQLRVRFAC 80

>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 = 64.0 bits (155), Expect = 8e-15
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
             F+G L +   + S+KE F                  + +GFG+  ++  +S  SA  +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 95  MDGQELNGRNIRVSFANDRPPRSDGGYGG 123
           ++ + L  + IRV  A+    +  G   G
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>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 = 63.1 bits (153), Expect = 1e-14
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 7/94 (7%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S   + +FVG  +    +  L+E FS +GD+ +  +         R F FVT+  ++ A 
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQ 56

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGG 123
           S     +   + G ++ +S A  +   + G   G
Sbjct: 57  SL--CGEDLIIKGISVHISNAEPKHNSNSGPSSG 88

>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 = 62.5 bits (151), Expect = 2e-14
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 34  TKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITE-RESGKSRGFGFVTYDSNESASSA 91
            ++ +  LS    D++ L+E+F  FG I +  +    +E   +    F+ +++ +SA  A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 92  QSAMDGQELNGRNIRVSFANDRP 114
              M+   L  R I VS A+ +P
Sbjct: 65  L-QMNRSLLGNREISVSLADKKP 86

>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 = 60.8 bits (147), Expect = 7e-14
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 8/81 (9%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L+V G       + L+ AFS FG+I +  +         R   FVTY+  ESA  A +
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVA 57

Query: 94  AMDGQELNGRNIRVSFANDRP 114
            ++G ++    ++V+ A  +P
Sbjct: 58  ELNGTQVESVQLKVNIARKQP 78

>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 = 60.8 bits (147), Expect = 9e-14
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            +++VG L        +++ F  +G I   + I  +       F FV ++    A  A  
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 71

Query: 94  AMDGQELNGRNIRVSFANDRPPRSDG 119
             DG + +G  +RV F   R  R  G
Sbjct: 72  GRDGYDYDGYRLRVEFP--RSGRGTG 95

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 8e-13
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 2/81 (2%)

Query: 32  SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSA 91
               +++ G         +KE   + G +     +        +G  FV +DS ESA   
Sbjct: 5   KNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 92  QSAMDGQELNGRNIRVSFAND 112
                GQ+    ++ + F +D
Sbjct: 64  V-ETPGQKYKETDLLILFKDD 83

>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 = 58.4 bits (141), Expect = 9e-13
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 4/64 (6%)

Query: 50  LKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF 109
           L+   S FG I +  +          G   V++   E A      +DG+   GR I    
Sbjct: 36  LRVECSKFGQIRKLLLFD----RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 91

Query: 110 ANDR 113
            +  
Sbjct: 92  WDGT 95

>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 = 58.1 bits (140), Expect = 1e-12
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
            ++ V  L +      L + FS FG + +    T+     ++    + Y    SA  A+ 
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKL 63

Query: 94  AMDGQEL--NGRNIRVSFAN 111
           ++DGQ +      +R+ F+ 
Sbjct: 64  SLDGQNIYNACCTLRIDFSK 83

>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 = 56.3 bits (135), Expect = 3e-12
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           L++ GL  GT D  L +    +G I   K I ++ + K +G+GFV +DS  +A  A +A+
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 96  DGQELNGRNIR 106
               +  +  +
Sbjct: 61  KASGVQAQMAK 71

>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 = 56.2 bits (135), Expect = 6e-12
 Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 1/81 (1%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           +  + + + +        +    E    +G++ E  V  +       G  +V +   E A
Sbjct: 23  LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDA 81

Query: 89  SSAQSAMDGQELNGRNIRVSF 109
             A   ++ +  NG+ I    
Sbjct: 82  EKAVIDLNNRWFNGQPIHAEL 102

>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 = 55.6 bits (133), Expect = 7e-12
 Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 35  KLFVGGLSWGTDDSSL---KEAFSNFGDITEAKVITERESGKS---RGFGFVTYDSNESA 88
            +FV GLS    D  +    E F  FG I +  +        S       +VTY  +E A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 89  SSAQSAMDGQELNGRNIRVS 108
             A   ++   ++GR ++ S
Sbjct: 70  LRAIQCVNNVVVDGRTLKAS 89

>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 = 56.0 bits (134), Expect = 9e-12
 Identities = 11/88 (12%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 29  MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESA 88
           ++ ++    +  + +      + +          A  +    +G+  G   V + + + A
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 89  SSAQSAMDGQELNGRNIRVSFANDRPPR 116
             ++  +  ++LNGR   V        R
Sbjct: 64  RKSE-RLHRKKLNGREAFVHVVTLEDMR 90

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.6 bits (133), Expect = 9e-12
 Identities = 22/94 (23%), Positives = 31/94 (32%), Gaps = 7/94 (7%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
            +S  ++ V GL        LK+     GD+  A V  +         G V Y   E   
Sbjct: 12  RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDME 64

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGG 123
            A   +D  +        S+    P RS G   G
Sbjct: 65  YALRKLDDTKFRSHEGETSYIRVYPERSSGPSSG 98

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 54.9 bits (131), Expect = 1e-11
 Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 3/77 (3%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
           T + V  L    + + + + F + G I    V       K+  F  + +      + A  
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFA-RYDGALAAI 57

Query: 94  AMDGQELNGRNIRVSFA 110
               + +    I VS  
Sbjct: 58  TKTHKVVGQNEIIVSHL 74

>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 = 55.2 bits (132), Expect = 2e-11
 Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 1/81 (1%)

Query: 31  QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASS 90
           Q  T L++  L    D+  L+           +  I    SG SRG GF   +S E   +
Sbjct: 16  QDPTNLYISNLPLSMDEQELEN-MLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 91  AQSAMDGQELNGRNIRVSFAN 111
                +G+ +       +   
Sbjct: 75  VIGHFNGKFIKTPPGVSAPTE 95

>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 = 54.6 bits (130), Expect = 3e-11
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S +   LF+G L+     + LK A S          + +  +G +R FG+V ++S E   
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLE 68

Query: 90  SAQSAMDGQELNGRNIRVSFANDR 113
            A   + G ++ G  I++     R
Sbjct: 69  KALE-LTGLKVFGNEIKLEKPKGR 91

>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 = 54.3 bits (130), Expect = 3e-11
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 30  SQSQTKLFV--GGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNES 87
           S +   L V  GGL  G   + L       G +    +   +       + F  Y + E 
Sbjct: 15  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEE 68

Query: 88  ASSAQSAMDGQEL-NGRNIRVSF 109
           +  A   ++G+E+ +    +++ 
Sbjct: 69  SKRAYVTLNGKEVVDDLGQKITL 91

>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 = 52.8 bits (126), Expect = 8e-11
 Identities = 13/94 (13%), Positives = 29/94 (30%), Gaps = 7/94 (7%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           S   + + V  L   ++   + +   ++               +++   FVT  + E A 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKY-------CYVDRNKRTAFVTLLNGEQAQ 54

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGG 123
           +A          G+++ V           G   G
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPTDALLCSGPSSG 88

>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 = 51.9 bits (124), Expect = 2e-10
 Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 9/82 (10%)

Query: 33  QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
            T + V G    +    L + F+ +G+I +  +        +  +  + Y S   A  A 
Sbjct: 4   DTWVTVFGFPQASASYILLQ-FAQYGNILKHVMS------NTGNWMHIRYQSKLQARKAL 56

Query: 93  SAMDGQELNGRN-IRVSFANDR 113
           S  DG+       I V    D+
Sbjct: 57  S-KDGRIFGESIMIGVKPCIDK 77

>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 = 52.3 bits (125), Expect = 2e-10
 Identities = 9/67 (13%), Positives = 23/67 (34%), Gaps = 2/67 (2%)

Query: 49  SLKEAFSNFGDITEAKVITER--ESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR 106
            +++  S +G +   ++            G  FV + S      A   + G++   R + 
Sbjct: 30  DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 89

Query: 107 VSFANDR 113
             + +  
Sbjct: 90  TKYCDPD 96

>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 = 51.7 bits (123), Expect = 3e-10
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 11/94 (11%)

Query: 30  SQSQTKLFVGGL-----SWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDS 84
           S   + L          S     +  +  F  +   T  +               + + +
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSN 55

Query: 85  NESASSAQSAMDGQELNGRNIRVSFANDRPPRSD 118
             SA+ A+  +   E  G+ +++ FA      S 
Sbjct: 56  PLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSS 89

>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 = 50.7 bits (120), Expect = 7e-10
 Identities = 15/89 (16%), Positives = 27/89 (30%), Gaps = 7/89 (7%)

Query: 35  KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           ++ V GL        LK+     GD+  A V  +         G V +   E  + A   
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 95  MDGQELNGRNIRVSFANDRPPRSDGGYGG 123
           +D  +        ++   +         G
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYG 83

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (120), Expect = 1e-09
 Identities = 16/83 (19%), Positives = 24/83 (28%), Gaps = 5/83 (6%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
              F G L   T    L   FSN G+I     +   + G          +  + A     
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEKAKEALGKAK 66

Query: 94  AMDGQELNGRNIRVSFANDRPPR 116
             +   L  RN  V++       
Sbjct: 67  DANNGNLQLRNKEVTWEVLEGEV 89

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             L +  +     +  LK  FS+ G + +     +++    R    +   S E A  A  
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALI 66

Query: 94  AMDGQEL-NGRNIRVSFANDR 113
            +   +L    ++RVSF+   
Sbjct: 67  DLHNHDLGENHHLRVSFSKST 87

>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 = 49.3 bits (117), Expect = 2e-09
 Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 8/87 (9%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           +   T+L+VGGL   T  ++L   F  FG I     +          F ++ Y+S ++A 
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQ 67

Query: 90  SAQSAMDGQELNGRN--IRVSFANDRP 114
           +A + M G  L G +  +RV FA   P
Sbjct: 68  AACAKMRGFPLGGPDRRLRVDFAKSGP 94

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (118), Expect = 2e-09
 Identities = 22/103 (21%), Positives = 41/103 (39%), Gaps = 8/103 (7%)

Query: 34  TKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQ 92
           + L V  L+       SL   F  +GD+   K++  +     +    V       A  A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 57

Query: 93  SAMDGQELNGRNIRVSFA--NDRPPRSDGGYGGGNDGSYGGNR 133
           S ++G +L+G+ IR++ +   +     +G    G    YG + 
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 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 = 47.6 bits (112), Expect = 2e-08
 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
            ++   +++ GL +  ++  + + F     + ++  I    +GK+ G GFV + +     
Sbjct: 15  HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 74

Query: 90  SAQSAMDGQELNGRNIRVSFANDR 113
           +A      Q +  R I+V     +
Sbjct: 75  AAL-CRHKQYMGNRFIQVHPITKK 97

>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 = 47.1 bits (111), Expect = 2e-08
 Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 1/94 (1%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
           + +   + + GL +G     + + FS    +     +     G+S G  FV + S E A 
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGG 123
            A      + +  R I +  ++    R+ G   G
Sbjct: 72  KALK-KHKERIGHRYIEIFKSSRAEVRTSGPSSG 104

>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 = 47.0 bits (111), Expect = 2e-08
 Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 3/97 (3%)

Query: 27  RFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
            F S +   + + GL +   ++ +   FS    +     I     G+  G   V + ++E
Sbjct: 9   SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEI--GPDGRVTGEADVEFATHE 66

Query: 87  SASSAQSAMDGQELNGRNIRVSFANDRPPRSDGGYGG 123
            A +A  A D   +  R + +   +       G   G
Sbjct: 67  DAVAAM-AKDKANMQHRYVELFLNSTAGTSGSGPSSG 102

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.5 bits (104), Expect = 1e-07
 Identities = 17/86 (19%), Positives = 40/86 (46%), Gaps = 10/86 (11%)

Query: 30  SQSQ----TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN 85
           +Q++      LF+  L   T++  L   F+ F    E +++  R         FV + + 
Sbjct: 1   AQTEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTE 55

Query: 86  ESASSAQSAMDGQEL-NGRNIRVSFA 110
             +++A+ A+ G ++     ++++FA
Sbjct: 56  LQSNAAKEALQGFKITPTHAMKITFA 81

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.9 bits (105), Expect = 2e-07
 Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 6/89 (6%)

Query: 30  SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESAS 89
            +S+T +    L  GT  + ++E FS FG +    +       +      V +     A 
Sbjct: 7   GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEAR 60

Query: 90  SAQSAMDGQELNGRNIRVSFANDRPPRSD 118
            A   +   + +   + + +A      + 
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPIGVFGAA 89

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (102), Expect = 3e-07
 Identities = 11/93 (11%), Positives = 32/93 (34%), Gaps = 8/93 (8%)

Query: 27  RFMSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNE 86
           +        L +  L     ++ +      FG +T   ++  +         F+   + E
Sbjct: 2   KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN------QAFLELATEE 55

Query: 87  SASSAQSAM--DGQELNGRNIRVSFANDRPPRS 117
           +A +  +        L  + I + ++N +  ++
Sbjct: 56  AAITMVNYYSAVTPHLRNQPIYIQYSNHKELKT 88

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 5e-07
 Identities = 15/91 (16%), Positives = 32/91 (35%), Gaps = 8/91 (8%)

Query: 34  TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS 93
             + V GL     ++ L EA   FG I    ++  +          V +++ +SA    +
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVT 69

Query: 94  AMDGQ--ELNGRNIRVSFANDRPPRSDGGYG 122
                   + G+    +++  +     G  G
Sbjct: 70  FAADVPVYIAGQQAFFNYSTSKRITRPGNSG 100

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.8 bits (97), Expect = 1e-06
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 7/76 (9%)

Query: 36  LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM 95
           + + GL     +  + +  S++               K +G  FVT  + E A +A +  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 96  DGQELNGRNIRVSFAN 111
               L  R + V    
Sbjct: 54  HQSRLRERELSVQLQP 69

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 1e-06
 Identities = 9/80 (11%), Positives = 23/80 (28%), Gaps = 5/80 (6%)

Query: 36  LFVGGL-SWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSA 94
           + +            L +    FG I+   ++ +        F  +    +  A+     
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEA----FIEMATTEDAQAAVDYYT 66

Query: 95  MDGQELNGRNIRVSFANDRP 114
                + G+ +RV  +    
Sbjct: 67  TTPALVFGKPVRVHLSQKYK 86

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {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: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 32.7 bits (73), Expect = 0.004
 Identities = 13/99 (13%), Positives = 31/99 (31%), Gaps = 5/99 (5%)

Query: 16  QAPKASLINAVRFMSQSQTKLFVGGL-SWGTDDSSLKEAFSNFGDITEAKVITERESGKS 74
           + P+           +    + +  L   G  DS++ +    +G I    ++  +    S
Sbjct: 1   KKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK----S 56

Query: 75  RGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR 113
           + F  +    +  A             GR ++V  +   
Sbjct: 57  QAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY 95

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	147
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.88
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.88
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.88
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.83
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.82
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.82
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.8
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.8
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.78
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.78
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.78
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.78
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.78
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.78
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.77
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.77
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.77
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.76
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.75
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.73
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.73
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.69
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
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	99.57
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.54
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.52
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.45
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.38
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.36
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.83
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.82
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.79
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.79

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.89  E-value=1.1e-22  Score=132.37  Aligned_cols=86  Identities=28%  Similarity=0.555  Sum_probs=80.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+.||+..|.|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34468999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      .....+
T Consensus       120 ~~~~~~  125 (139)
T d1u6fa1         120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876544

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2.3e-22  Score=122.33  Aligned_cols=85  Identities=29%  Similarity=0.441  Sum_probs=79.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|+.|++.|++..+.|++|.|+|
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +.+..
T Consensus        84 a~~~~   88 (93)
T d1h2vz_          84 DAGFK   88 (93)
T ss_dssp             ESCCC
T ss_pred             cCCCC
Confidence            87543

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.89  E-value=9.5e-23  Score=121.28  Aligned_cols=80  Identities=25%  Similarity=0.479  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+++++++|+++|++||.|..+.+++++.++++++||||+|.+.++|++||+.||+..+.++.|+|+++++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999864

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=1.5e-22  Score=124.53  Aligned_cols=85  Identities=29%  Similarity=0.484  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||+|||+++++++|+++|.+||.|..+.++.++.++.+++||||+|.+.++|++||+.||+..|.++.|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34578999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      ..+..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87654

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=5.5e-23  Score=124.15  Aligned_cols=86  Identities=40%  Similarity=0.627  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +...++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..||+..+.|++|.|++
T Consensus         2 a~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~   81 (89)
T d2cqba1           2 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   81 (89)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      ++++..
T Consensus        82 a~p~~~   87 (89)
T d2cqba1          82 AKPMRI   87 (89)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            986543

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.88  E-value=2e-22  Score=121.37  Aligned_cols=83  Identities=25%  Similarity=0.538  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .++.+|||+|||.++++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|+..||+..+.|+.|.|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34579999999999999999999999999999999999899999999999999999999999999999999999999998


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            764

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.7e-22  Score=119.24  Aligned_cols=80  Identities=29%  Similarity=0.564  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|++.|++..+.|++|+|.++++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46899999999999999999999999999999999988899999999999999999999999999999999999999874

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=1.7e-22  Score=122.18  Aligned_cols=86  Identities=44%  Similarity=0.810  Sum_probs=80.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +.+..+|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|+..|++..+.|++|.|++
T Consensus         2 ~~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   81 (90)
T d1x5sa1           2 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45668899999999999999999999999999999998888899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +.++..
T Consensus        82 a~~~~~   87 (90)
T d1x5sa1          82 AGKSSD   87 (90)
T ss_dssp             EECCCC
T ss_pred             cCCCCC
Confidence            987654

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=2.8e-22  Score=121.22  Aligned_cols=84  Identities=25%  Similarity=0.479  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+..+|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++||+.|++..+.|+.|+|+++
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      +++.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8653

>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=99.88  E-value=4.4e-22  Score=123.01  Aligned_cols=85  Identities=28%  Similarity=0.513  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +++++|||+|||+++++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|+.||+.||+..+.|++|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      .++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87654

>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=99.87  E-value=5.6e-22  Score=117.36  Aligned_cols=77  Identities=25%  Similarity=0.453  Sum_probs=74.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +|||+|||+++++++|+++|.+||.|..++++.++.++++++||||+|.+.++|+.|++.|++..+.|++|+|.+++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.87  E-value=3.6e-22  Score=121.43  Aligned_cols=82  Identities=32%  Similarity=0.507  Sum_probs=78.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||..+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.|++..+.|+.|+|+++++
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~   88 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA   88 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            47999999999999999999999999999999999989999999999999999999999999999999999999999987


Q ss_pred             CC
Q 032111          113 RP  114 (147)
Q Consensus       113 ~~  114 (147)
                      +.
T Consensus        89 ~~   90 (93)
T d1x5ua1          89 HN   90 (93)
T ss_dssp             TS
T ss_pred             CC
Confidence            54

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.4e-21  Score=116.39  Aligned_cols=77  Identities=38%  Similarity=0.642  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      .+.++|||+|||+.+++++|+++|++||.|.++.++.++.++++++||||+|.+.++|++|+..||+..+.|++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999986

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.4e-21  Score=116.99  Aligned_cols=84  Identities=32%  Similarity=0.589  Sum_probs=76.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .....+|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++||+..  ..+.|+.|.|++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~v~~   82 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEEEEC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeEEEe
Confidence            345578999999999999999999999999999999999999999999999999999999999843  489999999999


Q ss_pred             ecCCCC
Q 032111          110 ANDRPP  115 (147)
Q Consensus       110 ~~~~~~  115 (147)
                      +.++..
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            987654

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8e-22  Score=117.46  Aligned_cols=81  Identities=33%  Similarity=0.639  Sum_probs=75.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEE-EEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCCC
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEA-KVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDRP  114 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~~  114 (147)
                      |||+|||+++++++|+++|.+||.|..+ .++++..+++++|||||+|.+.++|++||+.|++..+.|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998664 678888889999999999999999999999999999999999999998766


Q ss_pred             CC
Q 032111          115 PR  116 (147)
Q Consensus       115 ~~  116 (147)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.86  E-value=2.2e-21  Score=116.00  Aligned_cols=79  Identities=29%  Similarity=0.564  Sum_probs=74.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~  109 (147)
                      ..++|||+|||+.+++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|++.||+..+.+  ++|.|++
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            44689999999999999999999999999999999998999999999999999999999999999999976  8899988


Q ss_pred             e
Q 032111          110 A  110 (147)
Q Consensus       110 ~  110 (147)
                      +
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.86  E-value=8.6e-22  Score=117.84  Aligned_cols=80  Identities=26%  Similarity=0.515  Sum_probs=77.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      .+|||+|||+.+++++|+++|.+||.|..++++.++.++++++||||+|.+.++|++|++.|++..+.|++|.|+++++.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999864

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=1.3e-21  Score=116.09  Aligned_cols=79  Identities=13%  Similarity=0.274  Sum_probs=69.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|++|++.||+..+.|++|.|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999998888877778889999999999999999999999999999999999999875

>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=99.86  E-value=3.8e-21  Score=114.70  Aligned_cols=80  Identities=36%  Similarity=0.654  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ +++..+.|+.|.|+.+.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34789999999999999999999999999999999999999999999999999999999998 68899999999998875


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      +
T Consensus        84 s   84 (84)
T d1l3ka1          84 S   84 (84)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.86  E-value=2.9e-21  Score=113.71  Aligned_cols=77  Identities=31%  Similarity=0.585  Sum_probs=73.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      +|||+|||+++++++|+++|.+||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..+.|++|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            59999999999999999999999999999998874 788999999999999999999999999999999999999864

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.8e-21  Score=119.48  Aligned_cols=82  Identities=34%  Similarity=0.618  Sum_probs=77.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ++|||+|||+.+++++|+++|.+||.|..+.++.++.++.++|||||+|.+.++|++||+ +++..|.|+.|.|.++.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            689999999999999999999999999999999998899999999999999999999997 7999999999999999887


Q ss_pred             CCC
Q 032111          114 PPR  116 (147)
Q Consensus       114 ~~~  116 (147)
                      +.+
T Consensus       100 e~~  102 (103)
T d1x4ba1         100 EES  102 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.85  E-value=3.4e-21  Score=115.23  Aligned_cols=78  Identities=32%  Similarity=0.639  Sum_probs=73.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEee
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVSFA  110 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~~  110 (147)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++.++.+++||||+|.+.++|++|++.||+..+.|  ++|.|+|+
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4789999999999999999999999999999999998899999999999999999999999999999987  56888875

>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=99.85  E-value=6.2e-21  Score=117.98  Aligned_cols=81  Identities=46%  Similarity=0.719  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+.++. .+.|++|.|+++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            346799999999999999999999999999999999989999999999999999999999998764 8999999999987


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=8.5e-21  Score=114.60  Aligned_cols=82  Identities=28%  Similarity=0.516  Sum_probs=74.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      +.++|||+|||..+++++|+++|++||.|..+.++.+..++  ++||||+|.+.++|++|+..|++..+.|+.|+|.+++
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999999999998876543  6799999999999999999999999999999999998


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      ++..
T Consensus        85 ~~~~   88 (90)
T d2cqia1          85 TPSS   88 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=4.1e-21  Score=116.93  Aligned_cols=83  Identities=25%  Similarity=0.577  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecC-CCCccceEEEEEeCCHHHHHHHHHHh-cCCeeCCeEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITER-ESGKSRGFGFVTYDSNESASSAQSAM-DGQELNGRNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~ai~~l-~~~~~~g~~l~v~~  109 (147)
                      ...+|||+|||+++++++|+++|.+||.|..+.++.+. .+++++|||||+|.+.++|++||..| ++..+.|++|.|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            44789999999999999999999999999999998764 47899999999999999999999998 88999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +++..
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98754

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3e-21  Score=119.61  Aligned_cols=81  Identities=33%  Similarity=0.706  Sum_probs=77.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|++..+.|+.|+|+++.+.
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            68999999999999999999999999999999999889999999999999999999999999999999999999998764


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      .
T Consensus        89 ~   89 (104)
T d1p1ta_          89 K   89 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=8.6e-21  Score=113.39  Aligned_cols=78  Identities=29%  Similarity=0.596  Sum_probs=72.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCC---ccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESG---KSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      |||+|||+++++++|+++|++||.|..+.++.++.++   .++|||||+|.+.++|++|++.||+..+.|+.|.|+++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999998876554   4689999999999999999999999999999999999864


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.84  E-value=7.5e-21  Score=117.13  Aligned_cols=87  Identities=25%  Similarity=0.517  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDIT--------EAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      ....+|||+|||+.+++++|+++|.+||.|.        .+.+..+..++++++||||+|.+.++|++||+.|++..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3457999999999999999999999999763        45566677788999999999999999999999999999999


Q ss_pred             eEEEEEeecCCCCCC
Q 032111          103 RNIRVSFANDRPPRS  117 (147)
Q Consensus       103 ~~l~v~~~~~~~~~~  117 (147)
                      +.|+|+++++++++.
T Consensus        86 r~i~V~~a~~~~p~~  100 (101)
T d2cpea1          86 SKLKVSLARKKPPMN  100 (101)
T ss_dssp             EECEEECSSCCCCST
T ss_pred             EEEEEEEcCCCCCCC
Confidence            999999999877653

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.5e-20  Score=113.16  Aligned_cols=82  Identities=30%  Similarity=0.617  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||+|||+++++++|+++|.+||.|..+.++.++.  .+++||||+|.+.++|++|+..|++..+.|+.|.|+++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3457899999999999999999999999999999988753  36899999999999999999999999999999999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      +++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8764

>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=99.84  E-value=1.8e-21  Score=114.32  Aligned_cols=76  Identities=36%  Similarity=0.699  Sum_probs=72.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ +++..+.|+.|.|+.+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999875

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=6.6e-21  Score=114.87  Aligned_cols=80  Identities=33%  Similarity=0.593  Sum_probs=73.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      .+|||+|||+++++++|+++|.+||.|..+.++.+.  ..++|||||+|.+.++|++||+.||+..+.|+.|.|.+++++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            579999999999999999999999999999998875  346799999999999999999999999999999999999876


Q ss_pred             CC
Q 032111          114 PP  115 (147)
Q Consensus       114 ~~  115 (147)
                      ..
T Consensus        87 ~~   88 (89)
T d1cvja2          87 KE   88 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.84  E-value=3e-20  Score=109.52  Aligned_cols=77  Identities=36%  Similarity=0.651  Sum_probs=73.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.+++++|+. +++..|.|+.|.|+.+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3789999999999999999999999999999999999999999999999999999999997 8999999999999875

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=6.4e-21  Score=111.40  Aligned_cols=75  Identities=39%  Similarity=0.748  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+ +++..+.|+.|.|+.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999998 7989999999988653

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=2.2e-20  Score=114.35  Aligned_cols=85  Identities=26%  Similarity=0.550  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc------CCeeCCeE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD------GQELNGRN  104 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~------~~~~~g~~  104 (147)
                      ...++|||+|||+++++++|+++|.+||.+..+.++.+..++.++|||||+|.+.++|++||+.|+      +..+.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            345799999999999999999999999999999999988889999999999999999999999887      56789999


Q ss_pred             EEEEeecCCCC
Q 032111          105 IRVSFANDRPP  115 (147)
Q Consensus       105 l~v~~~~~~~~  115 (147)
                      |+|.++.+++.
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999987643

>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=99.83  E-value=1.3e-20  Score=116.07  Aligned_cols=78  Identities=26%  Similarity=0.428  Sum_probs=74.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|++|++ |++..|.|+.|.|.++.+
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            689999999999999999999999999999999999999999999999999999999996 999999999999998764

>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=99.83  E-value=1.2e-20  Score=112.98  Aligned_cols=82  Identities=26%  Similarity=0.458  Sum_probs=71.1

Q ss_pred             CCCeEEEcCCCCCCC-HHHHHHHhhccCCeeEEEEEec-CCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           32 SQTKLFVGGLSWGTD-DSSLKEAFSNFGDITEAKVITE-RESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~-~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .+++|||+|||++++ +++|+++|++||.|..+.++.+ ..+++++|||||+|.+.++|++|++ ||+..+.|+.|.|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            468999999999876 5569999999999999988764 5678899999999999999999996 999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      ++++|
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98754

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=6.4e-20  Score=111.75  Aligned_cols=80  Identities=21%  Similarity=0.475  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+.+++++|+++|.+||.|..+.+..+   ...++||||+|.+.++|++||+.||+..+.+++|+|+++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            44578999999999999999999999999988876543   456789999999999999999999999999999999998


Q ss_pred             cCC
Q 032111          111 NDR  113 (147)
Q Consensus       111 ~~~  113 (147)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.3e-21  Score=118.46  Aligned_cols=86  Identities=22%  Similarity=0.403  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||.++++++|+++|.+||.|..+.+..+..++++++||||+|.+.++|++|++.||+..|.|++|.|+++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            34579999999999999999999999999988888887778899999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      +++..+
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            986554

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1e-19  Score=111.00  Aligned_cols=80  Identities=29%  Similarity=0.660  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ..+..++|||+|||..+++++|+++|++||.|..+.++.+      ++||||+|.+.++|++|+..|++..+.|+.|+|.
T Consensus        14 ~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~   87 (96)
T d1x4ga1          14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   87 (96)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445578999999999999999999999999999999865      5799999999999999999999999999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      |+++.+
T Consensus        88 ~ak~~p   93 (96)
T d1x4ga1          88 WGKESP   93 (96)
T ss_dssp             CCCCCC
T ss_pred             EcCCCC
Confidence            998654

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=9.5e-21  Score=110.57  Aligned_cols=75  Identities=27%  Similarity=0.520  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+ .++..+.|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999998 4668899999988764

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2.3e-20  Score=108.90  Aligned_cols=75  Identities=32%  Similarity=0.615  Sum_probs=71.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +|||+|||+++++++|+++|++||.+..+.++.++.++.+++||||+|.+.++|++|++ +++..+.|++|.|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            58999999999999999999999999999998888889999999999999999999997 9999999999999875

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1e-19  Score=114.29  Aligned_cols=81  Identities=20%  Similarity=0.378  Sum_probs=73.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ++...++|||+|||+.+++++|+++|++||.|..|.+..+   +.++|||||+|.+.++|..|++.||+..|.|+.|.|.
T Consensus         3 pp~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   79 (114)
T d2f9da1           3 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL   79 (114)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445679999999999999999999999999999988754   4568999999999999999999999999999999999


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      ++..
T Consensus        80 ~a~~   83 (114)
T d2f9da1          80 YYNA   83 (114)
T ss_dssp             ECCH
T ss_pred             EcCC
Confidence            9764

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=9.9e-20  Score=112.63  Aligned_cols=83  Identities=25%  Similarity=0.515  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecC-CCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITER-ESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      +.++|||+|||+.+++++|+++|.+|| +..+.++.+. .+++++|||||+|.+.++|++|+. ||+..|.++.|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            458999999999999999999999998 6677666654 467899999999999999987775 9999999999999999


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      .+....
T Consensus        92 ~~~~~~   97 (104)
T d1wi8a_          92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876443

>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=99.80  E-value=9.8e-20  Score=108.94  Aligned_cols=79  Identities=15%  Similarity=0.323  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ..+.|||+|||+.+++++|+++|..|+.+....++....+++++|+|||+|.+.++|++|++.||+..+.+++|+|+++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3467999999999999999999999998866434444467999999999999999999999999999999999999874

>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=99.80  E-value=3.2e-19  Score=110.28  Aligned_cols=84  Identities=20%  Similarity=0.298  Sum_probs=75.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ....|||+|||+++++++|+++|..++.+....++.+..+++++|+|||+|.+.++|++|++ +++..|.++.|.|.+++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            44689999999999999999999999988876666777788999999999999999999997 89999999999999998


Q ss_pred             CCCCC
Q 032111          112 DRPPR  116 (147)
Q Consensus       112 ~~~~~  116 (147)
                      ..+..
T Consensus        93 ~~~~~   97 (104)
T d1wg5a_          93 RAEVR   97 (104)
T ss_dssp             TTTSC
T ss_pred             HHHhc
Confidence            76544

>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=99.80  E-value=4e-19  Score=106.02  Aligned_cols=78  Identities=21%  Similarity=0.322  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      .++|||+|||.++++++|+++|+.+|.|..+.+..+ .+++++|||||+|.+.++|++||+ +++..+.|+.|.|++...
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~d   83 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDD   83 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcCC
Confidence            378999999999999999999999999999998776 478899999999999999999997 799999999999998653

>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=99.80  E-value=1.9e-19  Score=110.98  Aligned_cols=84  Identities=15%  Similarity=0.261  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +....+|||+|||+++++++|+++|..++ +..+.++.+ .++..++||||+|.+.++|++|++ +++..|.++.|+|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            44567999999999999999999999997 556777776 457899999999999999999997 899999999999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      ++.++..
T Consensus        89 s~~~~~~   95 (102)
T d1weza_          89 NSTAGTS   95 (102)
T ss_dssp             ECCCCCC
T ss_pred             cCCCCCC
Confidence            8876543

>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=99.80  E-value=1.2e-20  Score=114.06  Aligned_cols=82  Identities=27%  Similarity=0.451  Sum_probs=73.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +....+|||+|||+.+++++|+++|.+||.|..+.++.+ .+++++|||||+|.+.++|++||+ |++..+.|++|.|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            334568999999999999999999999999888777544 678899999999999999999997 999999999999999


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      ++++
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8764

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=3.5e-20  Score=111.18  Aligned_cols=74  Identities=20%  Similarity=0.326  Sum_probs=66.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      .+|||+|||+.+++++|+++|++||.|..+.+..+       |||||+|.+.++|++||+.||+..|.|+.|.|.+.+..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999987643       69999999999999999999999999999988876544


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>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=99.79  E-value=9.2e-20  Score=112.23  Aligned_cols=81  Identities=22%  Similarity=0.454  Sum_probs=72.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..+ .++.+++||||+|.+.++|++||+.||+..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34578999999999999999999999999999988877 57889999999999999999999999999999998877665


Q ss_pred             cC
Q 032111          111 ND  112 (147)
Q Consensus       111 ~~  112 (147)
                      ++
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=4.2e-19  Score=108.63  Aligned_cols=75  Identities=27%  Similarity=0.566  Sum_probs=67.3

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           31 QSQTKLFVGGLS-WGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      ....+|||.||| ..+++++|+++|.+||.|..+.+.        ++||||+|.+.++|++||..||+..+.|+.|+|++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344689999997 567888999999999999999873        57999999999999999999999999999999999


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      +..+
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9754

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2e-19  Score=108.26  Aligned_cols=77  Identities=26%  Similarity=0.401  Sum_probs=69.4

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHhhccCCeeEEEEEecCCCCc---cceEEEEEeCCHHHHHHHHHHhcCCeeCCeEE
Q 032111           32 SQTKLFVGGLSWGTDDSSL---KEAFSNFGDITEAKVITERESGK---SRGFGFVTYDSNESASSAQSAMDGQELNGRNI  105 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l---~~~f~~~g~i~~~~~~~~~~~~~---~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l  105 (147)
                      ..++|||+|||+.+++++|   .++|.+||.|..+.+++++.++.   +++||||+|.+.++|++|++.||+..+.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3478999999999999999   67899999999999998876554   45899999999999999999999999999999


Q ss_pred             EEE
Q 032111          106 RVS  108 (147)
Q Consensus       106 ~v~  108 (147)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            884

>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=99.79  E-value=3.6e-19  Score=108.53  Aligned_cols=80  Identities=23%  Similarity=0.498  Sum_probs=71.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .+.++|||+|||+.+++++|+++|.++|.|..+.     .++++++||||+|.+.++|++|++.||+..+.|++|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            3457999999999999999999999999776543     25678899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 032111          111 NDRPP  115 (147)
Q Consensus       111 ~~~~~  115 (147)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            87654

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.5e-18  Score=103.65  Aligned_cols=78  Identities=27%  Similarity=0.433  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ...++|||+|||+++++++|+++|++||.+..+.+..      +++||||+|.+.++|.+|+..||+..+.|+.|.|+++
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3447899999999999999999999999988776644      3579999999999999999999999999999999999


Q ss_pred             cCCC
Q 032111          111 NDRP  114 (147)
Q Consensus       111 ~~~~  114 (147)
                      +++.
T Consensus        80 kP~~   83 (86)
T d2cpda1          80 KPVD   83 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.9e-19  Score=105.46  Aligned_cols=77  Identities=26%  Similarity=0.479  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCC-eeCCeEEEEEeecC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQ-ELNGRNIRVSFAND  112 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~-~~~g~~l~v~~~~~  112 (147)
                      .+|||+|||+++++++|+++|.+||.+..+.+...      ++||||+|.+.++|++|++.|++. .+.|++|.|+++.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            47999999999999999999999998877655543      579999999999999999999985 79999999999997


Q ss_pred             CCCC
Q 032111          113 RPPR  116 (147)
Q Consensus       113 ~~~~  116 (147)
                      +..+
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            6543

>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=99.78  E-value=5.1e-19  Score=108.22  Aligned_cols=79  Identities=25%  Similarity=0.370  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ....+|||.|||+.+++++|+++|.+||.|..+.+..       ++||||+|.+.++|++||+.||+..|.++.|+|.+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3457899999999999999999999999999998754       379999999999999999999999999999999998


Q ss_pred             cCCCCC
Q 032111          111 NDRPPR  116 (147)
Q Consensus       111 ~~~~~~  116 (147)
                      +.++.+
T Consensus        86 ~~~~~~   91 (98)
T d1wg4a_          86 RVYPER   91 (98)
T ss_dssp             EEECCC
T ss_pred             ecCCCC
Confidence            765543

>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=99.78  E-value=6.2e-19  Score=105.39  Aligned_cols=77  Identities=27%  Similarity=0.587  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||.++++++|+++|++||.|..+.+.++      ++||||+|.+.++|++|+..||+..+.|+.|+|+++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999999988765      4699999999999999999999999999999999998


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      ...
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            653

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.5e-18  Score=104.06  Aligned_cols=79  Identities=22%  Similarity=0.354  Sum_probs=69.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee-CCeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL-NGRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~-~g~~l~v~~  109 (147)
                      ++.++|||+|||+++++++|+++|++||.|..+.+...    +.+++|||+|.+.++|.+|+..|++..+ .|+.|+|++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            45689999999999999999999999999988766543    3467999999999999999999999988 589999999


Q ss_pred             ecCC
Q 032111          110 ANDR  113 (147)
Q Consensus       110 ~~~~  113 (147)
                      ++++
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8763

>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=99.78  E-value=1.6e-18  Score=103.98  Aligned_cols=76  Identities=14%  Similarity=0.291  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ...+|||.|||+++++++|+++|.+|| +..+.+      .+.++||||+|.+.++|++|+..||+..+.|++|.|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            347899999999999999999999999 333333      2346899999999999999999999999999999999987


Q ss_pred             CCC
Q 032111          112 DRP  114 (147)
Q Consensus       112 ~~~  114 (147)
                      ...
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1e-19  Score=105.30  Aligned_cols=71  Identities=30%  Similarity=0.585  Sum_probs=67.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      |||+|||+++++++|+++|.+||.|..+.+..++.++.++++|||+|.+.++|++|++.||+..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999988999999999999999999999999999999988653

>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=99.77  E-value=6.5e-19  Score=107.39  Aligned_cols=83  Identities=25%  Similarity=0.438  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEEecC-CCCccceEEEEEeCCHHHHHHHHHHhcC--CeeCCeEEEEEe
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGD-ITEAKVITER-ESGKSRGFGFVTYDSNESASSAQSAMDG--QELNGRNIRVSF  109 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~ai~~l~~--~~~~g~~l~v~~  109 (147)
                      ++|||+|||..+++++|+++|++||. |..+.++.+. .++.++|||||+|.+.++|.+|++.|++  ..+.++.|.|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            58999999999999999999999995 8889888774 4678999999999999999999999864  466799999999


Q ss_pred             ecCCCCC
Q 032111          110 ANDRPPR  116 (147)
Q Consensus       110 ~~~~~~~  116 (147)
                      +++....
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9876544

>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=99.77  E-value=1.2e-18  Score=102.57  Aligned_cols=77  Identities=30%  Similarity=0.531  Sum_probs=69.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      +..+++|||+|++  +++++|+++|++||.|..+.+.++      ++||||+|.+.++|.+|+..||+..+.|++|+|+|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999986  899999999999999999988654      46999999999999999999999999999999999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      ++++|
T Consensus        74 a~~~P   78 (79)
T d2bz2a1          74 ARKQP   78 (79)
T ss_dssp             CCSSC
T ss_pred             ecCCC
Confidence            98654

>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=99.77  E-value=1.4e-18  Score=103.10  Aligned_cols=76  Identities=21%  Similarity=0.467  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeC-CeEEEEEe
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELN-GRNIRVSF  109 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~-g~~l~v~~  109 (147)
                      ++.++|||+|||.++++++|+++|.+||.|..+.++.++     +++|||+|.+.++|++|+..|++..+. ++.|+|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            345799999999999999999999999999999887542     579999999999999999999999984 68999999


Q ss_pred             ec
Q 032111          110 AN  111 (147)
Q Consensus       110 ~~  111 (147)
                      ++
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

>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=99.77  E-value=2e-18  Score=100.53  Aligned_cols=74  Identities=18%  Similarity=0.226  Sum_probs=67.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      ++|||+|||+++++++|+++|..+|.|..+.++.++..  .+++|||+|.+.++|++|+. +++..|.|++|.|+..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999887543  34699999999999999996 8999999999999865

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=1.7e-18  Score=108.05  Aligned_cols=76  Identities=18%  Similarity=0.201  Sum_probs=69.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+.+++++|+++|.+||.|..|.+..      .++||||+|.+.++|++||..||+..|.+++|.|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            347899999999999999999999999999987743      35799999999999999999999999999999999986


Q ss_pred             CC
Q 032111          112 DR  113 (147)
Q Consensus       112 ~~  113 (147)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=8.8e-19  Score=108.10  Aligned_cols=82  Identities=12%  Similarity=0.229  Sum_probs=72.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEe
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSF  109 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~  109 (147)
                      .....+|||+|||+++++++|+++|..+|.+..+.++....+++++|+|||+|.+.++|++||+ +++..|.|+.|.|.+
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3445789999999999999999999999988765455555789999999999999999999997 899999999999998


Q ss_pred             ecC
Q 032111          110 AND  112 (147)
Q Consensus       110 ~~~  112 (147)
                      +..
T Consensus        84 ~~~   86 (103)
T d2cpya1          84 VTL   86 (103)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            753

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.7e-18  Score=104.46  Aligned_cols=80  Identities=28%  Similarity=0.459  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEE
Q 032111           32 SQTKLFVGGLSWGTDDSSLKE----AFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRV  107 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v  107 (147)
                      +.++|||+|||+.+++++|++    +|++||.|..|.+..   ++++++||||+|.+.++|.+|++.||+..+.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            357999999999999998864    579999999887643   4567899999999999999999999999999999999


Q ss_pred             EeecCCC
Q 032111          108 SFANDRP  114 (147)
Q Consensus       108 ~~~~~~~  114 (147)
                      .+++++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9998653

>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=99.75  E-value=1.3e-18  Score=104.36  Aligned_cols=77  Identities=25%  Similarity=0.443  Sum_probs=67.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      ..++|||+|||+++++++|+++|.+||.|..+.+..     .+++||||+|.+.++|++|+.  ++..|.|++|.|+++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            457999999999999999999999999999987643     346899999999999999986  7789999999999997


Q ss_pred             CCCC
Q 032111          112 DRPP  115 (147)
Q Consensus       112 ~~~~  115 (147)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.75  E-value=2.6e-18  Score=106.93  Aligned_cols=75  Identities=24%  Similarity=0.442  Sum_probs=69.0

Q ss_pred             CeEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           34 TKLFVGGLSW-GTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        34 ~~i~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      ++|||.|||+ .+++++|+++|+.||.|..+.+++++     +|+|||+|.+.++|++|++.|++..|.|+.|.|++++.
T Consensus         3 ~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~   77 (109)
T d2adca1           3 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            6899999965 58999999999999999999998764     57999999999999999999999999999999999875


Q ss_pred             C
Q 032111          113 R  113 (147)
Q Consensus       113 ~  113 (147)
                      .
T Consensus        78 ~   78 (109)
T d2adca1          78 Q   78 (109)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=5.9e-18  Score=103.26  Aligned_cols=77  Identities=35%  Similarity=0.634  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCC--eEEEEEe
Q 032111           32 SQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNG--RNIRVSF  109 (147)
Q Consensus        32 ~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g--~~l~v~~  109 (147)
                      +.++|||+|||+++++++|+++|++||.|..+.+.++      +++|||+|.+.++|++|++.|++..|.+  ++|+|+|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4589999999999999999999999999999988654      4699999999999999999999999976  5799999


Q ss_pred             ecCCC
Q 032111          110 ANDRP  114 (147)
Q Consensus       110 ~~~~~  114 (147)
                      +++.+
T Consensus        90 ak~~~   94 (97)
T d1whya_          90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            88654

>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=99.74  E-value=1.1e-18  Score=109.26  Aligned_cols=83  Identities=18%  Similarity=0.312  Sum_probs=73.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      +.....+|||+|||+.+++++|+++|..+|.+..+.++.+..++.++|+|||+|.+.++|++|+. ||+..|.++.|.|.
T Consensus        14 ~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~   92 (112)
T d1wela1          14 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   92 (112)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEE
Confidence            34456799999999999999999999999988765566666789999999999999999999997 89999999999998


Q ss_pred             eecC
Q 032111          109 FAND  112 (147)
Q Consensus       109 ~~~~  112 (147)
                      .+..
T Consensus        93 ~~~~   96 (112)
T d1wela1          93 PITK   96 (112)
T ss_dssp             EECH
T ss_pred             EcCh
Confidence            8753

>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=99.74  E-value=1.4e-17  Score=96.93  Aligned_cols=71  Identities=21%  Similarity=0.368  Sum_probs=62.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           36 LFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        36 i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      |||+|||+++++++|+++|.+|| +..+.+      .+.+++|||+|.+.++|++|+..||+..+.|++|.|++++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999998 444433      235689999999999999999999999999999999998653

>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=99.73  E-value=8.2e-18  Score=104.53  Aligned_cols=80  Identities=21%  Similarity=0.355  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee--CCeEEEEE
Q 032111           31 QSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL--NGRNIRVS  108 (147)
Q Consensus        31 ~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~--~g~~l~v~  108 (147)
                      .+..+|||+|||+.+++++|+++|.+||.|..+.+..++    .+++|||+|.+.++|++||..|++..+  .+..|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            345689999999999999999999999999999888763    478999999999999999999999998  46788888


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      +++...
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            887543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.1e-17  Score=98.22  Aligned_cols=79  Identities=14%  Similarity=0.230  Sum_probs=70.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM--DGQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~~~~~~g~~l~v  107 (147)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.+..+      +++|||+|.+.++|++|++.+  ++..+.|++|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            345689999999999999999999999999999988755      369999999999999999865  567999999999


Q ss_pred             EeecCCC
Q 032111          108 SFANDRP  114 (147)
Q Consensus       108 ~~~~~~~  114 (147)
                      .+++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9998654

>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=99.73  E-value=6.2e-17  Score=99.83  Aligned_cols=80  Identities=16%  Similarity=0.245  Sum_probs=70.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc--CCeeCCeEEEE
Q 032111           30 SQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD--GQELNGRNIRV  107 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--~~~~~g~~l~v  107 (147)
                      ..+..+|||.|||+.+++++|.++|.+||.|..+.+.++      +++|||+|.+.++|++|+..|+  ...+.+++|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            345689999999999999999999999999999988754      4699999999999999999874  56788999999


Q ss_pred             EeecCCCC
Q 032111          108 SFANDRPP  115 (147)
Q Consensus       108 ~~~~~~~~  115 (147)
                      .+++..+.
T Consensus        86 ~~s~~~~~   93 (104)
T d1wexa_          86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEcCCCcc
Confidence            99976543

>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=99.69  E-value=5.1e-17  Score=99.37  Aligned_cols=78  Identities=14%  Similarity=0.264  Sum_probs=68.9

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHH--HhcCCeeCCeEEE
Q 032111           30 SQSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQS--AMDGQELNGRNIR  106 (147)
Q Consensus        30 ~~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~--~l~~~~~~g~~l~  106 (147)
                      ....++|||+|||.+ +++++|.++|++||.|..+.++.+      +++|||+|.+.++|.+|++  .+++..+.|+.|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345689999999986 899999999999999999988765      4699999999999999998  4678899999999


Q ss_pred             EEeecCC
Q 032111          107 VSFANDR  113 (147)
Q Consensus       107 v~~~~~~  113 (147)
                      |.+++.+
T Consensus        89 V~~s~~~   95 (99)
T d1x4fa1          89 VDLSEKY   95 (99)
T ss_dssp             EEEECSC
T ss_pred             EEEcCCc
Confidence            9999754

>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=99.68  E-value=2.8e-16  Score=105.62  Aligned_cols=85  Identities=33%  Similarity=0.587  Sum_probs=77.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      .....++|||+|||+.+++++|+++|..||.|..+.++.+..++.++|||||+|.+.++|++|++ +++..+.|+.|.|.
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            34456799999999999999999999999999999999998889999999999999999999998 78889999999999


Q ss_pred             eecCCC
Q 032111          109 FANDRP  114 (147)
Q Consensus       109 ~~~~~~  114 (147)
                      ++.++.
T Consensus       172 ~A~~k~  177 (183)
T d1u1qa_         172 KALSKQ  177 (183)
T ss_dssp             ECCCHH
T ss_pred             ecCCcc
Confidence            987643

>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=99.67  E-value=2e-16  Score=94.88  Aligned_cols=77  Identities=16%  Similarity=0.254  Sum_probs=68.2

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHh--cCCeeCCeEEEE
Q 032111           31 QSQTKLFVGGLSWG-TDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAM--DGQELNGRNIRV  107 (147)
Q Consensus        31 ~~~~~i~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~~~~~~g~~l~v  107 (147)
                      ...++|||+|||.. +++++|.++|++||.|..+.+..++      ++|||+|.+.++|..|+..|  ++..+.|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            45688999999986 7899999999999999999887653      48999999999999999966  577899999999


Q ss_pred             EeecCC
Q 032111          108 SFANDR  113 (147)
Q Consensus       108 ~~~~~~  113 (147)
                      .++++.
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            999854

>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=99.67  E-value=9.2e-19  Score=105.47  Aligned_cols=79  Identities=16%  Similarity=0.438  Sum_probs=67.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEE-----EecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEE
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKV-----ITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVS  108 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~-----~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~  108 (147)
                      ++|||+|||+++++++|+++|..+|.+..+.+     ..+..++++++||||+|.+.++|++|++ |++..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            68999999999999999999999987655433     2344567788999999999999999996 99999999999997


Q ss_pred             eecCC
Q 032111          109 FANDR  113 (147)
Q Consensus       109 ~~~~~  113 (147)
                      +++..
T Consensus        81 r~k~~   85 (90)
T d1u2fa_          81 RPHDY   85 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            65543

>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=99.64  E-value=8.6e-16  Score=94.54  Aligned_cols=78  Identities=13%  Similarity=0.160  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCC-CH----HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEE
Q 032111           32 SQTKLFVGGLSWGT-DD----SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIR  106 (147)
Q Consensus        32 ~~~~i~v~nlp~~~-~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~  106 (147)
                      ...+|||+||+.++ ++    ++|+++|..||.|..+.+.+.      +++|||+|.+.++|.+|+..||+..|.|++|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45789999999876 33    468999999999999988753      46999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 032111          107 VSFANDRPP  115 (147)
Q Consensus       107 v~~~~~~~~  115 (147)
                      |.+++....
T Consensus        78 v~~a~~~~~   86 (104)
T d1weya_          78 LYFAQTLHI   86 (104)
T ss_dssp             EECCCCSSC
T ss_pred             EeecccCCC
Confidence            999976544

>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=99.57  E-value=2.4e-16  Score=97.05  Aligned_cols=75  Identities=16%  Similarity=0.214  Sum_probs=68.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEee
Q 032111           35 KLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFA  110 (147)
Q Consensus        35 ~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~  110 (147)
                      .++|.+++.++++++|+++|++||.|..|.++++ .+++++|++||+|.+.++|.+|+..||+..+.|++|.|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4667788888899999999999999999998766 57899999999999999999999999999999999999875

>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=99.54  E-value=4.4e-14  Score=94.64  Aligned_cols=80  Identities=38%  Similarity=0.677  Sum_probs=72.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFANDR  113 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~~  113 (147)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..++.++++|||+|.+.++|++|+. +++..+..+.+.+......
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~~   85 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVSR   85 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCCT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhhc
Confidence            689999999999999999999999999999999998899999999999999999999999 5667888888888776544


Q ss_pred             C
Q 032111          114 P  114 (147)
Q Consensus       114 ~  114 (147)
                      .
T Consensus        86 ~   86 (183)
T d1u1qa_          86 E   86 (183)
T ss_dssp             T
T ss_pred             c
Confidence            3

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=2.5e-14  Score=87.41  Aligned_cols=67  Identities=19%  Similarity=0.354  Sum_probs=59.2

Q ss_pred             hCCCCCCeEEEcC--CCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           28 FMSQSQTKLFVGG--LSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        28 ~~~~~~~~i~v~n--lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      ..+.+..+++|.|  ||..+++++|+++|++||.|..+.++.+      ++||||+|.+.++|++|+..||+..+
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3455667889965  9999999999999999999999887654      46999999999999999999999987

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=3.6e-14  Score=88.39  Aligned_cols=72  Identities=22%  Similarity=0.264  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCH-HHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSN-ESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~-~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      -.+||+|||+.+|+++|+++|.+||.|..|.++.+      +++|||.|.+. ++|..|+..+++..+.++.+.|.+..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            35699999999999999999999999999998754      57999999985 78999999999998877776666654

>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=99.45  E-value=3.2e-13  Score=82.12  Aligned_cols=79  Identities=18%  Similarity=0.308  Sum_probs=66.2

Q ss_pred             CCCeEEEcCC--CCCC---------CHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCee
Q 032111           32 SQTKLFVGGL--SWGT---------DDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQEL  100 (147)
Q Consensus        32 ~~~~i~v~nl--p~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~  100 (147)
                      ..++|+|.||  |.++         ..++|++.|++||.|..+.+..+    ..+|++||+|.+.++|.+|+..||+..+
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            4578999998  5432         12578888999999999987654    3468999999999999999999999999


Q ss_pred             CCeEEEEEeecCCC
Q 032111          101 NGRNIRVSFANDRP  114 (147)
Q Consensus       101 ~g~~l~v~~~~~~~  114 (147)
                      .|++|.|.+..++.
T Consensus        83 ~gr~i~v~~~~g~~   96 (99)
T d2dita1          83 GGRQITAQAWDGTT   96 (99)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCEEEEEEEeCCcC
Confidence            99999999987654

>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=99.38  E-value=6.1e-13  Score=77.85  Aligned_cols=72  Identities=24%  Similarity=0.265  Sum_probs=59.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeE-EEEEeec
Q 032111           33 QTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRN-IRVSFAN  111 (147)
Q Consensus        33 ~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~-l~v~~~~  111 (147)
                      .+.|+|.++|++++++.| +.|.+||.|.++.+..+      ++|+||+|.+.++|++||+ +|+..+.|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999886544 67999999999877543      5799999999999999997 8999999974 5677664


Q ss_pred             C
Q 032111          112 D  112 (147)
Q Consensus       112 ~  112 (147)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.36  E-value=5.7e-13  Score=81.66  Aligned_cols=80  Identities=13%  Similarity=0.196  Sum_probs=66.4

Q ss_pred             CCCeEEEcCC--CCCCC--------HHHHHHHhhccCCeeEEEEEecCCCC--ccceEEEEEeCCHHHHHHHHHHhcCCe
Q 032111           32 SQTKLFVGGL--SWGTD--------DSSLKEAFSNFGDITEAKVITERESG--KSRGFGFVTYDSNESASSAQSAMDGQE   99 (147)
Q Consensus        32 ~~~~i~v~nl--p~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~ai~~l~~~~   99 (147)
                      +++.|.|.||  |.++.        .++|++.|.+||.|..+.++++..+.  ...|++||+|.+.++|.+|+..||+..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4578889998  44432        24688899999999999988764432  345899999999999999999999999


Q ss_pred             eCCeEEEEEeec
Q 032111          100 LNGRNIRVSFAN  111 (147)
Q Consensus       100 ~~g~~l~v~~~~  111 (147)
                      ++|+.|.+.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999875

>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=97.83  E-value=3.9e-05  Score=44.21  Aligned_cols=55  Identities=24%  Similarity=0.431  Sum_probs=48.4

Q ss_pred             HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeec
Q 032111           48 SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAN  111 (147)
Q Consensus        48 ~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~  111 (147)
                      .+|.+.|.+||.|.-+++..+        --+|+|.+-+.|.+|++ +++.++.|+.|+|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            367778899999998888876        58999999999999999 89999999999998654

>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=97.82  E-value=0.0001  Score=40.34  Aligned_cols=62  Identities=19%  Similarity=0.292  Sum_probs=51.2

Q ss_pred             HHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhcCCeeCCeEEEEEeecC
Q 032111           48 SSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMDGQELNGRNIRVSFAND  112 (147)
Q Consensus        48 ~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~~~~~~g~~l~v~~~~~  112 (147)
                      +.|.+.|.+++.|.++.+....   .....|-|...+.++|.-|+..||..+++.++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~---dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC---STTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc---CCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            3456678899999998775432   2234799999999999999999999999999999998764

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.79  E-value=0.00013  Score=42.31  Aligned_cols=69  Identities=12%  Similarity=0.146  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCcc--ceEEEEEeCCHHHHHHHHHHhcCCeeCC
Q 032111           34 TKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKS--RGFGFVTYDSNESASSAQSAMDGQELNG  102 (147)
Q Consensus        34 ~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~--~g~afv~f~~~~~a~~ai~~l~~~~~~g  102 (147)
                      +.|-|+.||+..+++++.+.+...+.+........+.+.+.  ..-|+|.|.+.++.....+.+++..+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            46889999999999999999998888777777665444332  2679999999999999999999998843

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.79  E-value=0.0034  Score=36.44  Aligned_cols=60  Identities=20%  Similarity=0.276  Sum_probs=48.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHhhccCCeeEEEEEecCCCCccceEEEEEeCCHHHHHHHHHHhc
Q 032111           29 MSQSQTKLFVGGLSWGTDDSSLKEAFSNFGDITEAKVITERESGKSRGFGFVTYDSNESASSAQSAMD   96 (147)
Q Consensus        29 ~~~~~~~i~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~   96 (147)
                      +.+.+..||....|.++...+|.++|..||.| .|.++.+.       .|||...+.+.++.++..+.
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            44566789999999999999999999999875 34455442       69999999999999888655