Citrus Sinensis ID: 036201

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110--
Protein Sequence
MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE
Secondary Structure (PSIPRED)
ccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccccHHHHHHcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEEccHHHHHHHHHHHHHccccccEEEEEEccHHHccccccHHHHHHHHcccccHHHHHHHHHHHHccccccccccccccHcccEEEEEccccccEEEEcc
Coil and Loop (DISEMBL)
mkfgnhrgFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE
Flexible Loop (DISEMBL)
MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTaaqftdevngfqnstklskkrkhmtildegtmkferiae
Low Complexity Region (SEG)
MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE
Disordered region (IsUnstruct)
******RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVM*******************************************************
Disordered Region (DISOPRED)
***GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH*********************************************************************
Disordered Region (DISEMBL)
MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE
Disordered Region (DISPRO)
****NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFT***************RKHMTILDEGTMKFERI**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	112	2.2.26 [Sep-21-2011]
Q54PB2	895	Multiple RNA-binding doma	yes	no	0.348	0.043	0.615	8e-10
Q9Y4C8	960	Probable RNA-binding prot	yes	no	0.625	0.072	0.34	5e-08
Q4PC17	858	Multiple RNA-binding doma	N/A	no	0.375	0.048	0.604	7e-08
O13620	833	Multiple RNA-binding doma	yes	no	0.321	0.043	0.638	3e-07
Q8R3C6	952	Probable RNA-binding prot	yes	no	0.446	0.052	0.438	6e-07
Q4WJT7	825	Multiple RNA-binding doma	yes	no	0.553	0.075	0.359	2e-06
Q5BGA9	819	Multiple RNA-binding doma	yes	no	0.330	0.045	0.513	7e-06
P0CR16	769	Multiple RNA-binding doma	yes	no	0.339	0.049	0.552	8e-06
P0CR17	769	Multiple RNA-binding doma	N/A	no	0.339	0.049	0.552	8e-06
Q6CEW9	828	Multiple RNA-binding doma	yes	no	0.330	0.044	0.540	2e-05

>sp|Q54PB2|MRD1_DICDI Multiple RNA-binding domain-containing protein 1 OS=Dictyostelium discoideum GN=mrd1 PE=3 SV=1

 Score = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 24/39 (61%), Positives = 32/39 (82%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           G HRGF FVE++T++EA+NA+EAL N+H YGRHL+   A
Sbjct: 832 GGHRGFGFVEFLTEEEAKNAMEALGNSHFYGRHLVLQYA 870

Dictyostelium discoideum (taxid: 44689)

>sp|Q9Y4C8|RBM19_HUMAN Probable RNA-binding protein 19 OS=Homo sapiens GN=RBM19 PE=1 SV=3

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/100 (34%), Positives = 49/100 (49%), Gaps = 30/100 (30%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALS-NTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKE 62
           G HRGF FV+++TKQ+A+ A  AL  +THLYGR L+   A  ++                
Sbjct: 871 GTHRGFGFVDFLTKQDAKRAFNALCHSTHLYGRRLVLEWADSEV---------------- 914

Query: 63  GESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDE 102
             +L+ LR +TAA F +             K+K   +LDE
Sbjct: 915 --TLQALRRKTAAHFHE-----------PPKKKRSVVLDE 941

Plays a role in embryo pre-implantation development.

Homo sapiens (taxid: 9606)

>sp|Q4PC17|MRD1_USTMA Multiple RNA-binding domain-containing protein 1 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=MRD1 PE=3 SV=1

 Score = 55.8 bits (133), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 32/43 (74%), Gaps = 1/43 (2%)

Query: 2   KFGNH-RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
           KF N  RGF FVEY T +EAQ+A+EAL +THL GRHL+   +H
Sbjct: 753 KFDNTTRGFGFVEYSTVREAQSAMEALKHTHLLGRHLVLQWSH 795

Involved in pre-rRNA processing.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

>sp|O13620|MRD1_SCHPO Multiple RNA-binding domain-containing protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mrd1 PE=3 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/36 (63%), Positives = 27/36 (75%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           RGFAF E+VT +EA NA+ AL NTHL GRHL+   A
Sbjct: 761 RGFAFAEFVTAREAANAMRALKNTHLLGRHLVLQYA 796

Involved in pre-rRNA processing.

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

>sp|Q8R3C6|RBM19_MOUSE Probable RNA-binding protein 19 OS=Mus musculus GN=Rbm19 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 7/57 (12%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALS-NTHLYGRHLIFSVAHDQIISIIAPTFQVMER 59
           G HRGF FV+++TKQ+A+ A  AL  +THLYGR L+   A  ++      T Q + R
Sbjct: 863 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV------TVQTLRR 913

Plays a role in embryo pre-implantation development.

Mus musculus (taxid: 10090)

>sp|Q4WJT7|MRD1_ASPFU Multiple RNA-binding domain-containing protein 1 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=mrd1 PE=3 SV=1

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 41/64 (64%), Gaps = 2/64 (3%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESL 66
           RGF F ++V+ +EA+NA++AL NTHL GR L+   A+++ +       Q+ ++   GE L
Sbjct: 742 RGFGFADFVSAREAENAMDALKNTHLLGRRLVLEFANEEAVDPEQEIEQIEKKV--GEQL 799

Query: 67  EELR 70
           + ++
Sbjct: 800 DRVK 803

Involved in pre-rRNA processing.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

>sp|Q5BGA9|MRD1_EMENI Multiple RNA-binding domain-containing protein 1 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=mrd1 PE=3 SV=1

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 28/37 (75%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
           RGF F ++V+ +EA+NA++AL NTHL GR L+   A+
Sbjct: 737 RGFGFADFVSAREAENAMDALKNTHLLGRRLVLEFAN 773

Involved in pre-rRNA processing.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

>sp|P0CR16|MRD1_CRYNJ Multiple RNA-binding domain-containing protein 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=MRD1 PE=3 SV=1

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/38 (55%), Positives = 28/38 (73%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD 44
           RGFAF+E+ T  EA  A+EAL +THL GRHL+   A++
Sbjct: 686 RGFAFLEFTTHTEAARAMEALKHTHLLGRHLVLQWANE 723

Involved in pre-rRNA processing.

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

>sp|P0CR17|MRD1_CRYNB Multiple RNA-binding domain-containing protein 1 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=MRD1 PE=3 SV=1

 Score = 49.3 bits (116), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/38 (55%), Positives = 28/38 (73%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD 44
           RGFAF+E+ T  EA  A+EAL +THL GRHL+   A++
Sbjct: 686 RGFAFLEFTTHTEAARAMEALKHTHLLGRHLVLQWANE 723

Involved in pre-rRNA processing.

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

>sp|Q6CEW9|MRD1_YARLI Multiple RNA-binding domain-containing protein 1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=MRD1 PE=3 SV=1

 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/37 (54%), Positives = 26/37 (70%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
           RGFAF EYV+ +EA++A+ AL  THL GR L+   A 
Sbjct: 743 RGFAFAEYVSAKEAEHAMSALQGTHLLGRRLVLQYAQ 779

Involved in pre-rRNA processing.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	112
255582596	181	RNA binding motif protein, putative [Ric	0.830	0.513	0.684	3e-35
297738037	767	unnamed protein product [Vitis vinifera]	0.794	0.116	0.705	6e-35
359472780	983	PREDICTED: probable RNA-binding protein	0.794	0.090	0.705	7e-35
356551226	847	PREDICTED: LOW QUALITY PROTEIN: multiple	0.839	0.110	0.669	5e-34
38345802	904	OSJNBa0085I10.19 [Oryza sativa Japonica	0.812	0.100	0.633	2e-31
125549686	904	hypothetical protein OsI_17353 [Oryza sa	0.812	0.100	0.633	2e-31
125591601	867	hypothetical protein OsJ_16124 [Oryza sa	0.812	0.104	0.633	2e-31
357168436	894	PREDICTED: probable RNA-binding protein	0.812	0.101	0.633	2e-31
115460478	536	Os04g0611500 [Oryza sativa Japonica Grou	0.812	0.169	0.633	3e-31
356554642	824	PREDICTED: probable RNA-binding protein	0.839	0.114	0.616	1e-30

>gi|255582596|ref|XP_002532080.1| RNA binding motif protein, putative [Ricinus communis] gi|223528250|gb|EEF30303.1| RNA binding motif protein, putative [Ricinus communis]

 Score =  152 bits (383), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 76/111 (68%), Positives = 87/111 (78%), Gaps = 18/111 (16%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           +KFGNHRGFAFVEYVTKQEAQNAL+ALS+THLYGRHL                  V+ERA
Sbjct: 88  VKFGNHRGFAFVEYVTKQEAQNALQALSSTHLYGRHL------------------VLERA 129

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIA 111
           KEGESLEELRARTAA F+DE++G  N  K+SKKRK+M +LDEGTMKF+RIA
Sbjct: 130 KEGESLEELRARTAAHFSDELSGMHNPAKVSKKRKNMAVLDEGTMKFQRIA 180

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738037|emb|CBI27238.3| unnamed protein product [Vitis vinifera]

 Score =  151 bits (381), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 79/112 (70%), Positives = 86/112 (76%), Gaps = 23/112 (20%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+ALS+THLYGRHL                  VMERA
Sbjct: 679 MKFGSHRGFAFVEFVTKQEAQNALQALSSTHLYGRHL------------------VMERA 720

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGESLEELRARTAAQFTD     QN TKLS+KRKHM  LDEGT+KFERIA+
Sbjct: 721 KEGESLEELRARTAAQFTD-----QNPTKLSRKRKHMAALDEGTVKFERIAD 767

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359472780|ref|XP_002275485.2| PREDICTED: probable RNA-binding protein 19-like [Vitis vinifera]

 Score =  150 bits (380), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 79/112 (70%), Positives = 86/112 (76%), Gaps = 23/112 (20%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+ALS+THLYGRHL                  VMERA
Sbjct: 895 MKFGSHRGFAFVEFVTKQEAQNALQALSSTHLYGRHL------------------VMERA 936

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGESLEELRARTAAQFTD     QN TKLS+KRKHM  LDEGT+KFERIA+
Sbjct: 937 KEGESLEELRARTAAQFTD-----QNPTKLSRKRKHMAALDEGTVKFERIAD 983

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356551226|ref|XP_003543978.1| PREDICTED: LOW QUALITY PROTEIN: multiple RNA-binding domain-containing protein 1-like [Glycine max]

 Score =  147 bits (372), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 75/112 (66%), Positives = 85/112 (75%), Gaps = 18/112 (16%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFGNHRGFAFVEYVT+QEAQNAL+ALS+THLYGRHL                  V+ERA
Sbjct: 754 MKFGNHRGFAFVEYVTQQEAQNALKALSSTHLYGRHL------------------VIERA 795

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KE ESLEELRARTAAQF+DE NGFQ++ K SKKRK +  LDEG MKF R+A+
Sbjct: 796 KEAESLEELRARTAAQFSDEQNGFQSAMKFSKKRKQVDFLDEGKMKFGRMAD 847

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|38345802|emb|CAE03574.2| OSJNBa0085I10.19 [Oryza sativa Japonica Group] gi|38568013|emb|CAE05198.3| OSJNBa0070C17.5 [Oryza sativa Japonica Group]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 21/112 (18%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+AL++THLYGRHL                  V+ERA
Sbjct: 814 MKFGSHRGFAFVEFVTKQEAQNALQALASTHLYGRHL------------------VIERA 855

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGE+LEELRARTAAQF DE +GFQ   +LSKKRK  +++DEG++KF RI E
Sbjct: 856 KEGETLEELRARTAAQFVDEQSGFQ---RLSKKRKQTSLVDEGSVKFSRIVE 904

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125549686|gb|EAY95508.1| hypothetical protein OsI_17353 [Oryza sativa Indica Group]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 21/112 (18%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+AL++THLYGRHL                  V+ERA
Sbjct: 814 MKFGSHRGFAFVEFVTKQEAQNALQALASTHLYGRHL------------------VIERA 855

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGE+LEELRARTAAQF DE +GFQ   +LSKKRK  +++DEG++KF RI E
Sbjct: 856 KEGETLEELRARTAAQFVDEQSGFQ---RLSKKRKQTSLVDEGSVKFSRIVE 904

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125591601|gb|EAZ31951.1| hypothetical protein OsJ_16124 [Oryza sativa Japonica Group]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 21/112 (18%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+AL++THLYGRHL                  V+ERA
Sbjct: 777 MKFGSHRGFAFVEFVTKQEAQNALQALASTHLYGRHL------------------VIERA 818

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGE+LEELRARTAAQF DE +GFQ   +LSKKRK  +++DEG++KF RI E
Sbjct: 819 KEGETLEELRARTAAQFVDEQSGFQ---RLSKKRKQTSLVDEGSVKFSRIVE 867

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357168436|ref|XP_003581646.1| PREDICTED: probable RNA-binding protein 19-like [Brachypodium distachyon]

 Score =  139 bits (351), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 21/112 (18%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+AL++THLYGRHL                  V+ERA
Sbjct: 804 MKFGSHRGFAFVEFVTKQEAQNALQALASTHLYGRHL------------------VIERA 845

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGE+LEELRARTAAQF DE +GFQ   ++SKKRK  ++LDEG++KF RI E
Sbjct: 846 KEGETLEELRARTAAQFVDEQSGFQ---RMSKKRKQTSLLDEGSVKFSRIVE 894

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115460478|ref|NP_001053839.1| Os04g0611500 [Oryza sativa Japonica Group] gi|113565410|dbj|BAF15753.1| Os04g0611500, partial [Oryza sativa Japonica Group]

 Score =  139 bits (349), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 71/112 (63%), Positives = 85/112 (75%), Gaps = 21/112 (18%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVE+VTKQEAQNAL+AL++THLYGRHL                  V+ERA
Sbjct: 446 MKFGSHRGFAFVEFVTKQEAQNALQALASTHLYGRHL------------------VIERA 487

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KEGE+LEELRARTAAQF DE +GFQ   +LSKKRK  +++DEG++KF RI E
Sbjct: 488 KEGETLEELRARTAAQFVDEQSGFQ---RLSKKRKQTSLVDEGSVKFSRIVE 536

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356554642|ref|XP_003545653.1| PREDICTED: probable RNA-binding protein 19-like [Glycine max]

 Score =  137 bits (344), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 69/112 (61%), Positives = 84/112 (75%), Gaps = 18/112 (16%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
           MKFG+HRGFAFVEYVT+QEA+NA EAL++THLYGRHL+                  +E A
Sbjct: 731 MKFGSHRGFAFVEYVTQQEAKNAREALASTHLYGRHLL------------------IEHA 772

Query: 61  KEGESLEELRARTAAQFTDEVNGFQNSTKLSKKRKHMTILDEGTMKFERIAE 112
           KE E+LEELRA+TAAQF+DE NGFQ++ KLSKKR  + ILDEG MKF R+A+
Sbjct: 773 KEDETLEELRAKTAAQFSDEQNGFQSAMKLSKKRNQVDILDEGNMKFGRMAD 824

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	112
WB|WBGene00004315	872	rbd-1 [Caenorhabditis elegans	0.348	0.044	0.475	3e-09
UNIPROTKB|F1P1R2	621	RBM19 "Uncharacterized protein	0.348	0.062	0.55	6.6e-09
DICTYBASE|DDB_G0284663	895	mrd1 "RNA-binding region RNP-1	0.348	0.043	0.615	8.5e-09
UNIPROTKB|F1NEC5	945	RBM19 "Uncharacterized protein	0.348	0.041	0.55	1.8e-08
TAIR|locus:2122990	816	AT4G19610 [Arabidopsis thalian	0.678	0.093	0.417	3.3e-08
ZFIN|ZDB-GENE-031125-3	927	rbm19 "RNA binding motif prote	0.348	0.042	0.525	4.6e-08
UNIPROTKB|H0YIL2	110	RBM19 "Probable RNA-binding pr	0.633	0.645	0.367	1.4e-07
ASPGD|ASPL0000061066	819	AN0421 [Emericella nidulans (t	0.553	0.075	0.406	3.9e-07
POMBASE|SPBP22H7.02c	833	SPBP22H7.02c "RNA-binding prot	0.526	0.070	0.423	5.1e-07
UNIPROTKB|F1RKD1	965	RBM19 "Uncharacterized protein	0.633	0.073	0.379	1.3e-06

WB|WBGene00004315 rbd-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 102 (41.0 bits), Expect = 3.0e-09, Sum P(2) = 3.0e-09
 Identities = 19/40 (47%), Positives = 27/40 (67%)

Query:     6 HRGFAFVEYVTKQEAQNALEAL-SNTHLYGRHLIFSVAHD 44
             HRGF FV++++  EA  A ++L  +THLYGR L+   A D
Sbjct:   789 HRGFGFVDFISADEAHRAFDSLVHSTHLYGRRLVLEWAKD 828

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0008406 "gonad development" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0006396 "RNA processing" evidence=IMP

GO:0040039 "inductive cell migration" evidence=IMP

GO:0005730 "nucleolus" evidence=IDA

GO:0000478 "endonucleolytic cleavage involved in rRNA processing" evidence=IMP

GO:0040025 "vulval development" evidence=IMP

GO:0040002 "collagen and cuticulin-based cuticle development" evidence=IMP

UNIPROTKB|F1P1R2 RBM19 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 116 (45.9 bits), Expect = 6.6e-09, Sum P(2) = 6.6e-09
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVA 42
             G+HRGF FV+++TKQ+A+ A  AL + THLYGR L+   A
Sbjct:   534 GSHRGFGFVDFLTKQDAKKAFNALCHSTHLYGRRLVLEWA 573

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IEA

DICTYBASE|DDB_G0284663 mrd1 "RNA-binding region RNP-1 domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 144 (55.7 bits), Expect = 8.5e-09, P = 8.5e-09
 Identities = 24/39 (61%), Positives = 32/39 (82%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             G HRGF FVE++T++EA+NA+EAL N+H YGRHL+   A
Sbjct:   832 GGHRGFGFVEFLTEEEAKNAMEALGNSHFYGRHLVLQYA 870

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0030515 "snoRNA binding" evidence=ISS

GO:0006364 "rRNA processing" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|F1NEC5 RBM19 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 116 (45.9 bits), Expect = 1.8e-08, Sum P(2) = 1.8e-08
 Identities = 22/40 (55%), Positives = 30/40 (75%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVA 42
             G+HRGF FV+++TKQ+A+ A  AL + THLYGR L+   A
Sbjct:   858 GSHRGFGFVDFLTKQDAKKAFNALCHSTHLYGRRLVLEWA 897

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0040019 "positive regulation of embryonic development" evidence=IEA

TAIR|locus:2122990 AT4G19610 [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 33/79 (41%), Positives = 48/79 (60%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEG 63
             G + G+AFVE+VTKQEA NA +AL++TH YGRHL+   A+D   S+ A   +    AK  
Sbjct:   739 GQYAGYAFVEFVTKQEALNAKKALASTHFYGRHLVLEWANDDN-SMEA--IRKRSAAKFD 795

Query:    64 ESLEELRARTAAQFTDEVN 82
             E  +  R R +++  +  N
Sbjct:   796 EENDNARKRKSSKAVEGKN 814

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-031125-3 rbm19 "RNA binding motif protein 19" [Danio rerio (taxid:7955)]

 Score = 115 (45.5 bits), Expect = 4.6e-08, Sum P(2) = 4.6e-08
 Identities = 21/40 (52%), Positives = 30/40 (75%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVA 42
             G+HRGF F++++TKQ+A+ A  AL + THLYGR L+   A
Sbjct:   843 GSHRGFGFIDFLTKQDAKKAFSALCHSTHLYGRRLVLEWA 882

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0048546 "digestive tract morphogenesis" evidence=IMP

UNIPROTKB|H0YIL2 RBM19 "Probable RNA-binding protein 19" [Homo sapiens (taxid:9606)]

 Score = 120 (47.3 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 29/79 (36%), Positives = 42/79 (53%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVAHDQIISIIAPTFQVMERAKE 62
             G HRGF FV+++TKQ+A+ A  AL + THLYGR L+   A  ++      T Q + R K 
Sbjct:    21 GTHRGFGFVDFLTKQDAKRAFNALCHSTHLYGRRLVLEWADSEV------TLQALRR-KT 73

Query:    63 GESLEELRARTAAQFTDEV 81
                  E   +  +   DE+
Sbjct:    74 AAHFHEPPKKKRSVVLDEI 92

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ASPGD|ASPL0000061066 AN0421 [Emericella nidulans (taxid:162425)]

 Score = 128 (50.1 bits), Expect = 3.9e-07, P = 3.9e-07
 Identities = 26/64 (40%), Positives = 42/64 (65%)

Query:     7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESL 66
             RGF F ++V+ +EA+NA++AL NTHL GR L+   A+++ I       Q +E+ K GE L
Sbjct:   737 RGFGFADFVSAREAENAMDALKNTHLLGRRLVLEFANEEAIDA-EEEIQRIEK-KVGEQL 794

Query:    67 EELR 70
             + ++
Sbjct:   795 DRVK 798

GO:0030686 "90S preribosome" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0042134 "rRNA primary transcript binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000472 "endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

GO:0000447 "endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

GO:0034462 "small-subunit processome assembly" evidence=IEA

GO:0000480 "endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" evidence=IEA

POMBASE|SPBP22H7.02c SPBP22H7.02c "RNA-binding protein Mrd1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 127 (49.8 bits), Expect = 5.1e-07, P = 5.1e-07
 Identities = 25/59 (42%), Positives = 35/59 (59%)

Query:     7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGES 65
             RGFAF E+VT +EA NA+ AL NTHL GRHL+   A +  +  +    + M +    E+
Sbjct:   761 RGFAFAEFVTAREAANAMRALKNTHLLGRHLVLQYASNATMDDMQHAIEKMAKEANAEA 819

GO:0003723 "RNA binding" evidence=ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0006364 "rRNA processing" evidence=ISO

GO:0030686 "90S preribosome" evidence=ISO

GO:0034462 "small-subunit processome assembly" evidence=ISO

UNIPROTKB|F1RKD1 RBM19 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 124 (48.7 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 30/79 (37%), Positives = 42/79 (53%)

Query:     4 GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVAHDQIISIIAPTFQVMERAKE 62
             G HRGF FV++ TKQ+A+ A  AL + THLYGR L+   A  ++      T Q + R K 
Sbjct:   876 GTHRGFGFVDFFTKQDAKRAFNALCHSTHLYGRRLVLEWADSEV------TLQALRR-KT 928

Query:    63 GESLEELRARTAAQFTDEV 81
              E   E   +  +   DE+
Sbjct:   929 AEHFHEPPKKKRSVVLDEI 947

GO:0040019 "positive regulation of embryonic development" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00030096001	SubName- Full=Chromosome chr1 scaffold_5, whole genome shotgun sequence; (789 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00034559001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (840 aa)				•	•		•		0.854
	GSVIVG00018070001	SubName- Full=Chromosome chr13 scaffold_17, whole genome shotgun sequence; (540 aa)				•	•		•		0.844
	GSVIVG00038815001	SubName- Full=Chromosome chr5 scaffold_98, whole genome shotgun sequence; (1139 aa)				•	•		•		0.837
	GSVIVG00000597001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (926 aa)				•	•		•		0.813
	GSVIVG00019376001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (1041 aa)				•			•		0.765
	GSVIVG00005498001	SubName- Full=Putative uncharacterized protein (Chromosome chr13 scaffold_152, whole genome sho [...] (293 aa)				•	•		•		0.758
	GSVIVG00000661001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (701 aa)				•			•		0.722
	GSVIVG00033408001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (430 aa)				•					0.712
	GSVIVG00021307001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (586 aa)				•			•		0.701
	GSVIVG00028481001	SubName- Full=Chromosome chr7 scaffold_44, whole genome shotgun sequence; (316 aa)				•					0.699

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	112
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	7e-19
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-11
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	9e-11
smart00360	73	smart00360, RRM, RNA recognition motif	8e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-06
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-05
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-05
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-05
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-05
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	7e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	7e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	7e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-04
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-04
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-04
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	5e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	5e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	7e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.001
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.002
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.002
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.002
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.002
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	0.002
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.003
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.003
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.004
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.004

>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 = 73.8 bits (182), Expect = 7e-19
 Identities = 29/35 (82%), Positives = 34/35 (97%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
          G+HRGFAFVE+VTKQEAQNA+EAL +THLYGRHL+
Sbjct: 38 GSHRGFAFVEFVTKQEAQNAMEALKSTHLYGRHLV 72

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 54.3 bits (131), Expect = 3e-11
 Identities = 21/36 (58%), Positives = 30/36 (83%), Gaps = 1/36 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALS-NTHLYGRHLI 38
          G+HRGF FV+++TKQ+A+ A +AL  +THLYGR L+
Sbjct: 40 GSHRGFGFVDFITKQDAKRAFKALCHSTHLYGRRLV 75

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

 Score = 53.3 bits (128), Expect = 9e-11
 Identities = 23/42 (54%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 2  KFGNH-RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          KF    RGFAFVE+ T +EA NA+ AL +THL GR L+   A
Sbjct: 35 KFDQSARGFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQYA 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|214636 smart00360, RRM, RNA recognition motif

 Score = 45.3 bits (108), Expect = 8e-08
 Identities = 17/34 (50%), Positives = 25/34 (73%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +GFAFVE+ ++++A+ ALEAL+   L GR L
Sbjct: 38 GKSKGFAFVEFESEEDAEKALEALNGKELDGRPL 71

Length = 73

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

 Score = 41.5 bits (98), Expect = 4e-06
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
          G  RG+ FV + TK+EA+ AL++L+     G+ L+   AH
Sbjct: 41 GQPRGYCFVTFETKEEAEKALKSLNGKTALGKKLVVRWAH 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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 4e-06
 Identities = 13/40 (32%), Positives = 21/40 (52%)

Query: 3  FGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
               GFAFVE+ T++ A+ A++ L+     GR L    +
Sbjct: 17 LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 40.8 bits (96), Expect = 5e-06
 Identities = 18/36 (50%), Positives = 25/36 (69%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          K G  +GFAFVE+ + ++A+ ALEAL+   L GR L
Sbjct: 34 KDGKSKGFAFVEFESPEDAEKALEALNGKELDGRKL 69

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

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 13/32 (40%), Positives = 22/32 (68%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
            HRGFAFVE+   ++A  A++ ++ + L+GR
Sbjct: 37 QKHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68

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

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 13/28 (46%), Positives = 20/28 (71%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTH 31
          G+ +GFAF+E+ T +EAQ A + L+N  
Sbjct: 38 GDIKGFAFIEFETPEEAQKACKHLNNPP 65

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

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 16/38 (42%), Positives = 26/38 (68%), Gaps = 1/38 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
          G  +G+AFVE+ T +EA+ A++AL+   L  +H  F+V
Sbjct: 47 GKTKGYAFVEFATPEEAKEAVKALNGYKLDKKH-TFAV 83

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

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 18/39 (46%), Positives = 22/39 (56%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          G  RGF FVE  T +EA  A+E L+ T   GR L  + A
Sbjct: 38 GRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTVNEA 76

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

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

 Score = 38.7 bits (91), Expect = 3e-05
 Identities = 16/32 (50%), Positives = 23/32 (71%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G  +GFAFVE+  +++A+ ALEAL+   L GR
Sbjct: 36 GRSKGFAFVEFEDEEDAEKALEALNGKELGGR 67

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

 Score = 38.7 bits (91), Expect = 3e-05
 Identities = 10/32 (31%), Positives = 23/32 (71%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
            H+G+ FVE++++++A  A++ ++   LYG+
Sbjct: 37 QAHQGYGFVEFLSEEDADYAIKIMNMIKLYGK 68

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

 Score = 38.5 bits (90), Expect = 4e-05
 Identities = 13/36 (36%), Positives = 25/36 (69%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          +G AF+ ++ +++A   ++AL+N  L+GR L  S+A
Sbjct: 43 KGVAFILFLDREDAHKCVKALNNKELFGRTLKCSIA 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 38.3 bits (90), Expect = 5e-05
 Identities = 15/32 (46%), Positives = 22/32 (68%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           RGFAFVE+ + ++A+ AL+ L+   L GR L
Sbjct: 37 PRGFAFVEFASPEDAEAALKKLNGLVLDGRTL 68

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

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

 Score = 38.3 bits (90), Expect = 6e-05
 Identities = 14/28 (50%), Positives = 21/28 (75%)

Query: 8  GFAFVEYVTKQEAQNALEALSNTHLYGR 35
          GF FVEY T+++A+NA++ L+ T L  R
Sbjct: 41 GFCFVEYYTREDAENAVKYLNGTKLDDR 68

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

 Score = 38.0 bits (89), Expect = 7e-05
 Identities = 11/32 (34%), Positives = 22/32 (68%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G  +GFAFV++ +K +A+ A++ ++   + GR
Sbjct: 37 GKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68

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|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 38.0 bits (88), Expect = 7e-05
 Identities = 17/30 (56%), Positives = 24/30 (80%), Gaps = 1/30 (3%)

Query: 1  MKF-GNHRGFAFVEYVTKQEAQNALEALSN 29
          M F GN+RG+AFV +  KQEA+NA++ L+N
Sbjct: 35 MDFNGNNRGYAFVTFSNKQEAKNAIKQLNN 64

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, 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. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

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

 Score = 37.9 bits (89), Expect = 7e-05
 Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 1/30 (3%)

Query: 1  MKF-GNHRGFAFVEYVTKQEAQNALEALSN 29
          M F G +RG+AFV Y  K+ AQ A++ L N
Sbjct: 35 MDFSGLNRGYAFVTYTNKEAAQRAVKQLHN 64

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

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

 Score = 37.7 bits (88), Expect = 9e-05
 Identities = 14/32 (43%), Positives = 22/32 (68%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
          RGFAFV +  K++A++A++A+    L GR L 
Sbjct: 40 RGFAFVRFYDKRDAEDAMDAMDGKELDGRELR 71

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

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 1   MKF-GNHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHL--IFSVAHDQIISIIAPTFQV 56
           M F G +RG+AFV +  K+EA+ A++ L+N  +  GR L    SV + ++     P  + 
Sbjct: 92  MDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDNCRLFVGGIPKNK- 150

Query: 57  MERAKEGESLEELRART 73
               K  E LEE    T
Sbjct: 151 ----KREEILEEFSKVT 163

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

 Score = 36.7 bits (86), Expect = 2e-04
 Identities = 18/38 (47%), Positives = 25/38 (65%), Gaps = 2/38 (5%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
          G  RGFAFV + T+++A+ A+E L N   Y  +LI SV
Sbjct: 38 GQSRGFAFVTFHTREDAERAIEKL-NGFGYD-NLILSV 73

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

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

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 8  GFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
          G+ FVE+ +K+ AQ AL+ L  T L G  L   +
Sbjct: 48 GYGFVEFKSKEAAQKALKRLQGTVLDGHALELKL 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 36.5 bits (85), Expect = 3e-04
 Identities = 13/34 (38%), Positives = 22/34 (64%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G H+G+ F+EY   Q AQ+A+ +++   L G+ L
Sbjct: 39 GKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQL 72

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|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 = 36.4 bits (85), Expect = 3e-04
 Identities = 12/28 (42%), Positives = 19/28 (67%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTH 31
          G  +G AFV++ +++EAQ A+EAL    
Sbjct: 38 GQSKGCAFVKFSSREEAQKAIEALHGKV 65

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

 Score = 36.1 bits (84), Expect = 3e-04
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  + FAFV +  +     A++ L+   L+GR L
Sbjct: 39 GKPKSFAFVTFKHEVSVPYAIQLLNGIRLFGREL 72

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

 Score = 38.0 bits (87), Expect = 4e-04
 Identities = 16/37 (43%), Positives = 24/37 (64%)

Query: 2   KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
           + G  RGFAFVE+ +++ A+ A+E L+   L GR L 
Sbjct: 152 ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR 188

Length = 306

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

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 13/37 (35%), Positives = 23/37 (62%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          MK G  RG+ FV + ++Q+A+NA+  ++   L  R +
Sbjct: 35 MKSGRSRGYGFVSFRSQQDAENAINEMNGKWLGSRPI 71

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

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.0 bits (83), Expect = 5e-04
 Identities = 17/30 (56%), Positives = 23/30 (76%), Gaps = 1/30 (3%)

Query: 1  MKF-GNHRGFAFVEYVTKQEAQNALEALSN 29
          M+F G +RG+AFV Y TK+EAQ A+  L+N
Sbjct: 35 MEFSGENRGYAFVMYTTKEEAQLAIRILNN 64

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

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 13/37 (35%), Positives = 26/37 (70%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          M+ G  +G+ FV +V K++A+NA+++++   L GR +
Sbjct: 35 MQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

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

 Score = 36.0 bits (84), Expect = 5e-04
 Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 3/39 (7%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLY---GRHLIFSVA 42
          RGFAFVE+ + ++A   ++AL+N   +   GR +  S A
Sbjct: 46 RGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 35.8 bits (83), Expect = 5e-04
 Identities = 15/32 (46%), Positives = 22/32 (68%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G  +GF +VE+ +++ AQ AL+AL  T L GR
Sbjct: 37 GRPKGFGYVEFSSQEAAQAALDALGGTDLLGR 68

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

 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 16/32 (50%), Positives = 22/32 (68%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          H+GFAFVEY   + AQ ALE ++   L GR++
Sbjct: 41 HKGFAFVEYEVPEAAQLALEQMNGVMLGGRNI 72

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

 Score = 35.3 bits (81), Expect = 7e-04
 Identities = 16/38 (42%), Positives = 22/38 (57%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
          G  RG AFV Y  ++EAQ A+ +L+ T   G  +  SV
Sbjct: 39 GLPRGVAFVRYDKREEAQAAISSLNGTIPPGSTMPLSV 76

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

 Score = 37.4 bits (86), Expect = 7e-04
 Identities = 17/34 (50%), Positives = 23/34 (67%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           G H+GFAFVEY   + AQ ALE ++   L GR++
Sbjct: 146 GKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNI 179

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

 Score = 34.9 bits (81), Expect = 0.001
 Identities = 12/37 (32%), Positives = 19/37 (51%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           RGF +V +  +++A+ ALE    T   GR +    A
Sbjct: 40 CRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHVEFA 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|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 = 34.5 bits (80), Expect = 0.001
 Identities = 10/35 (28%), Positives = 16/35 (45%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
          G  +G+AF EY+       A+  L+   L  + L 
Sbjct: 39 GLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKKLT 73

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

 Score = 34.5 bits (80), Expect = 0.002
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 1  MKFGNHR-GFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           K G    GFAFV +     A+NAL+ L+ T L GR +
Sbjct: 38 EKQGRLNNGFAFVTFKDASSAENALQ-LNGTELGGRKI 74

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

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 13/37 (35%), Positives = 17/37 (45%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             G  +G+ FVEY +K  A  A   L    + GR L
Sbjct: 35 ESTGESKGYGFVEYASKASALKAKNQLDGKQIGGRKL 71

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

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 18/41 (43%), Positives = 21/41 (51%), Gaps = 2/41 (4%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHL--IFSVAHD 44
          HRGF  V Y   + A+ A  AL  T L GR L   FS+  D
Sbjct: 37 HRGFIMVSYYDIRAARRAKRALQGTELGGRKLDIHFSIPKD 77

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

 Score = 34.1 bits (79), Expect = 0.002
 Identities = 14/28 (50%), Positives = 20/28 (71%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYG 34
          +G+A +EY TK+EAQ A+E L+   L G
Sbjct: 48 KGYALIEYETKKEAQAAIEGLNGKELLG 75

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

 Score = 34.3 bits (79), Expect = 0.002
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          RGFA+V++   ++A++AL  L  T   GR +
Sbjct: 42 RGFAYVQFEDVRDAEDALYYLDRTRFLGREI 72

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

 Score = 33.7 bits (78), Expect = 0.003
 Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 5/41 (12%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTH-----LYGRHLIFSVA 42
          +G AFV++ TK+ AQ  LEA  N       L GR LI ++A
Sbjct: 42 KGTAFVKFKTKESAQKCLEAADNAEDSGLSLDGRRLIVTLA 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 33.3 bits (77), Expect = 0.003
 Identities = 7/26 (26%), Positives = 18/26 (69%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEAL 27
          +    RG+A+VE+ + ++A+ A++ +
Sbjct: 35 EVNLPRGYAYVEFESPEDAEKAIKHM 60

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

 Score = 33.5 bits (77), Expect = 0.004
 Identities = 12/32 (37%), Positives = 21/32 (65%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G  RGF +V++ + ++A+ A+EA+    L GR
Sbjct: 38 GRSRGFGYVDFESPEDAKKAIEAMDGKELDGR 69

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

 Score = 33.3 bits (77), Expect = 0.004
 Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 6/37 (16%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
          +F   R F +V++ + + A  A+       L    L 
Sbjct: 36 RFNKTRRFCYVQFTSPESAAAAVA------LLNGKLG 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	112
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.27
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.95
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.81
smart00361	70	RRM_1 RNA recognition motif.	98.8
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.76
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	98.7
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.68
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	98.67
KOG0122	270	consensus Translation initiation factor 3, subunit	98.64
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.6
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.55
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.45
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.44
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.44
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	98.43
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.41
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	98.38
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.38
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	98.36
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	98.34
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.29
smart00360	71	RRM RNA recognition motif.	98.29
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.28
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.27
PLN03213	759	repressor of silencing 3; Provisional	98.24
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.2
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	98.2
smart00362	72	RRM_2 RNA recognition motif.	98.19
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.18
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.17
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.13
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.13
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.09
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.05
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	98.05
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.04
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	98.04
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	98.01
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	97.99
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	97.97
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	97.96
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	97.96
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.95
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.95
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	97.89
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.86
PLN03120	260	nucleic acid binding protein; Provisional	97.79
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.73
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	97.7
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	97.62
KOG0226	290	consensus RNA-binding proteins [General function p	97.57
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	97.56
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	97.52
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	97.46
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	97.42
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	97.32
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	97.28
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.22
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	97.13
PLN03121	243	nucleic acid binding protein; Provisional	97.06
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	96.96
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	96.91
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.9
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	96.87
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	96.78
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	96.76
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	96.35
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	96.25
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.23
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	96.14
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	96.13
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	96.11
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	95.97
KOG1457	284	consensus RNA binding protein (contains RRM repeat	95.84
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.52
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	95.25
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	95.17
KOG2314	698	consensus Translation initiation factor 3, subunit	94.86
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	94.65
KOG1548	382	consensus Transcription elongation factor TAT-SF1	94.56
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	93.84
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	93.67
KOG1548	382	consensus Transcription elongation factor TAT-SF1	93.54
KOG0533	243	consensus RRM motif-containing protein [RNA proces	93.47
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	92.79
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	92.64
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	92.42
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	92.41
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.33
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	91.65
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	91.36
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	91.01
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	88.75
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.51
KOG1995	351	consensus Conserved Zn-finger protein [General fun	87.91
KOG1996	378	consensus mRNA splicing factor [RNA processing and	87.44
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	87.09
KOG4660	549	consensus Protein Mei2, essential for commitment t	87.08
KOG0151	877	consensus Predicted splicing regulator, contains R	87.06
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	86.27
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	84.81
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	81.41

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

Probab=99.27  E-value=2e-12  Score=98.38  Aligned_cols=57  Identities=26%  Similarity=0.525  Sum_probs=50.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc------cccCcccchhcc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS------IIAPTFQVMERA   60 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k------~~~~~~~~~~~a   60 (112)
                      ++|||||||+|.-.++|..||.+||+..|+||+|+|++|.|.+++      .|++++|.-..+
T Consensus        49 qkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~kikegsqkPvWADDdWlkk~~  111 (298)
T KOG0111|consen   49 QKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKIKEGSQKPVWADDDWLKKQQ  111 (298)
T ss_pred             ccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccccCCCCCCcccCcHHHHHhc
Confidence            789999999999999999999999999999999999999999888      577765544443

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

Probab=98.95  E-value=5.6e-10  Score=95.14  Aligned_cols=63  Identities=54%  Similarity=0.900  Sum_probs=59.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCcccchhcccchhHHHHHHHHHHHhhchhccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNG   83 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~   83 (112)
                      +.|||||||+|.++.+|.+|+.+|.++||+||+|                  |++||..+..++.++.+.++.+.+....
T Consensus       652 ~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrL------------------VLEwA~~d~~~e~~r~r~Aak~~~~~~~  713 (725)
T KOG0110|consen  652 GAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRL------------------VLEWAKSDNTMEALRERTAAKFHDQEAA  713 (725)
T ss_pred             hhhccceeeeccCcHHHHHHHHhhcccceechhh------------------heehhccchHHHHHHHHHHHHhhccccc
Confidence            6789999999999999999999999999999999                  9999999999999999999998877665


Q ss_pred             c
Q 036201           84 F   84 (112)
Q Consensus        84 ~   84 (112)
                      .
T Consensus       714 ~  714 (725)
T KOG0110|consen  714 N  714 (725)
T ss_pred             c
Confidence            4

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

Probab=98.81  E-value=1.3e-08  Score=72.28  Aligned_cols=42  Identities=33%  Similarity=0.642  Sum_probs=39.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|+.|+..||+..|.|+.|+|.++.++
T Consensus        73 g~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~  114 (144)
T PLN03134         73 GRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDR  114 (144)
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcC
Confidence            789999999999999999999999999999999988877654

>smart00361 RRM_1 RNA recognition motif

Probab=98.80  E-value=1.2e-08  Score=63.65  Aligned_cols=36  Identities=19%  Similarity=0.391  Sum_probs=34.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      |.++|||||+|.+.++|..|+..|||..+.||.|++
T Consensus        34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       34 NHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678999999999999999999999999999999965

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.76  E-value=1.5e-08  Score=78.99  Aligned_cols=42  Identities=26%  Similarity=0.360  Sum_probs=39.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.+||||||+|.+.++|..|+..|||..|.||.|+|+|..++
T Consensus       308 ~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       308 NQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             CCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            789999999999999999999999999999999999887654

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

>PF13893 RRM_5: RNA recognition motif

Probab=98.71  E-value=5.7e-08  Score=57.68  Aligned_cols=36  Identities=47%  Similarity=0.752  Sum_probs=34.0

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      +|++||+|.+.++|..|+..|||..+.|++|+|++|
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            599999999999999999999999999999988775

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=98.70  E-value=4.4e-08  Score=76.41  Aligned_cols=66  Identities=21%  Similarity=0.376  Sum_probs=51.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc-----ccccCcccchhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII-----SIIAPTFQVMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~-----k~~~~~~~~~~~a~~~~~~~~~~~~   72 (112)
                      |+++|||||+|.+.++|..||..|||..|.|+.|.|.++.|...     .+++.   .+++..+.+++..+...
T Consensus        42 g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~~~~~~~l~v~---~l~~~~~~~~l~~~f~~  112 (352)
T TIGR01661        42 GQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVS---GLPKTMTQHELESIFSP  112 (352)
T ss_pred             CccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecccccccccceEEEC---CccccCCHHHHHHHHhc
Confidence            88999999999999999999999999999999999999987532     13333   44555555566665554

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

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

Probab=98.68  E-value=4e-08  Score=76.66  Aligned_cols=74  Identities=22%  Similarity=0.340  Sum_probs=59.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCccc--chhcccchhHHHHHHHHHHHhh
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQ--VMERAKEGESLEELRARTAAQF   77 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~   77 (112)
                      |.|-|||||.|..+++|+.||..|||..|..++|+|+||+|..-.+...-..  =++-..+..++|.+......-.
T Consensus        80 GqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrII  155 (360)
T KOG0145|consen   80 GQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRII  155 (360)
T ss_pred             ccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhh
Confidence            8999999999999999999999999999999999999999965443322222  2555677888999888765444

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=98.67  E-value=5e-08  Score=78.09  Aligned_cols=67  Identities=19%  Similarity=0.342  Sum_probs=55.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc-----ccccCcccchhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII-----SIIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~-----k~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      |+++|||||+|.+.++|..|+..|||..|.++.|+|.++.|...     ++++.   .|++..++++|.++..+.
T Consensus       146 g~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~~~~~~~lfV~---nLp~~vtee~L~~~F~~f  217 (346)
T TIGR01659       146 GYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKDTNLYVT---NLPRTITDDQLDTIFGKY  217 (346)
T ss_pred             CccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecccccccccccceeEEe---CCCCcccHHHHHHHHHhc
Confidence            78999999999999999999999999999999999999987432     23443   567777777787777654

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

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

Probab=98.64  E-value=4.7e-08  Score=75.19  Aligned_cols=44  Identities=25%  Similarity=0.348  Sum_probs=40.9

Q ss_pred             CC-CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            2 KF-GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         2 K~-g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |. |.+||||||.|.+.++|..||..|||+-.+.-.|+|.|+.|+
T Consensus       225 K~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwskP~  269 (270)
T KOG0122|consen  225 KETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSKPS  269 (270)
T ss_pred             cccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecCCC
Confidence            44 999999999999999999999999999999999988888875

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

Probab=98.60  E-value=8.6e-08  Score=75.52  Aligned_cols=50  Identities=22%  Similarity=0.523  Sum_probs=47.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPT   53 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~   53 (112)
                      |+++|||||+|....+...|.+..+|..|+|+.|.|++...+.+|.|.|-
T Consensus       140 gkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvERgRTvkgW~PR  189 (335)
T KOG0113|consen  140 GKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVERGRTVKGWLPR  189 (335)
T ss_pred             CCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEecccccccccccc
Confidence            99999999999999999999999999999999999999999999988763

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

Probab=98.55  E-value=7.2e-08  Score=76.80  Aligned_cols=44  Identities=25%  Similarity=0.388  Sum_probs=40.7

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      -|||||||+|++.++|++|-..|+|+++.||+|.|+.|.++.+-
T Consensus       134 GSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV~n  177 (376)
T KOG0125|consen  134 GSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARVHN  177 (376)
T ss_pred             CCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhhcc
Confidence            37999999999999999999999999999999999999887543

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

Probab=98.45  E-value=4.4e-07  Score=75.57  Aligned_cols=81  Identities=27%  Similarity=0.392  Sum_probs=57.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC----CeeEEEEeeeccccccccCcccchhcccchhHHHHHHHHHHHhhch
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY----GRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTD   79 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~----gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   79 (112)
                      |+++|||||.|.+.++|..|+..|||..+.    |+.|.|                  .|+....+.+........+...
T Consensus       216 g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v------------------~~a~~k~er~~~~~~~~~~~~~  277 (562)
T TIGR01628       216 GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYV------------------GRAQKRAEREAELRRKFEELQQ  277 (562)
T ss_pred             CCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEe------------------ecccChhhhHHHHHhhHHhhhh
Confidence            788999999999999999999999999999    999955                  4444444333333333333333


Q ss_pred             hcccccccccccccccccccccc
Q 036201           80 EVNGFQNSTKLSKKRKHMTILDE  102 (112)
Q Consensus        80 ~~~~~~~~~~~~~k~~~~~~~~~  102 (112)
                      ......++.+++.++...+++++
T Consensus       278 ~~~~~~~~~~l~V~nl~~~~~~~  300 (562)
T TIGR01628       278 ERKMKAQGVNLYVKNLDDTVTDE  300 (562)
T ss_pred             hhhcccCCCEEEEeCCCCccCHH
Confidence            33344556778888887777654

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

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

Probab=98.44  E-value=1.4e-07  Score=69.90  Aligned_cols=40  Identities=33%  Similarity=0.635  Sum_probs=38.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      ..++|||||+|.+.++|+.|++.||...|+||+|+|+.+.
T Consensus        48 ~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen   48 QKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             ccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            6789999999999999999999999999999999999887

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

Probab=98.44  E-value=4.6e-07  Score=77.37  Aligned_cols=48  Identities=21%  Similarity=0.360  Sum_probs=43.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIA   51 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~   51 (112)
                      |++||||||+|.+.++|..||..|||..|.|+.|+|.++.+.+...|.
T Consensus       243 gksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP~~~~~  290 (612)
T TIGR01645       243 RGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQ  290 (612)
T ss_pred             CCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCccccCC
Confidence            679999999999999999999999999999999999999886655544

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.

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

Probab=98.43  E-value=2.4e-07  Score=72.41  Aligned_cols=43  Identities=26%  Similarity=0.486  Sum_probs=39.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||||.|.+.++|++||..|||.-|.+|+|+-+||..++
T Consensus       101 ~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  101 GKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             CcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            8999999999999999999999999999999999888776544

>PF00076 RRM_1: RNA recognition motif

Probab=98.41  E-value=5.3e-07  Score=54.25  Aligned_cols=35  Identities=37%  Similarity=0.789  Sum_probs=33.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI   38 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~   38 (112)
                      +.++|||||+|.+.++|..|+..|||..+.|+.|+
T Consensus        36 ~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   36 GKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             ccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            67899999999999999999999999999999984

(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 ....

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

Probab=98.38  E-value=9e-07  Score=72.89  Aligned_cols=76  Identities=28%  Similarity=0.426  Sum_probs=56.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEeeeccccccccCcccchhcccchhHHHHHHHHHHHhhchhcc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVN   82 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~   82 (112)
                      |.+||||||.|.++++|+.||+.||++.|. |+.|.||.+..+- ..|+.   .++-.+.++++.+.-++..+-+.++..
T Consensus       122 G~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~-RLFiG---~IPK~k~keeIlee~~kVteGVvdViv  197 (506)
T KOG0117|consen  122 GDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANC-RLFIG---NIPKTKKKEEILEEMKKVTEGVVDVIV  197 (506)
T ss_pred             CCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecc-eeEec---cCCccccHHHHHHHHHhhCCCeeEEEE
Confidence            999999999999999999999999999885 9999998776531 12222   455556667766666666666665544


Q ss_pred             c
Q 036201           83 G   83 (112)
Q Consensus        83 ~   83 (112)
                      -
T Consensus       198 y  198 (506)
T KOG0117|consen  198 Y  198 (506)
T ss_pred             e
Confidence            3

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

Probab=98.38  E-value=4.3e-07  Score=68.25  Aligned_cols=44  Identities=32%  Similarity=0.471  Sum_probs=39.7

Q ss_pred             CCCCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            2 KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         2 K~g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.|.|+|||||+|++.+.|.-|.+.||++.|+++.|.|-+--|.
T Consensus        87 rTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmppe  130 (214)
T KOG4208|consen   87 RTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPPE  130 (214)
T ss_pred             ccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCch
Confidence            33999999999999999999999999999999999988766554

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

Probab=98.36  E-value=8.4e-07  Score=75.78  Aligned_cols=40  Identities=43%  Similarity=0.664  Sum_probs=37.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.||.|+|.+..
T Consensus       146 gkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       146 GKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            8899999999999999999999999999999999998654

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.

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

Probab=98.34  E-value=4.9e-07  Score=66.77  Aligned_cols=43  Identities=26%  Similarity=0.481  Sum_probs=38.9

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .+.|||||+|+++.+|+.|+..|||..|+|..|+|..+.-.+.
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            4689999999999999999999999999999999988876543

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

Probab=98.29  E-value=1e-06  Score=74.27  Aligned_cols=42  Identities=36%  Similarity=0.595  Sum_probs=38.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+.+|||||.|....+|..|++.+||..|.||+|.|+||.+.
T Consensus       155 gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  155 GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            777899999999999999999999999999999988777663

>smart00360 RRM RNA recognition motif

Probab=98.29  E-value=1.9e-06  Score=50.46  Aligned_cols=36  Identities=47%  Similarity=0.803  Sum_probs=33.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      +.++|||||+|.+.++|..|+..|++..+.|+.|.|
T Consensus        35 ~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360       35 GKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            567899999999999999999999999999999866

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

Probab=98.28  E-value=6.1e-07  Score=68.02  Aligned_cols=41  Identities=39%  Similarity=0.636  Sum_probs=37.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +.++|||||-|....+|+.|+++|+|..|+|+.|.|.+|.-
T Consensus        52 r~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   52 RQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             ccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            77999999999999999999999999999999998876643

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

Probab=98.27  E-value=3.9e-07  Score=67.82  Aligned_cols=40  Identities=25%  Similarity=0.510  Sum_probs=37.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+|+||||+.|++..+.--|+.+|||..|.||+|+|+...
T Consensus        74 GKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   74 GKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             CcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            9999999999999999999999999999999999997554

>PLN03213 repressor of silencing 3; Provisional

Probab=98.24  E-value=2.6e-06  Score=71.48  Aligned_cols=38  Identities=16%  Similarity=0.368  Sum_probs=35.4

Q ss_pred             cceEEEEeCCH--HHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            7 RGFAFVEYVTK--QEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         7 rGfgFVef~s~--eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      ||||||+|.+.  .++..||..|||..+.||.|+|..|.|
T Consensus        48 RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         48 RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            89999999987  689999999999999999998888876

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

Probab=98.20  E-value=2.8e-06  Score=69.46  Aligned_cols=41  Identities=27%  Similarity=0.337  Sum_probs=39.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
T Consensus       334 g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       334 GLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            78999999999999999999999999999999999999865

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

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

Probab=98.20  E-value=3.5e-06  Score=70.23  Aligned_cols=40  Identities=33%  Similarity=0.557  Sum_probs=36.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.
T Consensus       323 g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       323 GVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            7899999999999999999999999999999999554443

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

>smart00362 RRM_2 RNA recognition motif

Probab=98.19  E-value=4.7e-06  Score=49.00  Aligned_cols=36  Identities=47%  Similarity=0.802  Sum_probs=33.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      +.++|+|||+|.+.++|..|+..++|..+.|+.|.|
T Consensus        36 ~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362       36 GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            456899999999999999999999999999999865

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

Probab=98.18  E-value=3.1e-06  Score=68.46  Aligned_cols=41  Identities=34%  Similarity=0.658  Sum_probs=38.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++..
T Consensus       225 g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       225 GRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            68899999999999999999999999999999999999764

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.

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

Probab=98.17  E-value=2.4e-06  Score=70.47  Aligned_cols=43  Identities=28%  Similarity=0.580  Sum_probs=38.2

Q ss_pred             CC-CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            2 KF-GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         2 K~-g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      ++ |+.+||||++|.+.++|..|++.|||..+.||+|+|+|+..
T Consensus        54 ~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~   97 (435)
T KOG0108|consen   54 RETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASN   97 (435)
T ss_pred             ccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecccc
Confidence            35 99999999999999999999999999999999996655443

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

Probab=98.13  E-value=4.8e-06  Score=59.72  Aligned_cols=41  Identities=41%  Similarity=0.682  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |.++|||||+|.+.+++..|+..++|..|.|+.|.|.++.+
T Consensus       154 ~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         154 GKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            88999999999999999999999999999999999988653

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.13  E-value=5.6e-06  Score=50.48  Aligned_cols=34  Identities=47%  Similarity=0.859  Sum_probs=32.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL   37 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L   37 (112)
                      |.++|+|||+|.+.++|..|+..++|..+.|+.|
T Consensus        36 ~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l   69 (70)
T PF14259_consen   36 GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKL   69 (70)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEc
Confidence            5678999999999999999999999999999998

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 ....

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

Probab=98.09  E-value=2.6e-06  Score=60.97  Aligned_cols=41  Identities=37%  Similarity=0.575  Sum_probs=38.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |-.+||++|+|.+.++|+.|+..|||..|.|..|.|+|+-.
T Consensus       111 Gy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen  111 GYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             ccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            78899999999999999999999999999999998887754

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

Probab=98.05  E-value=6.8e-06  Score=69.92  Aligned_cols=65  Identities=29%  Similarity=0.487  Sum_probs=48.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEeeeccccccccCcccchhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~   72 (112)
                      |++||||||+|.+.++|+.||..||+..|. |+.|.|+.+.+. ...++.   .+++..++++|.++..+
T Consensus        96 G~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~~-~rLFVg---NLP~~~TeeeL~eeFsk  161 (578)
T TIGR01648        96 GQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVDN-CRLFVG---GIPKNKKREEILEEFSK  161 (578)
T ss_pred             CCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccccC-ceeEee---cCCcchhhHHHHHHhhc
Confidence            889999999999999999999999999885 888888766542 223333   45555555555554444

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.

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

Probab=98.05  E-value=1.6e-05  Score=64.28  Aligned_cols=40  Identities=28%  Similarity=0.497  Sum_probs=36.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..||. |+|..|.|+.|.|.++..
T Consensus       128 ~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~~  167 (457)
T TIGR01622       128 RRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQA  167 (457)
T ss_pred             CCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecch
Confidence            7899999999999999999996 899999999999987654

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=98.04  E-value=7.9e-06  Score=66.84  Aligned_cols=42  Identities=19%  Similarity=0.352  Sum_probs=37.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +...||+||+|.+.++|..|+..|||..|.|+.|.|.|..+.
T Consensus       461 ~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       461 TPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGED  502 (509)
T ss_pred             CCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHH
Confidence            345799999999999999999999999999999988887654

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

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

Probab=98.04  E-value=9.9e-06  Score=55.66  Aligned_cols=40  Identities=30%  Similarity=0.359  Sum_probs=37.5

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      .+|.|||.|++..+|..|+..|+|..++++.|.|-+.+|.
T Consensus        56 TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   56 TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            5899999999999999999999999999999999888774

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

Probab=98.01  E-value=1.1e-05  Score=68.65  Aligned_cols=42  Identities=24%  Similarity=0.446  Sum_probs=39.0

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ..+|||||+|.+.++|..|+..|||..|.|+.|.|+++.|..
T Consensus       267 ~~rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       267 KIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             eecCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            457999999999999999999999999999999999998854

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=97.99  E-value=1.4e-05  Score=64.16  Aligned_cols=41  Identities=39%  Similarity=0.606  Sum_probs=36.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..||..||+..|.+  +.|.|.++..
T Consensus       232 g~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       232 GTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEE  274 (346)
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCc
Confidence            7889999999999999999999999998876  6887776655

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

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

Probab=97.97  E-value=9.9e-06  Score=57.50  Aligned_cols=40  Identities=33%  Similarity=0.511  Sum_probs=36.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      -.+-||+||+|.+.++|..|+..+||+.|..++|+|++..
T Consensus        75 ktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   75 KTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             cCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            3467999999999999999999999999999999887654

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

Probab=97.96  E-value=6.3e-06  Score=67.09  Aligned_cols=39  Identities=44%  Similarity=0.682  Sum_probs=36.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+|+||+||+|+-++.|.-|++.|||..|.||.|+|..-
T Consensus       152 ~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  152 GKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             ccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            899999999999999999999999999999999999743

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

Probab=97.96  E-value=1.7e-05  Score=68.27  Aligned_cols=38  Identities=39%  Similarity=0.612  Sum_probs=36.5

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |.|||||+|.+.++|+.|+..|+|+.|.|+.|.|.++.
T Consensus       559 SmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  559 SMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             ccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            56999999999999999999999999999999999998

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

Probab=97.95  E-value=1.3e-05  Score=64.75  Aligned_cols=81  Identities=25%  Similarity=0.308  Sum_probs=65.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCcccchhcccchhHHHHHHHHHHHhhchhccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRARTAAQFTDEVNG   83 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~   83 (112)
                      |+++|||||.|.+.++|..|+..|||..+.+..+                  +|..++.+.+.+.+..+...+.......
T Consensus       205 g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~------------------~V~~aqkk~e~~~~l~~~~~~~~~~~~~  266 (369)
T KOG0123|consen  205 GKSKGFGFVNFENPEDAKKAVETLNGKIFGDKEL------------------YVGRAQKKSEREAELKRKFEQEFAKRSV  266 (369)
T ss_pred             CCCCCccceeecChhHHHHHHHhccCCcCCccce------------------eecccccchhhHHHHhhhhHhhhhhccc
Confidence            7899999999999999999999999999999999                  6666666666666666666666666666


Q ss_pred             ccccccccccccccccccc
Q 036201           84 FQNSTKLSKKRKHMTILDE  102 (112)
Q Consensus        84 ~~~~~~~~~k~~~~~~~~~  102 (112)
                      .++..+++.+++...+.++
T Consensus       267 ~~~~~nl~vknld~~~~~e  285 (369)
T KOG0123|consen  267 SLQGANLYVKNLDETLSDE  285 (369)
T ss_pred             cccccccccccCccccchh
Confidence            6778999999977666554

>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=97.95  E-value=3.1e-05  Score=45.65  Aligned_cols=36  Identities=44%  Similarity=0.716  Sum_probs=33.3

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEE
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFS   40 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~   40 (112)
                      .++|+|||+|.+.++|..|+..+++..+.|+.|.|.
T Consensus        38 ~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590          38 KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            458999999999999999999999999999999775

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

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

Probab=97.89  E-value=2.1e-05  Score=61.62  Aligned_cols=40  Identities=30%  Similarity=0.390  Sum_probs=37.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      .+++|||||.+.+..+|..||..|||+.|.+|.|.|++-.
T Consensus       317 nkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  317 NKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             ccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            6789999999999999999999999999999999988654

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

Probab=97.86  E-value=3.1e-05  Score=63.99  Aligned_cols=40  Identities=28%  Similarity=0.391  Sum_probs=37.3

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ++|||||+|.+.++|..|+..|||..|.|+.|+|.++...
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            4799999999999999999999999999999999988654

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=97.79  E-value=4.8e-05  Score=59.14  Aligned_cols=39  Identities=26%  Similarity=0.381  Sum_probs=35.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      .++|||||+|.+.++|..|+. |||..|.|+.|.|..+..
T Consensus        41 ~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120         41 ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            368999999999999999995 999999999999988763

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

Probab=97.73  E-value=4.3e-05  Score=64.20  Aligned_cols=42  Identities=38%  Similarity=0.712  Sum_probs=39.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|-||.|+|+....+
T Consensus       317 G~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  317 GRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             ccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            899999999999999999999999999999999999876553

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

Probab=97.70  E-value=2.6e-05  Score=59.78  Aligned_cols=42  Identities=24%  Similarity=0.366  Sum_probs=35.6

Q ss_pred             CC-CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            2 KF-GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         2 K~-g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |. |+|||||||+|.+.+.|.+|+...|.. |+||+..|+.|.-
T Consensus        48 ~~t~rskGyGfVTf~d~~aa~rAc~dp~pi-IdGR~aNcnlA~l   90 (247)
T KOG0149|consen   48 KNTGRSKGYGFVTFRDAEAATRACKDPNPI-IDGRKANCNLASL   90 (247)
T ss_pred             cCCccccceeeEEeecHHHHHHHhcCCCCc-ccccccccchhhh
Confidence            45 999999999999999999999876654 7999988876643

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

Probab=97.62  E-value=9e-05  Score=61.27  Aligned_cols=40  Identities=23%  Similarity=0.329  Sum_probs=36.9

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCee------EEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRH------LIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~------L~V~~a~~~   45 (112)
                      ++|||||+|.+.++|..|+..|||..|.++.      |+|+|+.++
T Consensus       435 ~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       435 RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            4799999999999999999999999999984      999999875

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).

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

Probab=97.57  E-value=8.8e-05  Score=57.70  Aligned_cols=36  Identities=17%  Similarity=0.431  Sum_probs=34.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      |+++|||||.|.+..++..|+..|||..+..|.|+.
T Consensus       229 gKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  229 GKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            999999999999999999999999999999999944

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

Probab=97.56  E-value=8e-05  Score=61.50  Aligned_cols=34  Identities=41%  Similarity=0.556  Sum_probs=30.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCee-C--CeeE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHL-Y--GRHL   37 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l-~--gr~L   37 (112)
                      |.|||+|||.|.+.+-|..||+.|||+.- .  ...|
T Consensus       162 ~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PL  198 (510)
T KOG0144|consen  162 GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPL  198 (510)
T ss_pred             ccccceeEEEEehHHHHHHHHHhhccceeeccCCCce
Confidence            88999999999999999999999999653 3  4578

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

Probab=97.52  E-value=0.00015  Score=53.98  Aligned_cols=46  Identities=24%  Similarity=0.439  Sum_probs=41.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISI   49 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~   49 (112)
                      |.++|||||.|.+.+.+..|+..|||..++.|+|+|+++.....|+
T Consensus       136 g~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~kg  181 (203)
T KOG0131|consen  136 GNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTKG  181 (203)
T ss_pred             CCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCCc
Confidence            7899999999999999999999999999999999999998765443

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

Probab=97.46  E-value=0.00018  Score=56.69  Aligned_cols=50  Identities=34%  Similarity=0.583  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC-C--eeEEEEeeeccccccccCcccchhcccchhH--HHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY-G--RHLIFSVAHDQIISIIAPTFQVMERAKEGES--LEELRA   71 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~-g--r~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~--~~~~~~   71 (112)
                      |.+||++||.|.+.-+|+.||.+|+|+.-. |  ..|                  ||.+|.+++|  +.+|++
T Consensus        57 g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSL------------------VVK~ADTdkER~lRRMQQ  111 (371)
T KOG0146|consen   57 GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSL------------------VVKFADTDKERTLRRMQQ  111 (371)
T ss_pred             CCCCCceEEEeccchHHHHHHHHhcccccCCCCccce------------------EEEeccchHHHHHHHHHH
Confidence            789999999999999999999999997544 3  456                  8888887765  444443

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

Probab=97.42  E-value=0.0001  Score=62.37  Aligned_cols=43  Identities=28%  Similarity=0.505  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.+||||||+|.-.++++.|+..++++.|.||.|.|.+|.++.
T Consensus        44 ~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~   86 (678)
T KOG0127|consen   44 SEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRA   86 (678)
T ss_pred             ccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccc
Confidence            5689999999999999999999999999999999999998754

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

Probab=97.32  E-value=0.00024  Score=57.56  Aligned_cols=42  Identities=19%  Similarity=0.361  Sum_probs=37.2

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |-|||||.|.++.+|..|+..||...+.|+.|++-|++..+.
T Consensus        36 slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~~   77 (369)
T KOG0123|consen   36 SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDPS   77 (369)
T ss_pred             ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCCc
Confidence            779999999999999999999999999999997766665443

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

Probab=97.28  E-value=0.00044  Score=54.40  Aligned_cols=40  Identities=30%  Similarity=0.518  Sum_probs=35.5

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +-+||+||-|.+++.|..||-.+|++.+.|..++++|-..
T Consensus       198 k~qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  198 KDQGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             cccceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            3579999999999999999999999999999997765543

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

Probab=97.22  E-value=0.00034  Score=53.19  Aligned_cols=42  Identities=31%  Similarity=0.464  Sum_probs=38.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      .+.||-|||.|.+.+.|-.|+.+|+|..++|+.+++.||+..
T Consensus        49 ~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~   90 (221)
T KOG4206|consen   49 PKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSD   90 (221)
T ss_pred             CCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCc
Confidence            578999999999999999999999999999999988888764

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

Probab=97.13  E-value=0.00019  Score=56.52  Aligned_cols=42  Identities=19%  Similarity=0.339  Sum_probs=38.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ..||.||||.|.+.-+++.||.+|||+.|..++|+|..-+|+
T Consensus       324 NQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPk  365 (371)
T KOG0146|consen  324 NQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPK  365 (371)
T ss_pred             ccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCcc
Confidence            678999999999999999999999999999999988766654

>PLN03121 nucleic acid binding protein; Provisional

Probab=97.06  E-value=0.0013  Score=50.82  Aligned_cols=39  Identities=15%  Similarity=0.204  Sum_probs=34.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      +.++|||||+|.+++++..|+ .|||..|.+++|.|..+.
T Consensus        41 ~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121         41 GEYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            556799999999999999998 699999999999987654

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

Probab=96.96  E-value=0.00098  Score=55.53  Aligned_cols=40  Identities=38%  Similarity=0.606  Sum_probs=37.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |++||+|.|+|.+++.++.|++.||-+.+.||.|.|.-.+
T Consensus        83 GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   83 GKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             CCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            8999999999999999999999999999999999875443

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

Probab=96.91  E-value=0.0015  Score=54.25  Aligned_cols=41  Identities=22%  Similarity=0.443  Sum_probs=38.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.|-||||-|.+.++|-.|++.+||..|.|..|.|..|.|.
T Consensus       291 k~rDYaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  291 KPRDYAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             cccceeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            45789999999999999999999999999999999999985

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

Probab=96.90  E-value=0.00096  Score=50.19  Aligned_cols=40  Identities=23%  Similarity=0.312  Sum_probs=36.9

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ...||||+|+++.+|+.||..-||..+.|.+|+|.+++--
T Consensus        44 ~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen   44 PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             CCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            3579999999999999999999999999999999998763

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

Probab=96.87  E-value=0.0014  Score=50.03  Aligned_cols=41  Identities=22%  Similarity=0.505  Sum_probs=37.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++||+||+|.+......|+. |||..|.|+.|.|.+..-+
T Consensus       140 ~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r~~  180 (231)
T KOG4209|consen  140 GHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKRTN  180 (231)
T ss_pred             CCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeeeee
Confidence            7899999999999999999999 9999999999998766543

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

Probab=96.78  E-value=0.0014  Score=53.46  Aligned_cols=42  Identities=19%  Similarity=0.395  Sum_probs=39.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.+--||||+|.+.++|+.|...|++..|..|+|.|+|++..
T Consensus       278 gdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSV  319 (479)
T KOG0415|consen  278 GDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSV  319 (479)
T ss_pred             cchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhhh
Confidence            777889999999999999999999999999999999998763

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

Probab=96.76  E-value=0.0012  Score=54.15  Aligned_cols=45  Identities=22%  Similarity=0.344  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      +.|||||||+|.+..+...||..||-+.|.|..|+|..+.-.+.-
T Consensus       249 ~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~a  293 (544)
T KOG0124|consen  249 RGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDA  293 (544)
T ss_pred             CCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCCch
Confidence            679999999999999999999999999999999999766544433

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

Probab=96.35  E-value=0.0053  Score=51.28  Aligned_cols=37  Identities=22%  Similarity=0.486  Sum_probs=34.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|  .|-|.++++|+.|+..|||..|.||.|.|.|+
T Consensus       572 GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  572 GKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             CCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            77777  99999999999999999999999999999763

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

Probab=96.25  E-value=0.0048  Score=53.10  Aligned_cols=39  Identities=33%  Similarity=0.497  Sum_probs=36.0

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.||||+|.+..+|..||..|+-+.|.||.|.|..+...
T Consensus       447 RCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  447 RCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             ceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            569999999999999999999999999999999887654

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=96.23  E-value=0.0091  Score=39.50  Aligned_cols=38  Identities=16%  Similarity=0.345  Sum_probs=29.4

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      +.|.|+|-|.+.+.|..|.+.|+|-.+.|+.|.|++..
T Consensus        38 ~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen   38 SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             -TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            56889999999999999999999999999999998763

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

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

Probab=96.14  E-value=0.0021  Score=48.81  Aligned_cols=38  Identities=32%  Similarity=0.614  Sum_probs=35.4

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      .||+||+|.+..+|..||..|||..|+|..+.|.++.+
T Consensus        35 ~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen   35 NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            59999999999999999999999999999988888874

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

Probab=96.13  E-value=0.011  Score=51.96  Aligned_cols=64  Identities=25%  Similarity=0.296  Sum_probs=50.9

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccc-----ccC--cccchhcccchhHHHH
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISI-----IAP--TFQVMERAKEGESLEE   68 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~-----~~~--~~~~~~~a~~~~~~~~   68 (112)
                      .+||+|||.+....+|++|+.+|+.+.+.+++|+|.|+...-++-     |.-  ..+++.|-+-..+++.
T Consensus       455 ~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~  525 (894)
T KOG0132|consen  455 PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGPKSEYKDYWDVELGVTYIPWEKLTDDLEA  525 (894)
T ss_pred             cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCcchhhhhhhhcccCeeEeehHhcCHHHHH
Confidence            368999999999999999999999999999999999998765553     221  2447888776655443

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

Probab=96.11  E-value=0.0029  Score=52.51  Aligned_cols=39  Identities=28%  Similarity=0.435  Sum_probs=35.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |-++-||||.|++..+|.+||..|||..+.+++|+|-..
T Consensus       463 nlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk  501 (510)
T KOG0144|consen  463 NLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLK  501 (510)
T ss_pred             CHhhhcCcccccchhhhHHHHHHhcchhhccccceEEee
Confidence            668899999999999999999999999999999987543

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

Probab=95.97  E-value=0.016  Score=38.86  Aligned_cols=30  Identities=23%  Similarity=0.362  Sum_probs=27.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY   33 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~   33 (112)
                      +.+.|||||.|.+++.+..-...++|..+.
T Consensus        42 ~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~   71 (97)
T PF04059_consen   42 KCNLGYAFVNFTSPQAAIRFYKAFNGKKWP   71 (97)
T ss_pred             CCceEEEEEEcCCHHHHHHHHHHHcCCccc
Confidence            457899999999999999999999998876

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

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

Probab=95.84  E-value=0.016  Score=44.81  Aligned_cols=39  Identities=26%  Similarity=0.393  Sum_probs=34.5

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeC---CeeEEEEeeecc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLY---GRHLIFSVAHDQ   45 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~---gr~L~V~~a~~~   45 (112)
                      +-+||++|.+.++|..|+.+|||..|+   +.+|.+.+|...
T Consensus        77 ~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiElAKSN  118 (284)
T KOG1457|consen   77 KPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIELAKSN  118 (284)
T ss_pred             cceEEEEecchHHHHHHHHHhcCeeeccccCceeEeeehhcC
Confidence            358999999999999999999999997   788988887653

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

Probab=95.52  E-value=0.017  Score=46.01  Aligned_cols=40  Identities=20%  Similarity=0.363  Sum_probs=36.4

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      -|-||||-.++...+..||.+|+|..|.|..|.|.-+..+
T Consensus        35 vKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen   35 VKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             ecccceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            4689999999999999999999999999999999877654

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

Probab=95.25  E-value=0.011  Score=49.92  Aligned_cols=45  Identities=29%  Similarity=0.462  Sum_probs=41.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.++||+|.+|.+......|+..|||..+.++.|.|-.|.+....
T Consensus       328 g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~  372 (500)
T KOG0120|consen  328 GNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASN  372 (500)
T ss_pred             ccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchh
Confidence            679999999999999999999999999999999999999886554

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

Probab=95.17  E-value=0.019  Score=45.72  Aligned_cols=40  Identities=23%  Similarity=0.500  Sum_probs=36.1

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      -++|+||-|.-.++|..|+..||++.|.|+++.|..+.-+
T Consensus       111 vkdy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsr  150 (346)
T KOG0109|consen  111 VKDYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSR  150 (346)
T ss_pred             ecceeEEEEeeccchHHHHhcccccccccceeeeeeeccc
Confidence            4799999999999999999999999999999998766543

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

Probab=94.86  E-value=0.043  Score=47.09  Aligned_cols=38  Identities=26%  Similarity=0.614  Sum_probs=33.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEe
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSV   41 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~   41 (112)
                      |.++||.|++|.+..+|..|++.|||..|+ .+++.|..
T Consensus       102 ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~~  140 (698)
T KOG2314|consen  102 GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVRL  140 (698)
T ss_pred             CCeeeEEEEEecChhhHHHHHHhcccceecccceEEeeh
Confidence            679999999999999999999999999988 45655543

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

Probab=94.65  E-value=0.051  Score=45.88  Aligned_cols=40  Identities=25%  Similarity=0.448  Sum_probs=34.9

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |--||+|.+.++++.|+.+|+|..+.+|++...|.-+.++
T Consensus       455 GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY  494 (500)
T KOG0120|consen  455 GKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKY  494 (500)
T ss_pred             ccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHh
Confidence            4569999999999999999999999999998877765543

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

Probab=94.56  E-value=0.2  Score=40.70  Aligned_cols=40  Identities=20%  Similarity=0.376  Sum_probs=35.2

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      .+.|.+-|.|.+.++|..||..|+|..|.||.|..+..-.
T Consensus       312 hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  312 HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            4569999999999999999999999999999997665443

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

Probab=93.84  E-value=0.035  Score=42.22  Aligned_cols=33  Identities=42%  Similarity=0.741  Sum_probs=31.9

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEE
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      ++++||+|...+++..|+..|+|..+.++.|.|
T Consensus       133 ~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  133 RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             ccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            799999999999999999999999999999977

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

Probab=93.67  E-value=0.021  Score=45.52  Aligned_cols=44  Identities=30%  Similarity=0.413  Sum_probs=35.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      +++|||+||+|.+.+....++.. .-++|.|+.|-+-.|.|+...
T Consensus        45 ~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av~r~~~   88 (311)
T KOG4205|consen   45 GRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAVSREDQ   88 (311)
T ss_pred             CCcccccceecCCCcchheeecc-cccccCCccccceeccCcccc
Confidence            88999999999998888777653 346689999988888876533

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

Probab=93.54  E-value=0.18  Score=40.95  Aligned_cols=42  Identities=26%  Similarity=0.404  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+.+|=|.|.|.-.++..-|+..|++..|.|+.|+|..|+-+
T Consensus       180 G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq  221 (382)
T KOG1548|consen  180 GKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQ  221 (382)
T ss_pred             CCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhh
Confidence            888999999999999999999999999999999999988764

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

Probab=93.47  E-value=0.15  Score=39.44  Aligned_cols=45  Identities=22%  Similarity=0.324  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.+.|.|=|.|...++|..|++.+||+.|+|+.|++....+..+.
T Consensus       121 G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~~~~  165 (243)
T KOG0533|consen  121 GRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSPSQS  165 (243)
T ss_pred             CCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCcccc
Confidence            889999999999999999999999999999999998776665444

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

Probab=92.79  E-value=0.15  Score=41.45  Aligned_cols=39  Identities=26%  Similarity=0.439  Sum_probs=33.0

Q ss_pred             CcceEEEEeCCHHHHHHHHH-hhCCCeeCCeeEEEEeeec
Q 036201            6 HRGFAFVEYVTKQEAQNALE-ALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~-~lng~~l~gr~L~V~~a~~   44 (112)
                      .+|.|||+|.+...|+.|.. .+|-..+.|++|+|-|..|
T Consensus       263 ~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  263 RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            46899999999999998665 5565778999999998888

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

Probab=92.64  E-value=0.16  Score=41.87  Aligned_cols=40  Identities=28%  Similarity=0.334  Sum_probs=35.6

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeeCCe--eEEEEeeeccccc
Q 036201            9 FAFVEYVTKQEAQNALEALSNTHLYGR--HLIFSVAHDQIIS   48 (112)
Q Consensus         9 fgFVef~s~eda~~Ai~~lng~~l~gr--~L~V~~a~~~~~k   48 (112)
                      -|.|+|.+.+.|++|-.+|||..|+.-  +|+|.||.|.+.-
T Consensus       161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~rln  202 (494)
T KOG1456|consen  161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLN  202 (494)
T ss_pred             eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcceee
Confidence            589999999999999999999999854  8999999996544

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

Probab=92.42  E-value=0.28  Score=41.39  Aligned_cols=67  Identities=19%  Similarity=0.198  Sum_probs=51.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc----cccC----ccc-----chhcccchhHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS----IIAP----TFQ-----VMERAKEGESLEELR   70 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k----~~~~----~~~-----~~~~a~~~~~~~~~~   70 (112)
                      |+..|=|||+|.+.++++.|++. +-.++..|-|.|-.+.+..++    ...+    .+.     =|+|+-++++|.+..
T Consensus        46 Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FF  124 (510)
T KOG4211|consen   46 GRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFF  124 (510)
T ss_pred             CCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHh
Confidence            88999999999999999999984 777788999999888775544    1111    122     278888888877654


Q ss_pred             H
Q 036201           71 A   71 (112)
Q Consensus        71 ~   71 (112)
                      +
T Consensus       125 a  125 (510)
T KOG4211|consen  125 A  125 (510)
T ss_pred             c
Confidence            3

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

Probab=92.41  E-value=0.074  Score=42.44  Aligned_cols=44  Identities=16%  Similarity=0.273  Sum_probs=37.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      .+++|||||+|.+.+....++. ...+.|+|+.+.|..|.|+-+.
T Consensus       136 ~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  136 SRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhc
Confidence            6789999999999988887765 4678899999999999996544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.33  E-value=0.18  Score=41.26  Aligned_cols=33  Identities=24%  Similarity=0.443  Sum_probs=30.8

Q ss_pred             EEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201           11 FVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus        11 FVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      ||+|.+.++|..||...+|+.++||.|+..|-.
T Consensus       169 YITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             EEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            999999999999999999999999999887653

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

Probab=91.65  E-value=0.24  Score=42.21  Aligned_cols=38  Identities=21%  Similarity=0.298  Sum_probs=34.5

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |-|+-||-|.+.+.|..|+.+|||..|.||.|+..|-.
T Consensus       489 s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  489 SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            34999999999999999999999999999999877654

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

Probab=91.36  E-value=0.12  Score=39.95  Aligned_cols=39  Identities=15%  Similarity=0.130  Sum_probs=33.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      ++.+ ||||.|.+.-...-|+..+||..|.++.|.|.+-+
T Consensus        47 ~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen   47 QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             CCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            5566 99999999999999999999999999988665443

>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=91.01  E-value=0.32  Score=30.42  Aligned_cols=35  Identities=31%  Similarity=0.479  Sum_probs=21.4

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      .-|+||+.... .+..++..|++..+.|++|+|..|
T Consensus        40 ~~~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   40 DNFSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             SS-EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             eeEEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            46899999875 688899999999999999987654

; PDB: 2G0C_A 3MOJ_B.

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

Probab=88.75  E-value=0.98  Score=32.47  Aligned_cols=37  Identities=24%  Similarity=0.335  Sum_probs=29.5

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +--+|+|.+-+.|-+|+. ++|..++|+.|+|..-.|.
T Consensus        71 ~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   71 DTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             TCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             CeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            346899999999999986 8999999999999877763

; PDB: 1UFW_A 2DNR_A.

>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=88.51  E-value=0.98  Score=28.18  Aligned_cols=29  Identities=14%  Similarity=0.303  Sum_probs=26.5

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeeCCeeEE
Q 036201           10 AFVEYVTKQEAQNALEALSNTHLYGRHLI   38 (112)
Q Consensus        10 gFVef~s~eda~~Ai~~lng~~l~gr~L~   38 (112)
                      =||.|.+..+|+.+..+.+|..+.+.+|.
T Consensus        36 fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~   64 (66)
T PF11767_consen   36 FYIVFNDSKEAERCFRAEDGTLFFTYRMQ   64 (66)
T ss_pred             EEEEECChHHHHHHHHhcCCCEEEEEEEE
Confidence            38999999999999999999999988873

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

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

Probab=87.91  E-value=0.36  Score=39.15  Aligned_cols=42  Identities=26%  Similarity=0.392  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.+||=|.|.|.+...|+.||..+++..+++.+|+|..|.-+
T Consensus       113 ~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  113 GAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERR  154 (351)
T ss_pred             cCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhc
Confidence            788999999999999999999999999999999988777654

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

Probab=87.44  E-value=0.7  Score=37.14  Aligned_cols=35  Identities=23%  Similarity=0.219  Sum_probs=31.8

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201           10 AFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus        10 gFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      -||+|...++|-.|+-.|||..|.||.+..+|.+-
T Consensus       332 iFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  332 IFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             eeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            59999999999999999999999999998777654

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

Probab=87.09  E-value=1  Score=37.27  Aligned_cols=40  Identities=28%  Similarity=0.377  Sum_probs=36.3

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      ...|.|.|++.+..+.++|+..||+..|.|.+|.|++++.
T Consensus       323 Tk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ  362 (494)
T KOG1456|consen  323 TKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQ  362 (494)
T ss_pred             cccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccc
Confidence            4469999999999999999999999999999999988754

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

Probab=87.08  E-value=0.31  Score=41.58  Aligned_cols=34  Identities=35%  Similarity=0.670  Sum_probs=31.9

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEE
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI   38 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~   38 (112)
                      .++|-.||+|.+..+|+.|+++||+.++.|+.|+
T Consensus       110 ~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen  110 NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3679999999999999999999999999999987

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

Probab=87.06  E-value=0.67  Score=41.03  Aligned_cols=42  Identities=17%  Similarity=0.309  Sum_probs=37.2

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.+-+|||-|-+..+++.|++.|+|..++++.+++.|..+.+
T Consensus       217 r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~V~  258 (877)
T KOG0151|consen  217 RERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKAVP  258 (877)
T ss_pred             cccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccccc
Confidence            345789999999999999999999999999999998886543

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

Probab=86.27  E-value=1.2  Score=37.27  Aligned_cols=38  Identities=29%  Similarity=0.482  Sum_probs=34.6

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +--|.|.|.+...|.-|+..|+|..|+|+.|+|.++.-
T Consensus       335 kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  335 KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            35699999999999999999999999999999988753

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

Probab=84.81  E-value=0.97  Score=37.56  Aligned_cols=37  Identities=38%  Similarity=0.530  Sum_probs=30.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEe
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV   41 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~   41 (112)
                      ++...||||+|.+..++..||.+ +-..|.+++|.|.-
T Consensus       327 ~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  327 GKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             CCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            44458999999999999999987 47788899997753

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

Probab=81.41  E-value=1.2  Score=34.89  Aligned_cols=38  Identities=26%  Similarity=0.430  Sum_probs=33.5

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +|=.||.|...++|+.|+..||+-.+.|++|...+...
T Consensus       110 ~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen  110 VGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             hhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            57789999999999999999999999999997665544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	112
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		3e-08

>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 = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 4   GNHRGFAFVEYVTKQEAQNALEALS-NTHLYGRHLIFSVAHDQIISIIAPT 53
           G HRGF FV+++TKQ+A+ A  AL  +THLYGR L+   A  ++     P+
Sbjct: 55  GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPS 105

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	112
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-09
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	6e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-09
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-05
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-09
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-05
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-05
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-08
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-08
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-07
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-07
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-06
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	5e-07
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	6e-07
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-07
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	7e-07
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	8e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-07
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-06
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-06
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-06
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	3e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-06
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-06
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-06
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-06
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	5e-06
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-06
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-06
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-06
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	7e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-06
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-05
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-05
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-05
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-05
2div_A	99	TRNA selenocysteine associated protein; structural	3e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-05
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-05
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	8e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	9e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-04
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-04
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-04
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-04
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	6e-04
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-04
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-04

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 58.9 bits (143), Expect = 6e-13
 Identities = 22/43 (51%), Positives = 30/43 (69%), Gaps = 1/43 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVAHDQ 45
          G HRGF FV+++TKQ+A+ A  AL + THLYGR L+   A  +
Sbjct: 55 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE 97

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 50.3 bits (121), Expect = 1e-09
 Identities = 11/42 (26%), Positives = 17/42 (40%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +    RG AFV +     A NAL ++     Y + +    A
Sbjct: 45 SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 50.4 bits (121), Expect = 1e-09
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
                 RG A+V Y    +A+NA++ LS  ++  R+L+    +          FQ M+  
Sbjct: 41  GNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNAN------RAFQKMDTK 94

Query: 61  KEGESLEELR 70
           K+ E L+ L+
Sbjct: 95  KKEEQLKLLK 104

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 47.9 bits (115), Expect = 6e-09
 Identities = 13/34 (38%), Positives = 23/34 (67%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
            HRGFAFVE+   ++A  A++ ++ + L+GR +
Sbjct: 46 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 79

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 50.0 bits (120), Expect = 6e-09
 Identities = 12/42 (28%), Positives = 18/42 (42%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
              G  +G+AF EYV       A+  L+   L  + L+   A
Sbjct: 150 SATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD 44
             + FAF+E+ +  E   A+ A       G+ L     HD
Sbjct: 48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHD 87

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 48.0 bits (115), Expect = 8e-09
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          + G  + F FV +   +    A+  L+   LYGR +  S  
Sbjct: 52 REGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 48.0 bits (115), Expect = 9e-09
 Identities = 13/34 (38%), Positives = 23/34 (67%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
            HRGFAFVE+   ++A  A++ ++ + L+GR +
Sbjct: 51 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 84

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 48.1 bits (115), Expect = 1e-08
 Identities = 12/44 (27%), Positives = 22/44 (50%)

Query: 2   KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           K    +G  F++Y T ++A   + AL+N    GR+L      ++
Sbjct: 58  KHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER 101

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 48.0 bits (115), Expect = 1e-08
 Identities = 11/34 (32%), Positives = 24/34 (70%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G H+G+ FVE++++++A  A++ +    LYG+ +
Sbjct: 54 GQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI 87

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

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 13/34 (38%), Positives = 23/34 (67%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             HRGFAFVE+   ++A  A++ ++ + L+GR +
Sbjct: 102 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 48.8 bits (117), Expect = 3e-08
 Identities = 11/41 (26%), Positives = 24/41 (58%)

Query: 2   KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +F   R FA+++  +K++A+  +E L+   + G  L+  V+
Sbjct: 154 RFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS 194

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             +   AF+ +  K  A+ AL+ ++ + L  R +  S+A
Sbjct: 251 SFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA 288

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 39.2 bits (92), Expect = 8e-05
 Identities = 5/35 (14%), Positives = 11/35 (31%), Gaps = 1/35 (2%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
                +  FA +E+     A  A+    +  +   
Sbjct: 75  DSLKKNFRFARIEFARYDGALAAITKT-HKVVGQN 108

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 45.7 bits (109), Expect = 5e-08
 Identities = 14/39 (35%), Positives = 23/39 (58%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             +G AF+ ++ K  AQN   A++N  L+GR +  S+A
Sbjct: 55 RKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 45.7 bits (109), Expect = 9e-08
 Identities = 14/38 (36%), Positives = 21/38 (55%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
          M  G  RG AF+ +  K+ A  AL  ++   LYG+ L+
Sbjct: 61 MMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV 98

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 45.3 bits (108), Expect = 1e-07
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G+  VEY T +EAQ A+E L+   L G+ +
Sbjct: 62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 45.5 bits (108), Expect = 1e-07
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
            H G A V + + + A+  ++ L  T + G  +
Sbjct: 45 RKHLGLARVLFTSTRGAKETVKNLHLTSVMGNII 78

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 47.3 bits (113), Expect = 1e-07
 Identities = 12/37 (32%), Positives = 16/37 (43%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
            + G  +G+ F EY+ K  A  A   L    L  R L
Sbjct: 131 ERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL 167

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 45.4 bits (108), Expect = 6e-07
 Identities = 14/39 (35%), Positives = 19/39 (48%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           G  +GFA +EY T + A+ A +      L G HL  S  
Sbjct: 223 GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 45.0 bits (107), Expect = 6e-07
 Identities = 10/36 (27%), Positives = 18/36 (50%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
              ++G AFV  +  ++A+ A+ A   + L  R L
Sbjct: 52 FVDKYKGTAFVTLLNGEQAEAAINAFHQSRLREREL 87

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 45.3 bits (108), Expect = 1e-07
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             RGFAFV +  +++AQ+A  A+    L GR L
Sbjct: 52 KAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.9 bits (107), Expect = 1e-07
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +GFAF+ +  +++A  A+  +S        L
Sbjct: 54 GQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL 87

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          G  +G+ F+ +   + A+ ALE L+   L GR +      ++
Sbjct: 44 GRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTER 85

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 45.4 bits (108), Expect = 2e-07
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G+  VEY T +EAQ A+E L+   L G+ +
Sbjct: 61 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 94

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 11/39 (28%), Positives = 24/39 (61%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          G+ +GF FV++ ++++A+ A EA+ +  + G  +    A
Sbjct: 51 GSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA 89

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G   G A V + ++ EA  A+  L++  +  R +
Sbjct: 54 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV 87

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.4 bits (109), Expect = 2e-07
 Identities = 11/42 (26%), Positives = 17/42 (40%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +    RG AFV +     A NAL ++     Y + +    A
Sbjct: 46 SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 38.3 bits (88), Expect = 1e-04
 Identities = 8/34 (23%), Positives = 15/34 (44%)

Query: 5   NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
                AFVE+  + +A  A +AL    +   + +
Sbjct: 242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 9/34 (26%), Positives = 17/34 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G   G A V + ++ EA  A+  L++  +  R +
Sbjct: 54 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV 87

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 44.5 bits (106), Expect = 2e-07
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G+AF+E+   + + +A+  L+   L  R L
Sbjct: 41 GRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 44.3 bits (105), Expect = 3e-07
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 2   KFGN------HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           K+G       H+G+AFV+Y  ++ A+ A+   +   L G+ L  ++A + 
Sbjct: 51  KYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP 100

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 2/42 (4%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          G  RG   V +    EA  A+   +   L+ R +   V  D+
Sbjct: 53 GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM--HVKMDE 92

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 44.9 bits (106), Expect = 3e-07
 Identities = 9/45 (20%), Positives = 20/45 (44%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
               ++ G A++ + T++ AQ  +EA       G  L+ + +   
Sbjct: 66  DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 43.9 bits (104), Expect = 3e-07
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 4/45 (8%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTH----LYGRHLIFSVAHD 44
            +RGFAFV+  +  +A   L+ L + H    + G+ +    A  
Sbjct: 50 QQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 44.1 bits (104), Expect = 3e-07
 Identities = 12/45 (26%), Positives = 18/45 (40%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          + +   R  AF+ Y     AQ A+  L    L    L  ++A  Q
Sbjct: 50 LTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 44.8 bits (106), Expect = 3e-07
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
               GF FVEY ++ +A+NA+  ++ T L  R +
Sbjct: 78  KTACGFCFVEYYSRADAENAMRYINGTRLDDRII 111

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 45.2 bits (108), Expect = 3e-07
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          K   +  +AFVEY    +A  AL+ L+   +   
Sbjct: 36 KNNKNVNYAFVEYHQSHDANIALQTLNGKQIENN 69

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 39.8 bits (94), Expect = 3e-05
 Identities = 12/32 (37%), Positives = 22/32 (68%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
           G+ RG+ FV + ++ +AQNA++++    L GR
Sbjct: 126 GSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR 157

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 9/42 (21%), Positives = 22/42 (52%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           G  +GFA V   ++  ++  ++ L    L+G++ + +  + Q
Sbjct: 109 GQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 44.3 bits (105), Expect = 4e-07
 Identities = 14/34 (41%), Positives = 22/34 (64%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
              RGFAFV +  K++A++A++A+    L GR L
Sbjct: 86  KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 43.4 bits (103), Expect = 5e-07
 Identities = 10/34 (29%), Positives = 15/34 (44%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             +GFAFV ++  + A  A   +      GR L
Sbjct: 47 KKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML 80

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 44.5 bits (106), Expect = 5e-07
 Identities = 9/34 (26%), Positives = 21/34 (61%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G   G+AFV++ ++ ++Q A++ L+   +  + L
Sbjct: 42 GYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 39.5 bits (93), Expect = 4e-05
 Identities = 15/32 (46%), Positives = 19/32 (59%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
           G  RG AFV Y  ++EAQ A+ AL+N    G 
Sbjct: 128 GRPRGVAFVRYNKREEAQEAISALNNVIPEGG 159

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 13/34 (38%), Positives = 21/34 (61%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           G  +G+A VEY T ++A  A EAL+   + G+ +
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTI 144

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 45.0 bits (107), Expect = 5e-07
 Identities = 16/32 (50%), Positives = 21/32 (65%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
            H+GFAFVEY   + AQ ALE +++  L GR
Sbjct: 67 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGR 98

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 12/34 (35%), Positives = 23/34 (67%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           G H+G+ F+EY   Q +Q+A+ +++   L G++L
Sbjct: 164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 43.4 bits (103), Expect = 5e-07
 Identities = 8/42 (19%), Positives = 20/42 (47%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          G  +G A+VEY  + +A  A+  +    +    +  ++++  
Sbjct: 55 GKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSG 96

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 43.3 bits (103), Expect = 5e-07
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             RGFAFV +    +A+ A E  +   L GR +
Sbjct: 54 RRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 44.5 bits (106), Expect = 5e-07
 Identities = 12/39 (30%), Positives = 18/39 (46%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           G  +G+AF EYV       A+  L+   L  + L+   A
Sbjct: 133 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 1/34 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             + FAF+E+ +  E   A+ A       G+ L
Sbjct: 48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL 80

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 43.4 bits (103), Expect = 6e-07
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          +GF F+   T+  A+ A   L N  L G+ L
Sbjct: 51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQL 81

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 43.5 bits (103), Expect = 6e-07
 Identities = 8/40 (20%), Positives = 21/40 (52%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           +G++FV + T + A +A+ +++ T + G  +      + 
Sbjct: 60 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 43.0 bits (102), Expect = 6e-07
 Identities = 10/36 (27%), Positives = 14/36 (38%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
               R  AFV Y   + A  A+  L+ T +    L
Sbjct: 44 SMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQL 79

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 43.4 bits (103), Expect = 7e-07
 Identities = 13/34 (38%), Positives = 21/34 (61%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G+A VEY T ++A  A EAL+   + G+ +
Sbjct: 65 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTI 98

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 43.4 bits (103), Expect = 7e-07
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           G  +G+ F+ +   + A+ ALE L+   L GR +      ++
Sbjct: 65  GRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 43.1 bits (102), Expect = 8e-07
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHL 32
          G H+G AF+ Y  ++ A  A  AL     
Sbjct: 52 GMHKGCAFLTYCERESALKAQSALHEQKT 80

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 42.5 bits (101), Expect = 8e-07
 Identities = 9/34 (26%), Positives = 19/34 (55%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             +G+A+VE+    EA+ AL+ +    + G+ +
Sbjct: 44 HLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.0 bits (102), Expect = 8e-07
 Identities = 11/32 (34%), Positives = 16/32 (50%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           +GF FV +    +A  A E L  T + GR +
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKI 85

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 42.6 bits (101), Expect = 8e-07
 Identities = 9/42 (21%), Positives = 21/42 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          G  +G A++E+ ++ +A+  LE      + GR +      ++
Sbjct: 50 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G+ F EY  ++ A +A+  L+     GR L
Sbjct: 47 GKPKGYGFCEYQDQETALSAMRNLNGREFSGRAL 80

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 42.8 bits (101), Expect = 1e-06
 Identities = 10/36 (27%), Positives = 19/36 (52%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF 39
          G  +GF FVE  +  +A+  +++     L  +H +F
Sbjct: 51 GKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF 86

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 8/42 (19%), Positives = 22/42 (52%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          G  +GFA V   ++  ++  ++ L    L+G++ + + ++  
Sbjct: 42 GQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKL 83

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.6 bits (101), Expect = 1e-06
 Identities = 8/30 (26%), Positives = 17/30 (56%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          +  + FVE+   ++A  AL A++   + G+
Sbjct: 54 NDPYCFVEFYEHRDAAAALAAMNGRKILGK 83

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 42.2 bits (100), Expect = 1e-06
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALS-NTHLYGRHL 37
              G+AFV+Y  +  A  A+E LS    L+G+ +
Sbjct: 41 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIM 75

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 42.2 bits (100), Expect = 1e-06
 Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 2/42 (4%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          G  +G   V++ + + A+ A   ++   L GR +   V  D+
Sbjct: 45 GKSKGCGVVKFESPEVAERACRMMNGMKLSGREI--DVRIDR 84

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 42.3 bits (100), Expect = 1e-06
 Identities = 10/34 (29%), Positives = 22/34 (64%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G+AF+E+ + ++A+ AL + +   + GR +
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAI 83

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 12/34 (35%), Positives = 17/34 (50%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
              RGFAFV +    +A+ A E  +   L GR +
Sbjct: 85  RRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 42.2 bits (100), Expect = 1e-06
 Identities = 10/40 (25%), Positives = 19/40 (47%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
             F F+++   Q  ++A+E  S    +G+ LI  V+   
Sbjct: 44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSN 83

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 42.7 bits (101), Expect = 1e-06
 Identities = 11/29 (37%), Positives = 18/29 (62%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHL 32
          G+ +G AFV++ +  EAQ A+ AL  +  
Sbjct: 53 GSSKGCAFVKFSSHTEAQAAIHALHGSQT 81

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 41.7 bits (99), Expect = 1e-06
 Identities = 8/34 (23%), Positives = 17/34 (50%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             +G+ FV++ +   AQ A+ AL  + +  +  
Sbjct: 44 NKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 42.2 bits (100), Expect = 1e-06
 Identities = 13/37 (35%), Positives = 19/37 (51%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
           GF FVEY   ++AQ AL+ L    + G  L   ++ 
Sbjct: 50 MGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE 86

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 43.2 bits (102), Expect = 1e-06
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           RG+ FV++ +   AQ A+  L+  ++  + L  ++A
Sbjct: 84  RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 41.6 bits (98), Expect = 2e-06
 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
          G  +G+ F+EY +   A +A++      L  +H  F V
Sbjct: 44 GKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH-TFRV 80

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 9/36 (25%), Positives = 17/36 (47%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF 39
          G  +G+ F+EY +   A +A++      L  +H   
Sbjct: 58 GKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR 93

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 41.7 bits (99), Expect = 2e-06
 Identities = 14/39 (35%), Positives = 25/39 (64%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          G+ RG+ FV + ++ +AQNA++++    L GR L  + A
Sbjct: 40 GSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 9/41 (21%), Positives = 20/41 (48%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD 44
           G  +G A++E+ ++ +A+  LE      + GR +      +
Sbjct: 133 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 41.4 bits (98), Expect = 9e-06
 Identities = 9/35 (25%), Positives = 21/35 (60%), Gaps = 1/35 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLI 38
          G +R F +V++ + ++ + ALE L+   ++G  + 
Sbjct: 51 GTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK 84

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 10/34 (29%), Positives = 13/34 (38%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G A V Y     A+ A+E        G  L
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKL 95

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 14/34 (41%), Positives = 22/34 (64%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
              RGFAFV +  K++A++A++A+    L GR L
Sbjct: 109 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 41.8 bits (99), Expect = 2e-06
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             RGF FV +    +A++A+ A++   + GR +
Sbjct: 51 QRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQI 84

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 7/32 (21%), Positives = 17/32 (53%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
              G+A+V +    +A+ AL+ ++   + G+
Sbjct: 54 RRSLGYAYVNFQQPADAERALDTMNFDVIKGK 85

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 9/32 (28%), Positives = 18/32 (56%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
              +G+ FV + T++ A+ A+E ++   L  R
Sbjct: 140 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 41.9 bits (99), Expect = 3e-06
 Identities = 10/34 (29%), Positives = 20/34 (58%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             RGFAF+ +    +A+NA + ++   L+G+ +
Sbjct: 45 SKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 11/42 (26%), Positives = 16/42 (38%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           G  +G+A V   ++      LE L    L G  +    A  Q
Sbjct: 96  GQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 41.5 bits (98), Expect = 3e-06
 Identities = 11/41 (26%), Positives = 23/41 (56%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          +    R +AFV +  +++A  A++AL+   L G  +  ++A
Sbjct: 46 RVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 42.1 bits (99), Expect = 3e-06
 Identities = 12/42 (28%), Positives = 22/42 (52%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           MK G  +G AF+    ++ A  AL+  +   L+G+ ++   A
Sbjct: 86  MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA 127

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

 Score = 41.6 bits (98), Expect = 3e-06
 Identities = 7/34 (20%), Positives = 13/34 (38%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G A V +     A+ A++        G  +
Sbjct: 54 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 87

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 42.6 bits (101), Expect = 3e-06
 Identities = 9/34 (26%), Positives = 18/34 (52%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G   G+ FV Y+  ++A+ A+  L+   L  + +
Sbjct: 41 GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 9/32 (28%), Positives = 16/32 (50%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
           G  RG  F+ +  + EA+ A++ L+     G 
Sbjct: 127 GVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 158

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 42.6 bits (100), Expect = 4e-06
 Identities = 13/84 (15%), Positives = 33/84 (39%)

Query: 5   NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGE 64
           N +  A V+     +AQ A+  L+   L+G+ +  +++  Q + +     +     K+  
Sbjct: 39  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 98

Query: 65  SLEELRARTAAQFTDEVNGFQNST 88
           +    R +       +     ++T
Sbjct: 99  NSPLHRFKKPGSKNFQNIFPPSAT 122

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 36.0 bits (83), Expect = 9e-04
 Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAHDQI 46
             F   R  A ++  + +EA  AL  L N  L    HL  S +   I
Sbjct: 152 KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.4 bits (97), Expect = 4e-06
 Identities = 8/34 (23%), Positives = 16/34 (47%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           +  G   +E+ +++    ALE L+N    G  +
Sbjct: 64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVI 97

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 41.2 bits (97), Expect = 4e-06
 Identities = 9/43 (20%), Positives = 15/43 (34%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
                  FAFVE+   ++A++A+         G  L      
Sbjct: 55 KNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 97

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 41.1 bits (97), Expect = 4e-06
 Identities = 9/34 (26%), Positives = 19/34 (55%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             +G+ FV + T++ A+ A+E ++   L  R +
Sbjct: 42 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 75

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 41.2 bits (97), Expect = 5e-06
 Identities = 8/39 (20%), Positives = 17/39 (43%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
              + F FV Y     AQ A+++++   +  + L   + 
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 41.6 bits (98), Expect = 5e-06
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           G   G A V +  + +A  A++      L GR +   +   Q
Sbjct: 73  GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 40.5 bits (95), Expect = 5e-06
 Identities = 10/39 (25%), Positives = 19/39 (48%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
            ++  AFV  +  ++AQNA++        G+ LI  + 
Sbjct: 37 DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ 75

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 40.7 bits (96), Expect = 5e-06
 Identities = 9/39 (23%), Positives = 19/39 (48%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          + +AFV     ++A  A+  L NT   G+ +   ++  +
Sbjct: 44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR 82

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 40.6 bits (96), Expect = 5e-06
 Identities = 8/37 (21%), Positives = 18/37 (48%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
          + + FV    K  A++A+  L +  L+G ++    + 
Sbjct: 42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK 78

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 40.7 bits (96), Expect = 5e-06
 Identities = 7/39 (17%), Positives = 19/39 (48%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          + +AFV    + +A+ A+  L+   + G+ +   ++   
Sbjct: 43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 40.4 bits (95), Expect = 7e-06
 Identities = 7/34 (20%), Positives = 13/34 (38%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G  +G A V +     A+ A++        G  +
Sbjct: 60 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 93

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 40.8 bits (96), Expect = 7e-06
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII 47
           +GF FV +    +A  A E L  T + GR +  + A  +++
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 109

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 40.4 bits (95), Expect = 7e-06
 Identities = 10/40 (25%), Positives = 19/40 (47%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
             F F+++   Q  ++A+E  S    +G+ LI  V+   
Sbjct: 56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN 95

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 41.8 bits (98), Expect = 7e-06
 Identities = 10/42 (23%), Positives = 17/42 (40%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           G   G A V +  + +A  A++      L GR +   +   Q
Sbjct: 126 GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 167

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 40.8 bits (96), Expect = 7e-06
 Identities = 8/39 (20%), Positives = 17/39 (43%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
              + F FV +     AQ A++A++   +  + L   + 
Sbjct: 79  SLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 40.3 bits (95), Expect = 8e-06
 Identities = 10/39 (25%), Positives = 21/39 (53%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          G  +GF FV + + +EA  A+  ++   +  + L  ++A
Sbjct: 52 GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 9/36 (25%), Positives = 18/36 (50%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
                  A+V Y+  ++A  A++ ++N  + GR L
Sbjct: 58 GSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 39.5 bits (93), Expect = 1e-05
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G  +G+ FV +  K +A+NA++ +    L GR
Sbjct: 45 GKSKGYGFVSFFNKWDAENAIQQMGGQWLGGR 76

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 39.9 bits (94), Expect = 1e-05
 Identities = 10/32 (31%), Positives = 20/32 (62%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          GN +G+AF+ + +   +  A+EA++  +L  R
Sbjct: 45 GNSKGYAFINFASFDASDAAIEAMNGQYLCNR 76

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 13/84 (15%), Positives = 33/84 (39%)

Query: 5   NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGE 64
           N +  A V+     +AQ A+  L+   L+G+ +  +++  Q + +     +     K+  
Sbjct: 70  NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 129

Query: 65  SLEELRARTAAQFTDEVNGFQNST 88
           +    R +       +     ++T
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSAT 153

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAHDQI 46
             F   R  A ++  + +EA  AL  L N  L    HL  S +   I
Sbjct: 183 KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 229

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 39.8 bits (93), Expect = 1e-05
 Identities = 9/33 (27%), Positives = 13/33 (39%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             G   VE+V K++   A+  L NT       
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEG 80

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 40.0 bits (94), Expect = 1e-05
 Identities = 10/29 (34%), Positives = 18/29 (62%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          +G+ FV +  K +A+NA++ +    L GR
Sbjct: 57 KGYGFVSFFNKWDAENAIQQMGGQWLGGR 85

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 9/31 (29%), Positives = 13/31 (41%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
             G   VE+V K++   A+  L NT     
Sbjct: 49 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSH 79

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 8/36 (22%), Positives = 18/36 (50%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          + +AF+ +  +  A  A+E ++   L G ++    A
Sbjct: 45 KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 39.6 bits (93), Expect = 2e-05
 Identities = 10/32 (31%), Positives = 15/32 (46%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G   G A V +  K +A  A++  +   L GR
Sbjct: 67 GRSLGTADVHFERKADALKAMKQYNGVPLDGR 98

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 9/41 (21%), Positives = 14/41 (34%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
               +G  FV + T++ A  A  AL N  +          
Sbjct: 42 NPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM 82

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHL 32
           G  RG AFV + T+  AQ A++A+     
Sbjct: 133 GLSRGCAFVTFTTRAMAQTAIKAMHQAQT 161

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 38.8 bits (91), Expect = 3e-05
 Identities = 9/33 (27%), Positives = 14/33 (42%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRH 36
          G   G+ FVE+     A+  L  ++   L G  
Sbjct: 49 GIPAGYCFVEFADLATAEKCLHKINGKPLPGAT 81

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 39.3 bits (92), Expect = 3e-05
 Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 6/45 (13%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTH------LYGRHLIFSVA 42
           + +G AF +++T++ AQ  L A S         L GR L   +A
Sbjct: 54 EHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 98

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.2 bits (92), Expect = 3e-05
 Identities = 4/39 (10%), Positives = 13/39 (33%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           G  RG  F    + ++ +  +   +   +     + +  
Sbjct: 63  GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 38.8 bits (91), Expect = 3e-05
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          N  GFAFVE+   ++A++A+  L    + G  +   ++   
Sbjct: 35 NPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM 75

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 39.0 bits (91), Expect = 3e-05
 Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 2/49 (4%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL-IFSVAHDQIISIIA 51
           G   G A V++  + +A+ +   L    L GR   +  V  + +  I  
Sbjct: 54  GQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEK 101

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.8 bits (90), Expect = 4e-05
 Identities = 6/32 (18%), Positives = 16/32 (50%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHL 32
          +    ++ ++F  Y T +E++ A   L+   +
Sbjct: 57 LLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 88

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 12/40 (30%), Positives = 21/40 (52%)

Query: 5   NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD 44
           N  GFAFVE+   ++A +A+  L    L G  +   +++ 
Sbjct: 108 NPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 38.2 bits (89), Expect = 7e-05
 Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSN--THLYGRHLI 38
            +RGFAFVEY + + A  A   L      L+G  + 
Sbjct: 49 MKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA 85

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 37.4 bits (87), Expect = 7e-05
 Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 1/36 (2%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          +    + FAF+E+ +  E   A+ A       G+ L
Sbjct: 48 QINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSL 82

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 38.9 bits (91), Expect = 8e-05
 Identities = 11/31 (35%), Positives = 15/31 (48%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          RGF F+   ++  A+ A   L  T L  R L
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPL 88

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 10/27 (37%), Positives = 13/27 (48%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNT 30
           G   G  FVE+  K  A+ ALE   + 
Sbjct: 134 GRATGKGFVEFAAKPPARKALERCGDG 160

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 37.7 bits (88), Expect = 8e-05
 Identities = 10/36 (27%), Positives = 16/36 (44%)

Query: 7   RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
            GFAFVE+   + A  A+E +       + L    +
Sbjct: 65  NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 37.6 bits (88), Expect = 9e-05
 Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 1/36 (2%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          +GF + E+       +AL  L+   L  R +   VA
Sbjct: 61 KGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVA 95

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 37.6 bits (88), Expect = 9e-05
 Identities = 8/31 (25%), Positives = 13/31 (41%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRH 36
             FA+++Y +   AQ A   +    L G  
Sbjct: 52 GDSFAYIQYESLDAAQAACAKMRGFPLGGPD 82

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 39.0 bits (90), Expect = 1e-04
 Identities = 9/44 (20%), Positives = 18/44 (40%)

Query: 2   KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           ++   +   FV++  +  A+ A EA+SN  L            +
Sbjct: 174 RYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRRE 217

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 37.1 bits (87), Expect = 1e-04
 Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 1/34 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
          G+ +GFA++E+  K+  + +L AL  +   GR +
Sbjct: 45 GHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQI 77

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 9/31 (29%), Positives = 14/31 (45%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
               V Y +K +A+ AL+ L+   L    L
Sbjct: 54 TAVVNVTYSSKDQARQALDKLNGFQLENFTL 84

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 37.1 bits (87), Expect = 1e-04
 Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
             +GF FVE   ++    A+  L NT   GR +  + A+ +
Sbjct: 40 KKPKGFGFVEM-QEESVSEAIAKLDNTDFMGRTIRVTEANPK 80

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 37.2 bits (87), Expect = 1e-04
 Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 1/36 (2%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          +GF + E+       +AL +L+   L  + +   VA
Sbjct: 57 KGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA 91

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 8/31 (25%), Positives = 14/31 (45%)

Query: 7  RGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             A VE++   EA+ A   L+ +  +   L
Sbjct: 46 GITAIVEFLEPLEARKAFRHLAYSKFHHVPL 76

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 5/35 (14%), Positives = 12/35 (34%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
                      +E+ +K +A   L  L++  +   
Sbjct: 159 SGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNP 193

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 36.2 bits (83), Expect = 7e-04
 Identities = 10/43 (23%), Positives = 18/43 (41%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII 47
          +  G A VE         A+  L+N  ++G+ +   V+    I
Sbjct: 40 SKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAI 82

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 36.5 bits (85), Expect = 2e-04
 Identities = 9/32 (28%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G +R F +V++ + ++ + ALE L+   ++G 
Sbjct: 55 GTNRKFGYVDFESAEDLEKALE-LTGLKVFGN 85

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 36.1 bits (84), Expect = 3e-04
 Identities = 10/32 (31%), Positives = 20/32 (62%), Gaps = 1/32 (3%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          GN  G+ FV++  ++E + AL+  +  ++ GR
Sbjct: 47 GNKTGYIFVDFSNEEEVKQALK-CNREYMGGR 77

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 36.1 bits (84), Expect = 3e-04
 Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 1/39 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             +GF +VE+      + AL       L  R L   +A
Sbjct: 53 DKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA 90

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 1/32 (3%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
             +G A+VE+   Q    A+  L+   L G 
Sbjct: 64 RRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGV 94

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G   G A VE+ T ++A  A+      ++  R
Sbjct: 52 GRVTGEADVEFATHEDAVAAMA-KDKANMQHR 82

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 35.6 bits (82), Expect = 7e-04
 Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 1/32 (3%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G   G  FVE+  + + + AL      ++  R
Sbjct: 64 GKATGEGFVEFRNEADYKAALC-RHKQYMGNR 94

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 35.5 bits (82), Expect = 7e-04
 Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 4   GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           G+ +G+A++E+  +     A+ A+  T   GR +
Sbjct: 75  GHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTI 107

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 35.5 bits (82), Expect = 7e-04
 Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 1/32 (3%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR 35
          G + G   V++++ Q+   AL+  +   +  R
Sbjct: 53 GRNNGNGLVKFLSPQDTFEALK-RNRMLMIQR 83

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 34.6 bits (80), Expect = 8e-04
 Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 7  RGFAFVEYVTKQEAQNALEALSN-THLYGRHL 37
          +  AF+++ T+Q A+ A E   N   + GR L
Sbjct: 48 QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL 79

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	112
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.21
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.12
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.11
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.08
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.05
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.04
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.04
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.03
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.02
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.02
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.01
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.01
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.0
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.0
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.99
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.99
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.98
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.98
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.98
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.98
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.97
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.97
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.97
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.97
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.97
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.96
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.96
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	98.96
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.96
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.95
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.95
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.95
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.95
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.95
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.95
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.94
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.94
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.94
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.93
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.93
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.93
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.93
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.92
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.92
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.92
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.92
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.92
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.92
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.92
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.91
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.91
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.91
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.91
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.91
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.91
1x5p_A	97	Negative elongation factor E; structure genomics,	98.9
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.9
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.9
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.89
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.89
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.89
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.89
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.89
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.89
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.88
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.88
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.88
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.88
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.88
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.88
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.88
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.87
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.87
2div_A	99	TRNA selenocysteine associated protein; structural	98.87
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.87
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.87
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.85
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.85
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.85
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.85
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.85
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.84
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.84
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.84
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.84
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.83
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.83
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.82
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.82
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.81
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	98.81
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.81
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.8
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.8
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.79
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.79
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.78
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.78
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.77
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.77
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.76
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.76
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.75
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.75
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.75
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.75
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	98.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.74
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.74
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.74
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.74
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.21
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.73
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.72
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.72
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.71
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.71
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.71
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.7
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.7
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	98.7
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.7
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.7
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.69
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.69
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.68
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.68
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.68
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.68
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.67
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.66
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.66
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.64
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.63
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.63
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.62
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.62
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.61
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	98.6
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.59
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.59
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.59
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	98.56
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.56
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	98.54
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.54
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.54
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	98.53
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	98.53
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	98.52
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.51
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.51
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	98.51
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.51
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.48
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.48
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.46
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.45
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	98.45
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.44
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	98.42
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.41
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.38
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	98.37
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.36
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.35
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	98.34
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.33
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.3
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.3
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.29
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	98.27
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.25
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.25
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	98.23
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.22
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.21
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	98.17
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	97.96
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	97.95
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	97.93
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.64
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	97.35
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	97.28
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	95.11
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	95.06
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	93.58

>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=99.21  E-value=2e-11  Score=79.73  Aligned_cols=41  Identities=32%  Similarity=0.581  Sum_probs=39.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|++|+|.+|.|
T Consensus        58 g~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           58 GHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            88999999999999999999999999999999999999887

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.12  E-value=8.2e-11  Score=75.44  Aligned_cols=43  Identities=30%  Similarity=0.515  Sum_probs=39.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhC-CCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALS-NTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~ln-g~~l~gr~L~V~~a~~~~   46 (112)
                      |.+||||||+|.+.++|..|++.++ +..|.|++|.|.+|.|++
T Consensus        41 ~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~   84 (91)
T 2lxi_A           41 GQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKP   84 (91)
T ss_dssp             CCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCC
T ss_pred             CCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCC
Confidence            8899999999999999999999874 568999999999998864

>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=99.11  E-value=2.6e-11  Score=77.09  Aligned_cols=45  Identities=18%  Similarity=0.360  Sum_probs=37.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|.+..
T Consensus        42 g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~~   86 (90)
T 3p5t_L           42 GQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEHH   86 (90)
T ss_dssp             CCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC------
T ss_pred             CccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCccc
Confidence            889999999999999999999999999999999999999886543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.08  E-value=1.4e-10  Score=75.89  Aligned_cols=39  Identities=28%  Similarity=0.386  Sum_probs=35.7

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      .|||||||+|.+.++|..|++.|||..|.||+|+|.+|.
T Consensus        41 ~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           41 LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            489999999999999999999999999999999766553

>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=99.08  E-value=1.8e-10  Score=72.00  Aligned_cols=43  Identities=28%  Similarity=0.533  Sum_probs=38.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+++
T Consensus        45 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~kp   87 (87)
T 3bs9_A           45 GKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP   87 (87)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC---
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCCC
Confidence            7789999999999999999999999999999999999887753

>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=99.05  E-value=2.5e-10  Score=75.11  Aligned_cols=64  Identities=27%  Similarity=0.318  Sum_probs=50.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCcccchhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      +.++|||||+|.+.++|..|+..|||..+.|+.|.|.++.|.....      .+.....++++++++.+.
T Consensus        44 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~------~~~~~~~~~~l~~~~~~~  107 (115)
T 3lqv_A           44 PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQ------KMDTKKKEEQLKLLKEKY  107 (115)
T ss_dssp             TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHTT------TSCHHHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChhhh------hhhHhHhHHHHHHHHHHh
Confidence            5679999999999999999999999999999999999998865442      233334445566555544

>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=99.05  E-value=2.9e-10  Score=70.42  Aligned_cols=42  Identities=33%  Similarity=0.654  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|+
T Consensus        40 ~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           40 GSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            778999999999999999999999999999999999988875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.04  E-value=2.1e-10  Score=74.79  Aligned_cols=40  Identities=28%  Similarity=0.483  Sum_probs=36.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCC----eeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNT----HLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~----~l~gr~L~V~~a~   43 (112)
                      |++||||||+|.+.++|..|++.|||.    .|.||+|.|++|.
T Consensus        50 g~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Ak   93 (95)
T 2lkz_A           50 QQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK   93 (95)
T ss_dssp             SSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECC
T ss_pred             CCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEcc
Confidence            889999999999999999999999997    4899999887765

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.04  E-value=4e-10  Score=72.56  Aligned_cols=47  Identities=32%  Similarity=0.599  Sum_probs=43.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISII   50 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~   50 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|...+.+
T Consensus        51 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~   97 (102)
T 2cqb_A           51 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKES   97 (102)
T ss_dssp             CCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCCCCC
Confidence            77899999999999999999999999999999999999998766543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.04  E-value=1.3e-10  Score=75.49  Aligned_cols=41  Identities=24%  Similarity=0.452  Sum_probs=38.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCC-eeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYG-RHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~g-r~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.| +.|.|.++.|
T Consensus        51 g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           51 GKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKD   92 (100)
T ss_dssp             TEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHH
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECch
Confidence            7899999999999999999999999999999 9997777765

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.03  E-value=4.9e-10  Score=71.31  Aligned_cols=45  Identities=27%  Similarity=0.496  Sum_probs=41.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...+
T Consensus        45 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   89 (96)
T 1x5t_A           45 GNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   89 (96)
T ss_dssp             CSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             CCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCCC
Confidence            788999999999999999999999999999999999999886544

>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=99.02  E-value=5.6e-10  Score=71.39  Aligned_cols=44  Identities=25%  Similarity=0.453  Sum_probs=41.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        41 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   84 (96)
T 2x1f_A           41 GRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDI   84 (96)
T ss_dssp             CCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSSG
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCCC
Confidence            78899999999999999999999999999999999999988643

>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=99.02  E-value=5.5e-10  Score=73.62  Aligned_cols=43  Identities=23%  Similarity=0.383  Sum_probs=40.0

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      +++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+++.
T Consensus        61 ~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           61 GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC  103 (111)
T ss_dssp             CCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCSC
T ss_pred             CCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEecccccc
Confidence            5679999999999999999999999999999999999988753

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.01  E-value=4.5e-10  Score=72.34  Aligned_cols=44  Identities=25%  Similarity=0.507  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|+..
T Consensus        51 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           51 GSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             CSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCS
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCC
Confidence            77899999999999999999999999999999999999988643

>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=99.01  E-value=7.1e-10  Score=72.39  Aligned_cols=44  Identities=30%  Similarity=0.422  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+++.
T Consensus        65 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  108 (110)
T 1oo0_B           65 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  108 (110)
T ss_dssp             SSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESSC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCCC
Confidence            78899999999999999999999999999999999999887643

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.00  E-value=5.5e-10  Score=74.21  Aligned_cols=40  Identities=20%  Similarity=0.291  Sum_probs=36.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        45 g~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A           45 RKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            7899999999999999999999999999999999665443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.00  E-value=3.9e-10  Score=77.20  Aligned_cols=43  Identities=21%  Similarity=0.400  Sum_probs=39.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.++.
T Consensus        69 ~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           69 DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ  111 (127)
T ss_dssp             CSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCC
T ss_pred             CCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcc
Confidence            6889999999999999999999999999999999888777643

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.99  E-value=4.4e-10  Score=74.45  Aligned_cols=44  Identities=16%  Similarity=0.126  Sum_probs=40.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      ++++|||||+|.+.++|..|+..|||..+.||.|.|.++.+..+
T Consensus        53 ~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~~~f   96 (105)
T 2pe8_A           53 DDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKF   96 (105)
T ss_dssp             TTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHHHH
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCHHHh
Confidence            57899999999999999999999999999999999999877543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.99  E-value=5.8e-10  Score=71.69  Aligned_cols=44  Identities=18%  Similarity=0.379  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|++.
T Consensus        55 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   98 (100)
T 2do4_A           55 GKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPS   98 (100)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCSC
T ss_pred             CCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            67899999999999999999999999999999999999988653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.98  E-value=6.4e-10  Score=70.35  Aligned_cols=42  Identities=24%  Similarity=0.430  Sum_probs=39.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+. |||..|.|+.|.|.++.+++
T Consensus        47 g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~~~   88 (91)
T 2dgw_A           47 GNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSGP   88 (91)
T ss_dssp             SCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESSCC
T ss_pred             CCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCcCC
Confidence            7889999999999999999999 99999999999999998764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.98  E-value=8e-10  Score=72.46  Aligned_cols=44  Identities=27%  Similarity=0.336  Sum_probs=41.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        62 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             CSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCC
Confidence            78899999999999999999999999999999999999887643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.98  E-value=4.7e-10  Score=72.00  Aligned_cols=44  Identities=27%  Similarity=0.261  Sum_probs=40.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      ++++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|++.
T Consensus        53 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   96 (97)
T 2e5j_A           53 QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD   96 (97)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCCCC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCCC
Confidence            56799999999999999999999999999999999999988643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.98  E-value=1e-09  Score=70.87  Aligned_cols=45  Identities=24%  Similarity=0.347  Sum_probs=41.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++...
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (103)
T 2cq0_A           54 GQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS   98 (103)
T ss_dssp             CSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCS
T ss_pred             CceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCCC
Confidence            788999999999999999999999999999999999999886543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.97  E-value=1.1e-09  Score=70.48  Aligned_cols=45  Identities=22%  Similarity=0.500  Sum_probs=41.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++...
T Consensus        50 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   94 (101)
T 2fc9_A           50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP   94 (101)
T ss_dssp             SCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCCCC
T ss_pred             CCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCCCC
Confidence            788999999999999999999999999999999999999886443

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.97  E-value=3.8e-10  Score=79.34  Aligned_cols=42  Identities=26%  Similarity=0.359  Sum_probs=39.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..||..|||..|.|+.|.|.++.+.
T Consensus        96 g~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           96 GQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            889999999999999999999999999999999988777654

>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=98.97  E-value=9.2e-10  Score=70.47  Aligned_cols=45  Identities=22%  Similarity=0.309  Sum_probs=41.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++...
T Consensus        47 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (99)
T 1whw_A           47 KKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA   91 (99)
T ss_dssp             CCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCSTT
T ss_pred             CCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCccc
Confidence            788999999999999999999999999999999999999886543

>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=98.97  E-value=7.7e-10  Score=69.06  Aligned_cols=41  Identities=22%  Similarity=0.470  Sum_probs=38.8

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|..
T Consensus        46 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   86 (88)
T 4a8x_A           46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPW   86 (88)
T ss_dssp             ECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCCC
T ss_pred             CCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCCC
Confidence            89999999999999999999999999999999999998754

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.97  E-value=5.7e-10  Score=71.10  Aligned_cols=43  Identities=21%  Similarity=0.474  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|+.
T Consensus        50 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           50 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            6789999999999999999999999999999999999988754

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=6.3e-10  Score=72.08  Aligned_cols=43  Identities=33%  Similarity=0.488  Sum_probs=40.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+++
T Consensus        62 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             SSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             CceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            7889999999999999999999999999999999999988754

>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=98.96  E-value=1.1e-09  Score=70.04  Aligned_cols=42  Identities=21%  Similarity=0.330  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++
T Consensus        54 g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           54 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             SCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            778999999999999999999999999999999999888754

>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=98.96  E-value=7.3e-10  Score=73.55  Aligned_cols=42  Identities=21%  Similarity=0.471  Sum_probs=38.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.+||||||+|.+.++|..|+..|||..|.|+.|.|.++.++
T Consensus        42 ~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A           42 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            457999999999999999999999999999999988777654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.96  E-value=1.1e-09  Score=69.53  Aligned_cols=45  Identities=24%  Similarity=0.492  Sum_probs=41.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.++...
T Consensus        44 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   88 (95)
T 2dnz_A           44 GRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLDG   88 (95)
T ss_dssp             CCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCCC
T ss_pred             CceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccCC
Confidence            788999999999999999999999999999999999999886543

>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=98.95  E-value=8.6e-10  Score=72.76  Aligned_cols=39  Identities=18%  Similarity=0.360  Sum_probs=36.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..+.||.|.|.++
T Consensus        65 ~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           65 DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            678999999999999999999999999999999988764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.95  E-value=1.2e-09  Score=70.71  Aligned_cols=44  Identities=50%  Similarity=0.961  Sum_probs=41.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhh-CCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEAL-SNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~l-ng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..| ||..|.|+.|.|.++.+...
T Consensus        55 ~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~   99 (107)
T 2cph_A           55 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   99 (107)
T ss_dssp             CSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             CCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCC
Confidence            788999999999999999999999 99999999999999988643

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.95  E-value=1.5e-09  Score=69.65  Aligned_cols=45  Identities=18%  Similarity=0.348  Sum_probs=41.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISI   49 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~   49 (112)
                      |+++|||||+|.+.++|..|+. |||..|.|+.|.|.++.|+....
T Consensus        49 ~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~~~   93 (99)
T 2dgs_A           49 QRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDSKS   93 (99)
T ss_dssp             CSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCCCC
T ss_pred             CCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEECCCCcccC
Confidence            7899999999999999999998 99999999999999998875543

>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=98.95  E-value=1.1e-09  Score=71.85  Aligned_cols=45  Identities=29%  Similarity=0.507  Sum_probs=41.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+....
T Consensus        64 g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~  108 (115)
T 2cpx_A           64 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR  108 (115)
T ss_dssp             SSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSCC
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCCC
Confidence            778999999999999999999999999999999999999886544

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.95  E-value=6.2e-10  Score=71.65  Aligned_cols=42  Identities=21%  Similarity=0.555  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+. |||..|.|+.|.|.++.++.
T Consensus        55 g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~   96 (101)
T 1fj7_A           55 GTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRD   96 (101)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECCSCCC
T ss_pred             CCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEcCCCC
Confidence            7889999999999999999999 99999999999999988754

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.95  E-value=1.3e-09  Score=70.52  Aligned_cols=44  Identities=23%  Similarity=0.379  Sum_probs=40.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.+....
T Consensus        53 g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2dng_A           53 DKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD   96 (103)
T ss_dssp             CSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECCCCCCC
T ss_pred             CccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEecCCCCC
Confidence            788999999999999999999 89999999999999999886544

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.94  E-value=8.2e-10  Score=70.97  Aligned_cols=39  Identities=23%  Similarity=0.335  Sum_probs=37.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.+|
T Consensus        60 g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           60 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             CSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            788999999999999999999999999999999988776

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=1.2e-09  Score=70.32  Aligned_cols=44  Identities=25%  Similarity=0.427  Sum_probs=41.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        51 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           51 QRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             CSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             CCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            77899999999999999999999999999999999999988643

>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=98.94  E-value=1.4e-09  Score=67.60  Aligned_cols=39  Identities=36%  Similarity=0.755  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.+|
T Consensus        46 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           46 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             TEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            778999999999999999999999999999999988765

>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=98.93  E-value=6.8e-10  Score=70.73  Aligned_cols=43  Identities=26%  Similarity=0.344  Sum_probs=39.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+
T Consensus        48 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           48 LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCC
Confidence            4678999999999999999999999999999999888887753

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.93  E-value=2e-09  Score=68.20  Aligned_cols=39  Identities=36%  Similarity=0.634  Sum_probs=36.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.+|
T Consensus        55 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           55 RKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            778999999999999999999999999999999988766

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.93  E-value=6.6e-10  Score=72.58  Aligned_cols=41  Identities=22%  Similarity=0.444  Sum_probs=38.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCe-eEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR-HLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr-~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+ .|.|.++.+
T Consensus        58 g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~   99 (105)
T 2nlw_A           58 GKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTD   99 (105)
T ss_dssp             TBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCC
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcch
Confidence            78999999999999999999999999999999 998887765

>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=98.93  E-value=1.3e-09  Score=72.07  Aligned_cols=43  Identities=19%  Similarity=0.295  Sum_probs=39.7

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      +++||+||+|.+.++|..|+..|||..+.||+|.|.++.+..+
T Consensus        57 ~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~~~~f   99 (105)
T 3v4m_A           57 PGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSY   99 (105)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECHHHH
T ss_pred             CCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeCHHHH
Confidence            5789999999999999999999999999999999999877544

>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=98.92  E-value=2.7e-09  Score=68.84  Aligned_cols=48  Identities=25%  Similarity=0.421  Sum_probs=43.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIA   51 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~   51 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+++...+.
T Consensus        52 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~   99 (103)
T 2cq3_A           52 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG   99 (103)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCCCCCS
T ss_pred             CCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCCCCCC
Confidence            347999999999999999999999999999999999999987665443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.92  E-value=1.4e-09  Score=71.45  Aligned_cols=45  Identities=27%  Similarity=0.499  Sum_probs=41.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+....
T Consensus        54 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           54 GKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA   98 (115)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCC
Confidence            778999999999999999999999999999999999999876443

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=1.5e-09  Score=71.39  Aligned_cols=43  Identities=28%  Similarity=0.471  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++.
T Consensus        66 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  108 (109)
T 2err_A           66 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV  108 (109)
T ss_dssp             TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCSC
T ss_pred             CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCc
Confidence            4579999999999999999999999999999999999988764

>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=98.92  E-value=1.1e-09  Score=70.84  Aligned_cols=45  Identities=27%  Similarity=0.611  Sum_probs=41.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+....
T Consensus        54 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   98 (105)
T 1x5u_A           54 GQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKN   98 (105)
T ss_dssp             CSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSCC
T ss_pred             CcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCcC
Confidence            789999999999999999999999999999999999998876443

>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=98.92  E-value=1.8e-09  Score=69.28  Aligned_cols=41  Identities=20%  Similarity=0.172  Sum_probs=38.5

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      +|||||+|.+.++|..|+..|||..|.|+.|+|.++.|.+.
T Consensus        52 rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~   92 (96)
T 2dgx_A           52 QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGASG   92 (96)
T ss_dssp             TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCSSC
T ss_pred             CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCCC
Confidence            89999999999999999999999999999999999988643

>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=98.92  E-value=1.6e-09  Score=71.28  Aligned_cols=45  Identities=20%  Similarity=0.267  Sum_probs=41.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.|+...
T Consensus        64 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~  108 (115)
T 2cpz_A           64 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS  108 (115)
T ss_dssp             CSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCCC
T ss_pred             CCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCcC
Confidence            788999999999999999999999999999999999999886543

>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=98.92  E-value=9.2e-10  Score=72.52  Aligned_cols=42  Identities=26%  Similarity=0.538  Sum_probs=39.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.|+
T Consensus        65 g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           65 GRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             TEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            778999999999999999999999999999999999888775

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.91  E-value=1.5e-09  Score=69.42  Aligned_cols=44  Identities=30%  Similarity=0.450  Sum_probs=40.4

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      .++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+....
T Consensus        48 ~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   91 (98)
T 2cpf_A           48 LSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATKP   91 (98)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSCC
T ss_pred             CcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCCC
Confidence            78899999999999999999999999999999999999876443

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.91  E-value=1.9e-09  Score=72.17  Aligned_cols=42  Identities=19%  Similarity=0.296  Sum_probs=38.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|+.||..|||..|.|+.|.|.++...
T Consensus        64 ~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNP  105 (111)
T ss_dssp             CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC-
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            357999999999999999999999999999999999887654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.91  E-value=2e-09  Score=68.19  Aligned_cols=40  Identities=33%  Similarity=0.449  Sum_probs=37.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           54 RRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCS
T ss_pred             CCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecC
Confidence            7889999999999999999999999999999999877664

>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=98.91  E-value=1.7e-09  Score=73.84  Aligned_cols=42  Identities=24%  Similarity=0.470  Sum_probs=39.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        89 g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A           89 GRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             TTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCS
T ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            789999999999999999999999999999999988888764

>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=98.91  E-value=1.9e-09  Score=69.83  Aligned_cols=44  Identities=20%  Similarity=0.323  Sum_probs=40.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.++...
T Consensus        54 g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           54 ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             TSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCCC
T ss_pred             CCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEccCCCCC
Confidence            678999999999999999999 99999999999999999886543

>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=98.91  E-value=8.8e-10  Score=71.03  Aligned_cols=42  Identities=29%  Similarity=0.541  Sum_probs=38.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        47 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   88 (104)
T 1p1t_A           47 GKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             TEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCc
Confidence            778999999999999999999999999999999977766654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.90  E-value=3.2e-09  Score=68.01  Aligned_cols=45  Identities=27%  Similarity=0.353  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      ++++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+++..
T Consensus        46 ~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~~   90 (97)
T 1x5p_A           46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPML   90 (97)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCCC
Confidence            367999999999999999999999999999999999999886543

>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=98.90  E-value=2.1e-09  Score=68.16  Aligned_cols=40  Identities=25%  Similarity=0.330  Sum_probs=37.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        54 g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           54 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            7789999999999999999999999999999999888764

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.90  E-value=1.8e-09  Score=69.64  Aligned_cols=44  Identities=23%  Similarity=0.425  Sum_probs=40.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        52 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2d9p_A           52 GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE   95 (103)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCC
T ss_pred             CCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeccccc
Confidence            57899999999999999999999999999999999999988643

>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=98.89  E-value=1.6e-09  Score=70.40  Aligned_cols=43  Identities=35%  Similarity=0.549  Sum_probs=39.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhC--CCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALS--NTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~ln--g~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..||  +..|.|+.|.|.++.|+.
T Consensus        49 g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~   93 (109)
T 2dis_A           49 MKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI   93 (109)
T ss_dssp             TTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSC
T ss_pred             CCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCC
Confidence            6899999999999999999999996  589999999999988754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.89  E-value=1e-09  Score=69.23  Aligned_cols=42  Identities=19%  Similarity=0.414  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        45 g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   86 (92)
T 2dgv_A           45 GKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA   86 (92)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            678999999999999999999999999999999988888775

>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=98.89  E-value=2.5e-09  Score=73.75  Aligned_cols=43  Identities=35%  Similarity=0.572  Sum_probs=40.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+
T Consensus       109 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A          109 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             TTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            8899999999999999999999999999999999999998754

>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=98.89  E-value=2.8e-09  Score=69.36  Aligned_cols=44  Identities=32%  Similarity=0.450  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhC------CCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALS------NTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~ln------g~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..||      |..|.|+.|.|.++.|+..
T Consensus        54 g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           54 EHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             CCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             CCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCcc
Confidence            7889999999999999999999999      9999999999999988643

>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=98.89  E-value=1.9e-09  Score=71.81  Aligned_cols=44  Identities=25%  Similarity=0.481  Sum_probs=40.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        45 g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   88 (116)
T 2fy1_A           45 SKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF   88 (116)
T ss_dssp             TTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSSC
T ss_pred             CCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCCC
Confidence            77899999999999999999999999999999999999887543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.89  E-value=1.3e-09  Score=70.32  Aligned_cols=44  Identities=36%  Similarity=0.498  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+.
T Consensus        52 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dnm_A           52 KAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRR   95 (103)
T ss_dssp             CSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSCCS
T ss_pred             CCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcCCC
Confidence            77899999999999999999999999999999999999987543

>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=98.88  E-value=1.3e-09  Score=70.50  Aligned_cols=41  Identities=24%  Similarity=0.408  Sum_probs=37.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.++
T Consensus        58 g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           58 ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             CCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEECCCS
T ss_pred             CccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEeccCC
Confidence            789999999999999999999 89999999999988777664

>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=98.88  E-value=3.9e-09  Score=68.08  Aligned_cols=44  Identities=20%  Similarity=0.391  Sum_probs=40.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        52 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2cqi_A           52 TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   95 (103)
T ss_dssp             CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCcc
Confidence            44789999999999999999999999999999999999988543

>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=98.88  E-value=2.2e-09  Score=67.17  Aligned_cols=41  Identities=27%  Similarity=0.584  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.+.
T Consensus        45 ~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           45 GHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             SSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            788999999999999999999 99999999999999888764

>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=98.88  E-value=3.1e-09  Score=69.31  Aligned_cols=43  Identities=21%  Similarity=0.264  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.++|||||+|.+.++|..|+..||+..|.|+.|.|.++.+.+
T Consensus        58 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           58 RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCC
Confidence            5689999999999999999999999999999999999998754

>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=98.88  E-value=2.3e-09  Score=71.46  Aligned_cols=45  Identities=31%  Similarity=0.450  Sum_probs=41.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+....
T Consensus        61 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  105 (126)
T 3ex7_B           61 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP  105 (126)
T ss_dssp             SSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSSC
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCCC
Confidence            788999999999999999999999999999999999998875433

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=98.88  E-value=2.3e-09  Score=74.13  Aligned_cols=43  Identities=21%  Similarity=0.474  Sum_probs=40.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|++
T Consensus       133 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          133 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             SSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             CCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCCC
Confidence            7899999999999999999999999999999999999998763

>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=98.88  E-value=1.1e-09  Score=69.02  Aligned_cols=44  Identities=27%  Similarity=0.437  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.+ |..|+..|||..+.|+.|.|.+|.+....
T Consensus        40 ~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~~~   83 (90)
T 2ki2_A           40 KKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKKSL   83 (90)
T ss_dssp             CCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC------
T ss_pred             CCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCCCC
Confidence            788999999999999 99999999999999999999988876443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.87  E-value=7.9e-10  Score=68.75  Aligned_cols=36  Identities=22%  Similarity=0.461  Sum_probs=34.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCe-eEEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR-HLIF   39 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr-~L~V   39 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+ +|+|
T Consensus        44 g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           44 GKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             TBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            78999999999999999999999999999999 8865

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.87  E-value=3.6e-09  Score=70.60  Aligned_cols=43  Identities=26%  Similarity=0.357  Sum_probs=40.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.+..
T Consensus        73 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  115 (124)
T 2kt5_A           73 GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  115 (124)
T ss_dssp             SSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTT
T ss_pred             CCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            6789999999999999999999999999999999999998753

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.87  E-value=1.6e-09  Score=69.35  Aligned_cols=42  Identities=24%  Similarity=0.409  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCee----EEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRH----LIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~----L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.    |+|.++.+.
T Consensus        49 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           49 GIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             CCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             CCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCC
Confidence            788999999999999999999999999999999    988888764

>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=98.87  E-value=2.2e-09  Score=69.39  Aligned_cols=44  Identities=30%  Similarity=0.471  Sum_probs=40.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCC---eeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYG---RHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~g---r~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+..|||..+.|   +.|.|.++.+.+.
T Consensus        53 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~   99 (105)
T 2dnh_A           53 GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE   99 (105)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCC
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCcc
Confidence            6789999999999999999999999999998   9999999987643

>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=98.87  E-value=3e-09  Score=67.47  Aligned_cols=44  Identities=27%  Similarity=0.433  Sum_probs=40.2

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCC-CeeCCeeEEEEeeecccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVAHDQIISI   49 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng-~~l~gr~L~V~~a~~~~~k~   49 (112)
                      ++|||||+|.+.++|..|+..||| ..|.|+.|.|.++.++....
T Consensus        43 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   87 (93)
T 2cqh_A           43 KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLRS   87 (93)
T ss_dssp             ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCccccC
Confidence            589999999999999999999999 99999999999998865543

>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=98.85  E-value=3.9e-09  Score=68.28  Aligned_cols=44  Identities=27%  Similarity=0.419  Sum_probs=40.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCee---CCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHL---YGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l---~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+..|||..+   .|+.|.|.++.+...
T Consensus        52 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           52 GMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR   98 (106)
T ss_dssp             CSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCcccc
Confidence            78999999999999999999999999988   899999999987643

>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=98.85  E-value=5.1e-09  Score=69.12  Aligned_cols=42  Identities=19%  Similarity=0.287  Sum_probs=39.2

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      .++|||||+|.+.++|..|+..|||..|.||.|.|.++.|..
T Consensus        62 ~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           62 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            478999999999999999999999999999999999998853

>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=98.85  E-value=2.6e-09  Score=72.63  Aligned_cols=43  Identities=28%  Similarity=0.414  Sum_probs=39.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+++
T Consensus        85 g~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~~  127 (129)
T 2kxn_B           85 RRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR  127 (129)
T ss_dssp             SCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSSS
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            7899999999999999999999999999999999888887653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=4.3e-09  Score=68.92  Aligned_cols=44  Identities=20%  Similarity=0.371  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        53 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   96 (114)
T 2do0_A           53 GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP   96 (114)
T ss_dssp             CSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCCCC
T ss_pred             CCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccCCC
Confidence            67899999999999999999999999999999999999876433

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.85  E-value=3e-09  Score=72.04  Aligned_cols=45  Identities=22%  Similarity=0.419  Sum_probs=41.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.+....
T Consensus        81 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  125 (139)
T 1u6f_A           81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            678999999999999999999999999999999999999875433

>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=98.84  E-value=3e-09  Score=67.45  Aligned_cols=40  Identities=28%  Similarity=0.484  Sum_probs=37.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        54 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           54 GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            6789999999999999999999999999999999877664

>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=98.84  E-value=4e-09  Score=73.84  Aligned_cols=43  Identities=30%  Similarity=0.452  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..||..|||..|.|+.|.|.++.+..
T Consensus       111 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  153 (165)
T 1rk8_A          111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  153 (165)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC
T ss_pred             CcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            7789999999999999999999999999999999888887754

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.84  E-value=2.2e-09  Score=69.00  Aligned_cols=40  Identities=28%  Similarity=0.454  Sum_probs=36.1

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +++|||||+|.+.++|..|+..|||..|.|+.|+|.++.+
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            5789999999999999999999999999999996666554

>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=98.84  E-value=3.9e-09  Score=66.62  Aligned_cols=41  Identities=24%  Similarity=0.435  Sum_probs=37.8

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +++|||||+|.+.++|..|+..|||..+.|++|+|.++...
T Consensus        38 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A           38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            57899999999999999999999999999999999887653

>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=98.83  E-value=4.7e-09  Score=68.00  Aligned_cols=40  Identities=25%  Similarity=0.347  Sum_probs=37.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.
T Consensus        67 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           67 GRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            6789999999999999999999999999999999887764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.83  E-value=7.3e-09  Score=66.42  Aligned_cols=43  Identities=26%  Similarity=0.407  Sum_probs=39.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|...
T Consensus        49 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            3689999999999999999999999999999999999988654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.82  E-value=6e-09  Score=69.26  Aligned_cols=42  Identities=21%  Similarity=0.536  Sum_probs=39.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.+..
T Consensus        75 ~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~  116 (124)
T 2jwn_A           75 GHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNM  116 (124)
T ss_dssp             SSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCCC
T ss_pred             CCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCCC
Confidence            788999999999999999999 899999999999999887643

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.82  E-value=1.7e-09  Score=73.13  Aligned_cols=44  Identities=27%  Similarity=0.382  Sum_probs=40.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCC----eeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNT----HLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~----~l~gr~L~V~~a~~~~~k   48 (112)
                      |++||||||+|.+. +|..|+..|||.    .|.||.|.|.++.|....
T Consensus        64 g~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~~  111 (131)
T 2m2b_A           64 QLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKRD  111 (131)
T ss_dssp             SSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCCC
T ss_pred             CCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCCC
Confidence            88999999999999 999999999999    999999999999886544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.81  E-value=1.8e-09  Score=69.66  Aligned_cols=43  Identities=26%  Similarity=0.418  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCe-eCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTH-LYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~-l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||.. |.|+.|.|.++.+..
T Consensus        48 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           48 GVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             CCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCC
Confidence            6789999999999999999999999999 999999888887754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=98.81  E-value=3.8e-09  Score=69.67  Aligned_cols=39  Identities=21%  Similarity=0.323  Sum_probs=36.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++
T Consensus        79 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           79 SLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             SCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            788999999999999999999999999999999977665

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

Probab=98.81  E-value=6e-09  Score=70.08  Aligned_cols=39  Identities=36%  Similarity=0.755  Sum_probs=36.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.+|
T Consensus       102 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A          102 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             CCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            789999999999999999999999999999999988764

>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=98.81  E-value=3.7e-09  Score=71.58  Aligned_cols=43  Identities=23%  Similarity=0.333  Sum_probs=39.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++++||+||+|.+.++|..|+..|||..+.||.|.|.++.+..
T Consensus        68 ~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~~~~  110 (118)
T 3ue2_A           68 AEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQER  110 (118)
T ss_dssp             CEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECHHH
T ss_pred             CcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcChHh
Confidence            4567999999999999999999999999999999999887643

>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=98.80  E-value=6.9e-09  Score=71.69  Aligned_cols=43  Identities=28%  Similarity=0.393  Sum_probs=40.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+
T Consensus        78 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z           78 KTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             CccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            6789999999999999999999999999999999999988753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.80  E-value=3.4e-09  Score=64.57  Aligned_cols=38  Identities=21%  Similarity=0.410  Sum_probs=35.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|+.|+. |||..|.|+.|.|.+|
T Consensus        38 ~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           38 NRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             TTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            7889999999999999999998 9999999999977654

>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=98.80  E-value=2.6e-09  Score=70.19  Aligned_cols=42  Identities=24%  Similarity=0.438  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.+..
T Consensus        64 g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~  105 (114)
T 2cq4_A           64 RRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEK  105 (114)
T ss_dssp             SSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHHH
T ss_pred             CccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCCc
Confidence            788999999999999999999 999999999999888877643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.80  E-value=3.1e-09  Score=70.95  Aligned_cols=41  Identities=24%  Similarity=0.314  Sum_probs=37.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+. |||..|.||.|.|.++.+.
T Consensus        58 g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           58 GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEEEEECHH
T ss_pred             CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEEEECCHH
Confidence            7889999999999999999999 9999999999977766543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.79  E-value=6.9e-09  Score=69.12  Aligned_cols=41  Identities=22%  Similarity=0.352  Sum_probs=37.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+ .+|+..|.||.|.|..+.+.
T Consensus        53 g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           53 GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            889999999999999999999 69999999999988777653

>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=98.79  E-value=1.1e-08  Score=66.00  Aligned_cols=40  Identities=25%  Similarity=0.535  Sum_probs=37.3

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+.
T Consensus        56 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            4899999999999999999999999999999999888764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.78  E-value=8e-09  Score=70.06  Aligned_cols=41  Identities=34%  Similarity=0.683  Sum_probs=38.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |.++|||||+|.+.++|..|+..|||..+.|+.|.|.+|.+
T Consensus       126 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          126 GSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            78899999999999999999999999999999998888753

>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=98.77  E-value=4e-09  Score=70.55  Aligned_cols=40  Identities=20%  Similarity=0.266  Sum_probs=36.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..||. |||..|.|+.|.|.++.+
T Consensus        64 g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           64 GKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             SSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             CCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECCH
Confidence            7889999999999999999999 999999999996665544

>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=98.77  E-value=2.3e-09  Score=70.15  Aligned_cols=41  Identities=27%  Similarity=0.332  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+. +||..|.||.|.|.++.+.
T Consensus        52 g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           52 GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCCEECCHH
T ss_pred             CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEEEECCHH
Confidence            7899999999999999999999 9999999999966665543

>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=98.77  E-value=4.8e-09  Score=69.34  Aligned_cols=41  Identities=22%  Similarity=0.357  Sum_probs=36.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..||.. ||..|.|+.|.|.++.+.
T Consensus        54 g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           54 GQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             SSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEEECHH
T ss_pred             CCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEECCHH
Confidence            78999999999999999999987 999999999977666553

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.76  E-value=8.2e-09  Score=68.41  Aligned_cols=42  Identities=19%  Similarity=0.225  Sum_probs=37.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCe--eCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTH--LYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~--l~gr~L~V~~a~~~~   46 (112)
                      ++||||||+|.+.++|..|+..|||..  |.||+|.|.++.++.
T Consensus        55 ~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k~   98 (100)
T 3r27_A           55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK   98 (100)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEeccccc
Confidence            468999999999999999999999976  779999999988753

>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=98.76  E-value=1.6e-08  Score=68.58  Aligned_cols=67  Identities=22%  Similarity=0.406  Sum_probs=53.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc-----cccCcccchhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS-----IIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k-----~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      |+++|||||+|.+.++|..|+..|||..+.|+.|.|.++.|....     .++.   .+++..+.++|.++..+.
T Consensus        41 ~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~---nl~~~~t~~~l~~~f~~~  112 (167)
T 1fxl_A           41 GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVS---GLPKTMTQKELEQLFSQY  112 (167)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCGGGTTCEEEEE---SCCTTCCHHHHHHHHGGG
T ss_pred             CcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcccCCCCcEEEC---CCCCcCCHHHHHHHHHhc
Confidence            788999999999999999999999999999999999999876433     2222   455556666777666543

>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=98.75  E-value=9.7e-09  Score=65.62  Aligned_cols=41  Identities=24%  Similarity=0.301  Sum_probs=38.2

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeC--CeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLY--GRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~--gr~L~V~~a~~~~   46 (112)
                      .+|||||+|.+.++|..|+..|||..|.  |+.|.|.++.|++
T Consensus        52 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           52 GDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             SSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            3799999999999999999999999999  9999999998864

>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=98.75  E-value=7.9e-09  Score=67.73  Aligned_cols=42  Identities=12%  Similarity=0.307  Sum_probs=38.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCee--------CCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHL--------YGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l--------~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|        .++.|.|.++.|.
T Consensus        63 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           63 GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             SCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            67899999999999999999999999999        5788988888765

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.75  E-value=5.3e-09  Score=71.52  Aligned_cols=43  Identities=35%  Similarity=0.572  Sum_probs=40.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+
T Consensus        86 g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           86 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             SSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            7899999999999999999999999999999999999988753

>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=98.75  E-value=1.5e-08  Score=66.17  Aligned_cols=42  Identities=19%  Similarity=0.368  Sum_probs=38.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .+|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+.
T Consensus        60 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           60 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            379999999999999999999999999999999999888643

>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=98.75  E-value=8.1e-09  Score=66.21  Aligned_cols=42  Identities=29%  Similarity=0.402  Sum_probs=38.9

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+..
T Consensus        49 ~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            458999999999999999999999999999999999998754

>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=98.75  E-value=1.5e-08  Score=66.97  Aligned_cols=43  Identities=21%  Similarity=0.186  Sum_probs=39.0

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .++|||||+|.+.++|..|+..|||..|.|+.|.|.++....+
T Consensus        44 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   86 (111)
T 1whx_A           44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVF   86 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTTT
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCcc
Confidence            4689999999999999999999999999999999998876533

>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=98.74  E-value=9.6e-09  Score=70.53  Aligned_cols=41  Identities=27%  Similarity=0.490  Sum_probs=38.5

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|++
T Consensus       109 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A          109 PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            68999999999999999999999999999999999988764

>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=98.74  E-value=3.8e-09  Score=73.07  Aligned_cols=41  Identities=24%  Similarity=0.309  Sum_probs=38.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+. |||..|.||.|.|.++.+.
T Consensus        85 g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           85 GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEEEECCHH
T ss_pred             CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEEEECChH
Confidence            7899999999999999999999 9999999999988877654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=1.2e-08  Score=67.09  Aligned_cols=41  Identities=24%  Similarity=0.362  Sum_probs=38.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..||+ .|.|+.|.|.++.+.
T Consensus        56 ~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           56 GKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             CCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             CccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEcccC
Confidence            78999999999999999999999999 899999999998663

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.74  E-value=1.3e-08  Score=67.03  Aligned_cols=40  Identities=25%  Similarity=0.378  Sum_probs=37.6

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  104 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA  104 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCCC
Confidence            7999999999999999999999999999999999888754

>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=98.74  E-value=2.1e-08  Score=65.94  Aligned_cols=45  Identities=16%  Similarity=0.246  Sum_probs=39.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhh--CCCeeCCeeEEEEeeeccccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEAL--SNTHLYGRHLIFSVAHDQIISII   50 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~l--ng~~l~gr~L~V~~a~~~~~k~~   50 (112)
                      .||||||+|.+.++|..|+..|  ++..|.|++|.|.++.++..+..
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~~~~   96 (101)
T 2cq1_A           50 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTS   96 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSCCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccCcCC
Confidence            4899999999999999999977  56789999999999998776643

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=1.2e-08  Score=67.09  Aligned_cols=43  Identities=26%  Similarity=0.322  Sum_probs=39.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+.. ||..|.|+.|.|.++.|+..
T Consensus        66 g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~  108 (116)
T 1x4b_A           66 KRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREE  108 (116)
T ss_dssp             SSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSSCCC
T ss_pred             CCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCCCcc
Confidence            78899999999999999999998 99999999999999988643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=1.2e-08  Score=64.32  Aligned_cols=42  Identities=19%  Similarity=0.366  Sum_probs=38.7

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      +|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+..
T Consensus        42 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~   83 (90)
T 2dnq_A           42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKA   83 (90)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCCC
Confidence            799999999999999999999999999999999999876543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.74  E-value=1.5e-08  Score=66.56  Aligned_cols=42  Identities=21%  Similarity=0.340  Sum_probs=38.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..+ +..|.|+.|.|.++.++.
T Consensus        64 g~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a~~~~  105 (109)
T 2rs2_A           64 KRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVAFPRR  105 (109)
T ss_dssp             CCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEECCCCC
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEccCCC
Confidence            789999999999999999999986 599999999999998764

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

Probab=98.21  E-value=1.1e-09  Score=72.27  Aligned_cols=43  Identities=21%  Similarity=0.305  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.++.
T Consensus        54 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   96 (116)
T 2lcw_A           54 GKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA   96 (116)
Confidence            7789999999999999999999999999999999888887754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.73  E-value=5.4e-09  Score=67.63  Aligned_cols=43  Identities=21%  Similarity=0.320  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |.++|||||+|.+.++|..|+.. |+..|.|+.|.|.++.|+..
T Consensus        55 g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           55 NQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             CCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCSCCSSC
T ss_pred             CCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEccCCCC
Confidence            78899999999999999999998 99999999998888877643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.73  E-value=5.6e-09  Score=68.59  Aligned_cols=38  Identities=16%  Similarity=0.237  Sum_probs=34.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |.++|||||+|.+.++|..|+. +||..|.|+.|.|.++
T Consensus        49 g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A           49 KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            7899999999999999999999 8999999999955443

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.72  E-value=9.6e-09  Score=67.96  Aligned_cols=40  Identities=18%  Similarity=0.384  Sum_probs=37.3

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      .|||||.|.+.++|.+|++.|||..|.||.|+|++|..++
T Consensus        46 gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~s   85 (96)
T 2diu_A           46 GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNR   85 (96)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSC
T ss_pred             cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCc
Confidence            3999999999999999999999999999999999988754

>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=98.72  E-value=2.3e-08  Score=68.15  Aligned_cols=66  Identities=21%  Similarity=0.385  Sum_probs=52.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc-----cccCcccchhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS-----IIAPTFQVMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k-----~~~~~~~~~~~a~~~~~~~~~~~~   72 (112)
                      |.++|||||+|.+.++|..|+..|||..+.|+.|.|.++.|....     .++.   .+++..++++|.++..+
T Consensus        42 ~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~~~~~~~l~v~---nl~~~~t~~~l~~~f~~  112 (168)
T 1b7f_A           42 GYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVT---NLPRTITDDQLDTIFGK  112 (168)
T ss_dssp             TEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSSTTTTCEEEEE---SCCTTCCHHHHHHHHTS
T ss_pred             CccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcccCCCCCEEEe---CCCCCCCHHHHHHhhhc
Confidence            778999999999999999999999999999999999999875433     2222   45566666667666644

>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=98.72  E-value=1.1e-08  Score=66.54  Aligned_cols=43  Identities=21%  Similarity=0.322  Sum_probs=39.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|..|+.. |+..|.||.|.|.++.+..+
T Consensus        54 g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~~~~~~~   96 (104)
T 1wg5_A           54 GRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFKSSRAEV   96 (104)
T ss_dssp             SCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEEECTTTS
T ss_pred             CCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEECCHHHH
Confidence            88999999999999999999998 99999999999998877543

>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=98.72  E-value=1.7e-08  Score=81.30  Aligned_cols=49  Identities=24%  Similarity=0.548  Sum_probs=45.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccC
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAP   52 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~   52 (112)
                      |+++|||||+|.+.++|..||..|||..|.|+.|.|.++.+.....|.+
T Consensus       141 g~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~~~~~~  189 (437)
T 3pgw_S          141 GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRP  189 (437)
T ss_pred             CCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCCCCCC
Confidence            7889999999999999999999999999999999999999987766543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.71  E-value=2.7e-08  Score=62.96  Aligned_cols=42  Identities=21%  Similarity=0.445  Sum_probs=38.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .+|||||+|.+.++|..|+..|||..|.|+.|.|.++.++..
T Consensus        43 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   84 (92)
T 2dgt_A           43 VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLR   84 (92)
T ss_dssp             CSSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCCS
T ss_pred             ECCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCCC
Confidence            368999999999999999999999999999999999988643

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.71  E-value=2.5e-08  Score=62.86  Aligned_cols=42  Identities=17%  Similarity=0.344  Sum_probs=38.5

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .+|||||+|.+.++|..|+..|||..|.|+.|.|.++.+...
T Consensus        42 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A           42 VKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             CSSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ECCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            367999999999999999999999999999999999988643

>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=98.71  E-value=5.6e-09  Score=77.38  Aligned_cols=42  Identities=21%  Similarity=0.452  Sum_probs=39.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |++||||||+|.+.++|..||..|||..|.|+.|+|.++.+.
T Consensus       109 g~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~~  150 (229)
T 3q2s_C          109 GQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ  150 (229)
T ss_dssp             CCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCHH
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCCC
Confidence            889999999999999999999999999999999988777654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.70  E-value=1.3e-08  Score=72.15  Aligned_cols=45  Identities=29%  Similarity=0.502  Sum_probs=41.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+..
T Consensus       164 g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMP  208 (216)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSST
T ss_pred             CCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCCC
Confidence            778999999999999999999999999999999999999886543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=1.1e-08  Score=68.20  Aligned_cols=44  Identities=16%  Similarity=0.293  Sum_probs=38.3

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCC--CeeCCeeEEEEeeecccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSN--THLYGRHLIFSVAHDQIISI   49 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng--~~l~gr~L~V~~a~~~~~k~   49 (112)
                      .||||||+|.+.++|..|+..|++  ..|.|++|+|.++.++..+.
T Consensus        51 ~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~~~   96 (105)
T 1sjq_A           51 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT   96 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCCCc
Confidence            489999999999999999998864  78999999998888765553

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.70  E-value=7.9e-09  Score=66.37  Aligned_cols=41  Identities=24%  Similarity=0.467  Sum_probs=38.4

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+.+
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            68999999999999999999999999999999999888754

>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=98.70  E-value=2.6e-08  Score=64.36  Aligned_cols=43  Identities=19%  Similarity=0.351  Sum_probs=39.0

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      .+|||||+|.+.++|..|+..|||..|.|+.|.|.++.+....
T Consensus        44 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~   86 (103)
T 2dgu_A           44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQK   86 (103)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCccc
Confidence            4789999999999999999999999999999999999875433

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=98.70  E-value=3.1e-08  Score=68.35  Aligned_cols=68  Identities=16%  Similarity=0.347  Sum_probs=51.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCccc----chhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQ----VMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~----~~~~a~~~~~~~~~~~~   72 (112)
                      |.++|||||+|.+.++|..|++ |||..|.|+.|.|.++.+.......+...    .+++..++++|.++...
T Consensus        51 ~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~  122 (175)
T 1fje_B           51 GTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFED  122 (175)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTT
T ss_pred             CccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            7899999999999999999994 99999999999999998754331111111    45666666666666554

>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=98.70  E-value=1.3e-08  Score=69.56  Aligned_cols=41  Identities=22%  Similarity=0.380  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+. ++|..|.|+.|.|.+|.|+
T Consensus       126 g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          126 GQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             STTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            7899999999999999999998 8999999999999998875

>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=98.70  E-value=1.5e-08  Score=68.23  Aligned_cols=42  Identities=17%  Similarity=0.184  Sum_probs=38.3

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      ++||+||+|.+.++|..|+..|||..+.||.|.|.++.+..+
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~~~y   95 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTY   95 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECHHHH
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcHHHH
Confidence            589999999999999999999999999999999988876443

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.69  E-value=1.2e-08  Score=71.43  Aligned_cols=43  Identities=28%  Similarity=0.454  Sum_probs=40.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|+.
T Consensus       153 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          153 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             CSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            7789999999999999999999999999999999999998864

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.69  E-value=1.5e-08  Score=64.85  Aligned_cols=41  Identities=24%  Similarity=0.524  Sum_probs=37.8

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+..
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            47999999999999999999999999999999998887753

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.69  E-value=1.3e-08  Score=73.42  Aligned_cols=41  Identities=22%  Similarity=0.470  Sum_probs=36.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.|
T Consensus       140 ~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          140 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45799999999999999999999999999999996655544

>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=98.68  E-value=1.6e-08  Score=66.88  Aligned_cols=41  Identities=24%  Similarity=0.415  Sum_probs=36.0

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCC--eeCCeeEEEEeeecc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNT--HLYGRHLIFSVAHDQ   45 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~--~l~gr~L~V~~a~~~   45 (112)
                      +.+|||||+|.+.++|..|+..||+.  .|.||+|.|.+|.+.
T Consensus        50 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~   92 (102)
T 1x4d_A           50 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   92 (102)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCC
Confidence            35799999999999999999999864  599999999988753

>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=98.68  E-value=1e-08  Score=67.02  Aligned_cols=42  Identities=24%  Similarity=0.250  Sum_probs=38.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|| .+|+..|.||.|.|..+.+..
T Consensus        52 g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           52 GRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             SCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEEECCCC
T ss_pred             CCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEECCCCC
Confidence            789999999999999999999 479999999999998887653

>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=98.68  E-value=1.4e-08  Score=66.40  Aligned_cols=41  Identities=29%  Similarity=0.503  Sum_probs=37.8

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.+
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            58999999999999999999999999999999999987543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=98.68  E-value=5.3e-08  Score=65.92  Aligned_cols=69  Identities=22%  Similarity=0.280  Sum_probs=52.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCccc----chhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQ----VMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~----~~~~a~~~~~~~~~~~~   72 (112)
                      |+++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+.......+...    .+++..+.++|.++..+
T Consensus        38 ~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~  110 (166)
T 3md3_A           38 NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD  110 (166)
T ss_dssp             -CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTT
T ss_pred             CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhc
Confidence            6789999999999999999999999999999999999997754332221111    45666677777766644

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.68  E-value=3.4e-09  Score=66.04  Aligned_cols=38  Identities=24%  Similarity=0.364  Sum_probs=35.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEe
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV   41 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~   41 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|+|++
T Consensus        44 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A           44 NKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            78899999999999999999999999999999995543

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=98.67  E-value=1.6e-08  Score=69.39  Aligned_cols=39  Identities=31%  Similarity=0.543  Sum_probs=37.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|
T Consensus       133 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          133 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             CSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            778999999999999999999999999999999988876

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.67  E-value=1.1e-08  Score=62.40  Aligned_cols=38  Identities=24%  Similarity=0.386  Sum_probs=35.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..++ ..+.|+.|.|.+|
T Consensus        39 ~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           39 KRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             SSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            7889999999999999999999999 9999999988765

>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=98.67  E-value=2.5e-08  Score=61.93  Aligned_cols=37  Identities=27%  Similarity=0.376  Sum_probs=34.0

Q ss_pred             CcceEEEEeCCHHHHHHHHHhh-CCCeeCCeeEEEEee
Q 036201            6 HRGFAFVEYVTKQEAQNALEAL-SNTHLYGRHLIFSVA   42 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~l-ng~~l~gr~L~V~~a   42 (112)
                      ++|||||+|.+.++|..|+..| ||..+.|+.|.|.++
T Consensus        47 ~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           47 RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            5799999999999999999999 999999999977665

>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=98.66  E-value=1.6e-08  Score=68.13  Aligned_cols=43  Identities=16%  Similarity=0.240  Sum_probs=37.5

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCC--CeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSN--THLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng--~~l~gr~L~V~~a~~~~~   47 (112)
                      ++||||||+|.+.++|..|+..||+  ..|.||+|+|.++.+...
T Consensus        60 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccc
Confidence            5789999999999999999998864  569999999999987543

>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=98.66  E-value=2.5e-08  Score=67.48  Aligned_cols=40  Identities=18%  Similarity=0.348  Sum_probs=36.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCee-----CCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHL-----YGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l-----~gr~L~V~~a~~~   45 (112)
                      .||||||+|.+.++|..|+..|||..|     .|+.|.|+++.+.
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV  106 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEecccC
Confidence            489999999999999999999999998     6899999998843

>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=98.64  E-value=3.9e-08  Score=64.19  Aligned_cols=39  Identities=26%  Similarity=0.347  Sum_probs=36.9

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCC-----eeEEEEeeeccc
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYG-----RHLIFSVAHDQI   46 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~g-----r~L~V~~a~~~~   46 (112)
                      |||||+|.+.++|..||..|||..|.|     +.|.|.++.|+.
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRS   94 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCS
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCC
Confidence            999999999999999999999999999     999999988854

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.63  E-value=4.4e-08  Score=69.92  Aligned_cols=43  Identities=26%  Similarity=0.357  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+..
T Consensus       126 g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~~  168 (177)
T 2f3j_A          126 GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  168 (177)
T ss_dssp             SSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSGG
T ss_pred             CCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            7789999999999999999999999999999999999987754

>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=98.63  E-value=2.7e-08  Score=67.61  Aligned_cols=44  Identities=16%  Similarity=0.293  Sum_probs=39.5

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCC--CeeCCeeEEEEeeecccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSN--THLYGRHLIFSVAHDQIISI   49 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng--~~l~gr~L~V~~a~~~~~k~   49 (112)
                      .||||||+|.+.++|..|+..|++  ..|.|++|+|.++.++..+.
T Consensus        66 ~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~~~  111 (119)
T 2ad9_A           66 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKT  111 (119)
T ss_dssp             GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCCCc
Confidence            379999999999999999999884  68999999999999877664

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.62  E-value=4.6e-08  Score=64.41  Aligned_cols=43  Identities=26%  Similarity=0.221  Sum_probs=37.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      ++++|||||+|.+.++|..|+..+++  +.|+.|+|.++.+++..
T Consensus        51 ~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           51 SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            57899999999999999999998554  68999999998876543

>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=98.62  E-value=2.3e-08  Score=65.94  Aligned_cols=43  Identities=16%  Similarity=0.312  Sum_probs=38.0

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCC--eeCCeeEEEEeeeccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNT--HLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~--~l~gr~L~V~~a~~~~~k   48 (112)
                      .||||||+|.+.++|..|+..|++.  .|.|++|.|.++.++..+
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~~   94 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCcccc
Confidence            4899999999999999999988764  589999999999887655

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=98.62  E-value=5.2e-08  Score=60.56  Aligned_cols=36  Identities=25%  Similarity=0.476  Sum_probs=33.4

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEe
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV   41 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~   41 (112)
                      +++|||||+|.+.++|..|+ .|||..|.|+.|+|.+
T Consensus        51 ~~kg~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           51 QDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             SSSSEEEEEESSHHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             CCCcEEEEEcCCHHHHHHHH-hcCCCEECCeEEEEeC
Confidence            45899999999999999999 9999999999998863

>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=98.61  E-value=4.4e-08  Score=61.13  Aligned_cols=38  Identities=26%  Similarity=0.452  Sum_probs=34.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+. +++..|.|+.|.|.+|
T Consensus        50 g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           50 GRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             CCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            7889999999999999999996 4888999999988654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=98.61  E-value=4.6e-08  Score=72.91  Aligned_cols=41  Identities=24%  Similarity=0.349  Sum_probs=38.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.|+
T Consensus       251 g~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          251 SFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             -CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            678999999999999999999 99999999999999998875

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=98.60  E-value=7.7e-08  Score=65.89  Aligned_cols=66  Identities=20%  Similarity=0.322  Sum_probs=51.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc-----ccccCcccchhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII-----SIIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~-----k~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      ++++|||||+|.+.++|..|+ .|||..+.|+.|.|.++.+...     ..++.   .+++.-++++|.++..+.
T Consensus        48 ~~~~g~afV~f~~~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~~~~~~~l~v~---nlp~~~t~~~l~~~f~~~  118 (172)
T 2g4b_A           48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIG---GLPNYLNDDQVKELLTSF  118 (172)
T ss_dssp             ETTTTEEEEEESSHHHHHHHG-GGTTCEETTEECEEECCSSCCCCTTTTCEEEE---CCCTTCCHHHHHHHHHTT
T ss_pred             cCCCCEEEEEeCCHHHHHHHH-HhCCcEecCceeeecCCcccCCCCCCCEEEEE---cCCCcCCHHHHHHHHHhc
Confidence            567999999999999999999 8999999999999998876432     23333   466666777777776643

>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=98.59  E-value=5.4e-08  Score=69.73  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=38.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a~~~~   46 (112)
                      .++|||||+|.+.++|..|+..|||..|+|  ++|+|.++.+..
T Consensus        82 ~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~  125 (164)
T 1sjr_A           82 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  125 (164)
T ss_dssp             SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSS
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCc
Confidence            467999999999999999999999999976  999999999864

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.59  E-value=7.5e-08  Score=61.91  Aligned_cols=41  Identities=17%  Similarity=0.397  Sum_probs=37.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+.  ++..|.|+.|.|.++.++.
T Consensus        54 g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a~~~~   94 (103)
T 2cqg_A           54 GHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQ   94 (103)
T ss_dssp             CSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCCTTC
T ss_pred             CCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEecCCCC
Confidence            7889999999999999999998  4789999999999888753

>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=98.59  E-value=2.5e-08  Score=60.50  Aligned_cols=38  Identities=18%  Similarity=0.352  Sum_probs=34.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+.. ++..+.|+.|.|.+|
T Consensus        38 ~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           38 NKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             SSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            78999999999999999999985 899999999977654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.58  E-value=6.9e-08  Score=66.69  Aligned_cols=43  Identities=21%  Similarity=0.339  Sum_probs=39.0

Q ss_pred             CCcce-EEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEeeecccc
Q 036201            5 NHRGF-AFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGf-gFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a~~~~~   47 (112)
                      +++|| |||+|.+.++|..|+..|||..|+|  ++|+|.|+.+...
T Consensus        63 ~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~l  108 (130)
T 3zzy_A           63 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  108 (130)
T ss_dssp             ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSSC
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCce
Confidence            35788 9999999999999999999999998  9999999988643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=98.56  E-value=1.1e-07  Score=68.57  Aligned_cols=67  Identities=13%  Similarity=0.261  Sum_probs=53.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc-------cccCcccchhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS-------IIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k-------~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      |+++|||||+|.+.++|..|+..+|+..+.|+.|+|.++.+....       +++.   .+++..++++|.++..+.
T Consensus        54 g~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~l~v~---nl~~~~t~~~l~~~F~~~  127 (213)
T 4f02_A           54 RRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIK---NLDKSIDNKALYDTFSAF  127 (213)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHHHHCTTEEEEE---SCCTTCCHHHHHHHHGGG
T ss_pred             CCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccccccccccccccceEC---CcccccHHHHHHHHHhhc
Confidence            789999999999999999999999999999999999988765432       3333   466666777777666543

>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=98.56  E-value=7e-08  Score=71.65  Aligned_cols=42  Identities=33%  Similarity=0.455  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|.
T Consensus       223 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~  264 (284)
T 3smz_A          223 GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG  264 (284)
T ss_dssp             CCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             CCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCC
Confidence            778999999999999999999999999999999977777664

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=98.54  E-value=9.7e-08  Score=66.76  Aligned_cols=41  Identities=27%  Similarity=0.497  Sum_probs=38.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ++++|||||+|.+.++|..|+ .|||..|.|+.|.|.++.+.
T Consensus        48 ~~~~g~afV~F~~~~~A~~Al-~l~g~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           48 NQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             ETTTTEEEEEESCSHHHHHHG-GGTTEEETTEEEEEECCCCC
T ss_pred             cCCCCEEEEEeCCHHHHHHHH-HhcCCEEcCceEEEeCCCCC
Confidence            678999999999999999999 89999999999999998764

>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=98.54  E-value=1.1e-07  Score=70.49  Aligned_cols=43  Identities=26%  Similarity=0.344  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+..
T Consensus        49 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   91 (282)
T 3pgw_A           49 LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   91 (282)
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEEeccCc
Confidence            7789999999999999999999999999999999999997654

>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=98.54  E-value=2.2e-08  Score=68.56  Aligned_cols=41  Identities=22%  Similarity=0.323  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+.. ++..|.||.|.|.++.+.
T Consensus        81 GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~~a~~~  121 (126)
T 2hgm_A           81 GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVFKSSQE  121 (126)
T ss_dssp             SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCEEECHH
T ss_pred             CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEEECCHH
Confidence            88999999999999999999985 779999999988777654

>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=98.53  E-value=7.1e-08  Score=65.68  Aligned_cols=39  Identities=44%  Similarity=0.622  Sum_probs=36.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a   42 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|  ++|.|.+|
T Consensus       128 ~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          128 GRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            6789999999999999999999999999988  99988765

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=98.53  E-value=1e-07  Score=67.46  Aligned_cols=43  Identities=37%  Similarity=0.511  Sum_probs=38.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+..
T Consensus        67 g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~  109 (216)
T 2qfj_A           67 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIG  109 (216)
T ss_dssp             -CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCG
T ss_pred             CccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCcc
Confidence            7789999999999999999999999999999999998876643

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=98.52  E-value=1.2e-07  Score=68.85  Aligned_cols=40  Identities=23%  Similarity=0.422  Sum_probs=37.4

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      .++|||||+|.+.++|..||..|||..|.|+.|.|.++..
T Consensus        40 ~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A           40 SKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             TSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            3589999999999999999999999999999999999864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.51  E-value=2.3e-08  Score=68.02  Aligned_cols=40  Identities=30%  Similarity=0.300  Sum_probs=35.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+.. |+..|.||.|.|..+.+
T Consensus        65 gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~~a~~  104 (123)
T 2dha_A           65 GRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELFRSTA  104 (123)
T ss_dssp             SCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCEEECH
T ss_pred             CCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEEECCH
Confidence            88999999999999999999986 99999999996666554

>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=98.51  E-value=2.2e-08  Score=69.51  Aligned_cols=42  Identities=24%  Similarity=0.252  Sum_probs=38.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|| .+|+..|.||.|.|..+.+..
T Consensus        83 g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           83 GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSC
T ss_pred             CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCC
Confidence            789999999999999999999 789999999999888887754

>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=98.51  E-value=8.6e-08  Score=64.93  Aligned_cols=39  Identities=26%  Similarity=0.492  Sum_probs=35.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCee--EEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRH--LIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~--L~V~~a   42 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.  |.|+||
T Consensus       127 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          127 GVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            678999999999999999999999999999975  766654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.51  E-value=1.3e-07  Score=64.58  Aligned_cols=40  Identities=30%  Similarity=0.357  Sum_probs=36.8

Q ss_pred             cce-EEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEeeeccc
Q 036201            7 RGF-AFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVAHDQI   46 (112)
Q Consensus         7 rGf-gFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a~~~~   46 (112)
                      .|| |||+|.+.++|..|+..|||..|+|  +.|+|.+|.|..
T Consensus        61 ~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            386 9999999999999999999999998  699999998864

>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=98.48  E-value=1.2e-07  Score=64.79  Aligned_cols=39  Identities=31%  Similarity=0.517  Sum_probs=35.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC---CeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY---GRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~---gr~L~V~~a   42 (112)
                      |.++|||||+|.+.++|..|+..|||..+.   ++.|.|.+|
T Consensus       133 g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          133 GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEEC
T ss_pred             CCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEec
Confidence            778999999999999999999999998777   499988776

>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=98.48  E-value=1.4e-07  Score=65.77  Aligned_cols=41  Identities=22%  Similarity=0.377  Sum_probs=36.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+.. +|..|.|+.|.|.++.|+
T Consensus       143 g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k  183 (196)
T 1l3k_A          143 GKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSK  183 (196)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC--
T ss_pred             CCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCCh
Confidence            77899999999999999999986 899999999988777764

>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=98.46  E-value=1.1e-07  Score=68.99  Aligned_cols=43  Identities=23%  Similarity=0.333  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++||+||+|.+.++|..|+..|||..+.||.|.|.++....
T Consensus       172 ~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~  214 (222)
T 3dxb_A          172 AEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQER  214 (222)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHH
T ss_pred             cCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHH
Confidence            6889999999999999999999999999999999999887543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.45  E-value=2.9e-07  Score=58.26  Aligned_cols=40  Identities=25%  Similarity=0.314  Sum_probs=36.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ..|.|||+|.+.++|..|+..|||..|.|+.|.|.++.|.
T Consensus        53 ~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           53 ETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             SSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            3456999999999999999999999999999999998875

>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=98.45  E-value=2.7e-07  Score=64.34  Aligned_cols=65  Identities=26%  Similarity=0.324  Sum_probs=49.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc-----------cccCcccchhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS-----------IIAPTFQVMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k-----------~~~~~~~~~~~a~~~~~~~~~~~~   72 (112)
                      |.++|||||+|.+.++|..|+.. ++..|.|+.|.|.++.+....           +++.   .+++.-++++|.++..+
T Consensus        52 g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~---nLp~~~t~~~l~~~F~~  127 (196)
T 1l3k_A           52 KRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG---GIKEDTEEHHLRDYFEQ  127 (196)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC-----------CCSEEEEE---CCTTTCCHHHHHHHHTT
T ss_pred             CCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecccCcccccccccCCCcceEEEe---CCCCCCCHHHHHHHHhc
Confidence            77899999999999999999986 999999999999998775322           1222   45666677777776654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.44  E-value=6.5e-08  Score=62.13  Aligned_cols=40  Identities=25%  Similarity=0.511  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+.  +|..|.|+.|.|.++.+.
T Consensus        47 g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~~~   86 (102)
T 2xs2_A           47 GVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAIRK   86 (102)
T ss_dssp             SCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEEEC
T ss_pred             CCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECCcC
Confidence            6789999999999999999998  999999999988888764

>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=98.42  E-value=4.3e-07  Score=67.36  Aligned_cols=65  Identities=20%  Similarity=0.300  Sum_probs=48.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCcccchhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~   72 (112)
                      ++++|||||+|.+.++|..|+..|||..+.|+.|.|.++.+. ...++.   .+++.-+.++|.++...
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~~-~~l~v~---nlp~~~t~~~l~~~f~~  118 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD-ALLCVA---NLPPSLTQQQFEELVRP  118 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCS-CEEEEE---SCCTTCCHHHHHHHHGG
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCCC-CEEEEc---CCCCcCCHHHHHHHHHh
Confidence            578999999999999999999999999999999999986543 223332   34455555555555443

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=98.41  E-value=4e-07  Score=67.56  Aligned_cols=65  Identities=23%  Similarity=0.291  Sum_probs=49.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccccCcccchhcccchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERAKEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~   72 (112)
                      ++++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.. .+++.   .+++..+.++|.++...
T Consensus        55 ~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~~~-~l~v~---nl~~~~t~~~l~~~F~~  119 (261)
T 3sde_A           55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA-ALTVK---NLSPVVSNELLEQAFSQ  119 (261)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCSS-EEEEE---SCCTTCCHHHHHHHHGG
T ss_pred             eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecccCC-ccccc---CCCCCCCHHHHHHHHHh
Confidence            4578999999999999999999999999999999999998732 22222   34445555555555543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.38  E-value=2.5e-07  Score=65.15  Aligned_cols=40  Identities=30%  Similarity=0.354  Sum_probs=37.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~a~~~   45 (112)
                      ++|||||+|.+.++|..|+..|||..+. |+.|.|+++.|.
T Consensus       157 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            5899999999999999999999999999 999999988875

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=98.38  E-value=3.6e-07  Score=66.44  Aligned_cols=41  Identities=29%  Similarity=0.352  Sum_probs=38.2

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEeeecc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAHDQ   45 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~a~~~   45 (112)
                      .++|||||+|.+.++|..|+..|||..+. |+.|.|+|+.|+
T Consensus       187 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          187 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            36899999999999999999999999999 999999998875

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=98.37  E-value=4.5e-07  Score=67.47  Aligned_cols=69  Identities=19%  Similarity=0.227  Sum_probs=49.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccccc----Cccc-----chhcc-cchhHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIA----PTFQ-----VMERA-KEGESLEELRAR   72 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~~----~~~~-----~~~~a-~~~~~~~~~~~~   72 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|.......    ....     .+++. .+.++|.++...
T Consensus       156 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~  234 (292)
T 2ghp_A          156 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG  234 (292)
T ss_dssp             ---CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGG
T ss_pred             CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhc
Confidence            678999999999999999999999999999999999999886433111    1101     45666 666777766654

>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=98.36  E-value=3.7e-07  Score=60.39  Aligned_cols=37  Identities=27%  Similarity=0.403  Sum_probs=32.7

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCCee-----EEEEeeec
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYGRH-----LIFSVAHD   44 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~gr~-----L~V~~a~~   44 (112)
                      |||||+|.+.++|..||..|||..|.|+.     |+|..+.|
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~   93 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP   93 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC-
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCC
Confidence            99999999999999999999999999998     66665554

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.35  E-value=3.6e-07  Score=68.83  Aligned_cols=40  Identities=30%  Similarity=0.431  Sum_probs=35.3

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCee------------CCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHL------------YGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l------------~gr~L~V~~a~~   44 (112)
                      .++|||||+|.+.++|+.|+.+|+|..|            .|+.|.|.+|.+
T Consensus       177 ~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~  228 (240)
T 3u1l_A          177 ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANE  228 (240)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC-
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccC
Confidence            3689999999999999999999999999            899997766654

>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=98.34  E-value=5.2e-07  Score=61.58  Aligned_cols=66  Identities=15%  Similarity=0.259  Sum_probs=50.8

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeC---CeeEEEEeeeccccc------cccCcccchhcccchhHHHHHHHHH
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLY---GRHLIFSVAHDQIIS------IIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~---gr~L~V~~a~~~~~k------~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      +++|||||+|.+.++|..|+..|||..+.   ++.|.|.++.+....      .++.   .+++..++++|.++..+.
T Consensus        45 ~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~---nl~~~~t~~~l~~~F~~~  119 (175)
T 3nmr_A           45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIG---MISKKCTENDIRVMFSSF  119 (175)
T ss_dssp             EEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCSCGGGSEEEEE---SCCTTCCHHHHHHHHGGG
T ss_pred             CcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccccCCCCeEEEc---CCCCcCCHHHHHHHHHhC
Confidence            78999999999999999999999998876   678888887765432      2222   466667777777776543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.33  E-value=4.5e-07  Score=59.70  Aligned_cols=39  Identities=15%  Similarity=0.245  Sum_probs=33.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|+  .++|+.|.|..+.+
T Consensus        49 g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~~~~~   87 (114)
T 2dnl_A           49 FPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCVSSPT   87 (114)
T ss_dssp             SCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEECCSS
T ss_pred             CCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEeccCCC
Confidence            6889999999999999999999985  47888888876654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=98.30  E-value=8.6e-07  Score=64.44  Aligned_cols=39  Identities=23%  Similarity=0.354  Sum_probs=37.2

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~  110 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ  110 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCc
Confidence            799999999999999999999999999999999999764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.30  E-value=7.3e-07  Score=62.71  Aligned_cols=39  Identities=23%  Similarity=0.354  Sum_probs=37.1

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +|||||+|.+.++|..|+..|||..+.|+.|.|.++.+.
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~   79 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   79 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCC
Confidence            799999999999999999999999999999999998764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.29  E-value=5.3e-07  Score=57.16  Aligned_cols=39  Identities=23%  Similarity=0.218  Sum_probs=35.0

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            9 FAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         9 fgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      ||||+|.+.++|..|+. |||..|.|+.|.|.++.++...
T Consensus        47 ~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~~~~   85 (94)
T 2e5g_A           47 FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQKEFQ   85 (94)
T ss_dssp             EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCSCCC
T ss_pred             EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcCCCC
Confidence            99999999999999999 9999999999988877765443

>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=98.27  E-value=6.9e-07  Score=60.75  Aligned_cols=65  Identities=17%  Similarity=0.228  Sum_probs=50.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc-----cccCcccchhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS-----IIAPTFQVMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k-----~~~~~~~~~~~a~~~~~~~~~~~~~   73 (112)
                      |+++|||||+|.+.++|..|+..  +..+.|+.|.|.++.+....     .++.   .+++..++++|.++..+.
T Consensus        42 g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~~~~~~~~~l~V~---nlp~~~t~~~l~~~F~~~  111 (167)
T 2cjk_A           42 GRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAIPRDEQDKTGKIFVG---GIGPDVRPKEFEEFFSQW  111 (167)
T ss_dssp             SSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECCCHHHHHHCEEEEEE---EECTTCCHHHHHHHHHTT
T ss_pred             CCccceEEEEEccHHHHHHHHhc--ccccCCeEcccccccchhhccCCCeEEEC---CCCCCCCHHHHHHHHHhC
Confidence            88999999999999999999984  67899999999988775422     3333   466667777777776643

>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=98.25  E-value=1.4e-06  Score=55.30  Aligned_cols=39  Identities=31%  Similarity=0.387  Sum_probs=29.1

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCee--CCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHL--YGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l--~gr~L~V~~a~~~~~   47 (112)
                      .+||||||+|.+.++|..    |+|..+  .|+.|.|.++.|+..
T Consensus        46 ~srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           46 PFRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             SCCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEECC----
T ss_pred             CCCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEcCCCCc
Confidence            479999999999998873    567654  599999998887643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.25  E-value=5.8e-07  Score=62.72  Aligned_cols=42  Identities=12%  Similarity=0.159  Sum_probs=34.6

Q ss_pred             CCCcceEEEEeCC----HHH----HHHHHH--hhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVT----KQE----AQNALE--ALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s----~ed----a~~Ai~--~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.|+|||||+|.+    +.+    |..|+.  .|||..|.||+|+|.+....
T Consensus        45 g~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           45 ALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILNKHS   96 (136)
T ss_dssp             CCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEECCTT
T ss_pred             CceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEECccc
Confidence            8999999999995    323    788888  78999999999999876653

>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=98.23  E-value=1.4e-06  Score=64.48  Aligned_cols=37  Identities=27%  Similarity=0.356  Sum_probs=34.5

Q ss_pred             cceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEeee
Q 036201            7 RGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAH   43 (112)
Q Consensus         7 rGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~a~   43 (112)
                      +|||||+|.+.++|..|+..|||..|. |+.|+|+|+.
T Consensus       244 ~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          244 HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            599999999999999999999999999 9999887764

>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=98.22  E-value=1.1e-06  Score=63.22  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=33.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |.++|||||+|.+.++|..|+..++ ..+.|+.|.|.++.
T Consensus       147 ~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          147 KAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILFKD  185 (193)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEETT
T ss_pred             CCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEEhH
Confidence            6789999999999999999998765 58999999776544

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.21  E-value=1.4e-06  Score=56.97  Aligned_cols=37  Identities=19%  Similarity=0.340  Sum_probs=34.6

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.+||+|.+.++|.+|+. |||..++||+|+|..+.|.
T Consensus        50 d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~LkV~lkt~d   86 (91)
T 2dnr_A           50 DKMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSPS   86 (91)
T ss_dssp             SSEEEEESSHHHHHHGGG-GTTCEETTEEEEEEECCCS
T ss_pred             CCEEEEECChHHHHHHHh-cCCeEeCCeEEEEEeCCCC
Confidence            569999999999999998 9999999999999999874

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=98.17  E-value=3.4e-06  Score=62.49  Aligned_cols=42  Identities=31%  Similarity=0.445  Sum_probs=36.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCC-CeeC---CeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSN-THLY---GRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng-~~l~---gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..||+ ..+.   +++|.|.++.+.
T Consensus       134 g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          134 GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             SCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             CCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence            77899999999999999999999954 4444   999999998774

>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=97.96  E-value=9.5e-06  Score=58.69  Aligned_cols=32  Identities=16%  Similarity=0.260  Sum_probs=29.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCe
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR   35 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr   35 (112)
                      |.++|||||+|.+.++|..||..|||..|.|+
T Consensus       162 ~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          162 SERSSSGLLEWDSKSDALETLGFLNHYQMKNP  193 (205)
T ss_dssp             SSSSEEEEEECSSHHHHHHHHHHHTTCEECCS
T ss_pred             CCCceEEEEEeCCHHHHHHHHHHhCCCCccCC
Confidence            45679999999999999999999999999987

>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=97.95  E-value=1e-05  Score=63.71  Aligned_cols=40  Identities=20%  Similarity=0.449  Sum_probs=34.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeC---Ce--eEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLY---GR--HLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~---gr--~L~V~~a~~~   45 (112)
                      +||||||+|.+.++|..|++.|||..+.   |+  .|.|+|+...
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~~~~   99 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV   99 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEECSSE
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEeecc
Confidence            6899999999999999999999999883   55  6788888543

>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=97.93  E-value=3.7e-06  Score=52.45  Aligned_cols=39  Identities=28%  Similarity=0.313  Sum_probs=31.3

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCC--eeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNT--HLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~--~l~gr~L~V~~a~~~~~   47 (112)
                      .++|||||+|.+.++|+.|    ++.  .+.|+.|.|.++.|+..
T Consensus        40 ~~~g~afV~f~~~~~a~~~----~~~~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A           40 PFRAFAFVTFADDQIAQSL----CGEDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCSCCEEECSCHHHHHHT----TTCEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEEECCHHHHHHH----hcCCceeCCEEEEEEecCCCCC
Confidence            4689999999999998753    454  45899999999888643

>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=97.64  E-value=4.5e-05  Score=50.14  Aligned_cols=34  Identities=18%  Similarity=0.294  Sum_probs=31.0

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            9 FAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         9 fgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      -+||+|.+.++|.+||. |||..++||.|+|.+-.
T Consensus        60 ~~fVtF~d~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           60 QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             cEEEEEcChHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            38999999999999998 99999999999997543

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=97.35  E-value=0.00016  Score=49.28  Aligned_cols=67  Identities=12%  Similarity=0.136  Sum_probs=42.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc------------------ccccccCcccchhcccchhH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ------------------IISIIAPTFQVMERAKEGES   65 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~------------------~~k~~~~~~~~~~~a~~~~~   65 (112)
                      .+++|||||+|.+.++|+.|+..+++.......+.+....+.                  ...+++.   .+++..++++
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~---nl~~~~~~~~   86 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVD---NLTYRTSPDT   86 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEE---SCCTTCCHHH
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEe---CCCCCCCHHH
Confidence            468999999999999999999888764332222222211111                  0112222   5677778888


Q ss_pred             HHHHHHHH
Q 036201           66 LEELRART   73 (112)
Q Consensus        66 ~~~~~~~~   73 (112)
                      |.++..+.
T Consensus        87 l~~~F~~~   94 (158)
T 2kn4_A           87 LRRVFEKY   94 (158)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            88887654

>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=97.28  E-value=0.00012  Score=49.66  Aligned_cols=66  Identities=12%  Similarity=0.128  Sum_probs=52.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhh-CCCeeCCeeEEEEeeeccccc---------------------cccCcccchhccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEAL-SNTHLYGRHLIFSVAHDQIIS---------------------IIAPTFQVMERAK   61 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~l-ng~~l~gr~L~V~~a~~~~~k---------------------~~~~~~~~~~~a~   61 (112)
                      ...+|+++|+|.+.++|+.|+..| ||..+.| .|.|+++.+....                     +++.   .++|..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~---nl~~~~   85 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVG---NLGNNG   85 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEE---SCCSCC
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEe---CCCCCC
Confidence            456899999999999999999999 9999999 9999988763210                     1222   577778


Q ss_pred             chhHHHHHHHHH
Q 036201           62 EGESLEELRART   73 (112)
Q Consensus        62 ~~~~~~~~~~~~   73 (112)
                      ++++|.++..+.
T Consensus        86 t~~~l~~~F~~~   97 (150)
T 2i2y_A           86 NKTELERAFGYY   97 (150)
T ss_dssp             SCHHHHHHHHHH
T ss_pred             CHHHHHHHHHhh
Confidence            888888887664

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=95.11  E-value=0.059  Score=36.32  Aligned_cols=33  Identities=12%  Similarity=0.198  Sum_probs=27.8

Q ss_pred             ceEEEEeCC-HHHHHHHHHhhC--CCeeCCeeEEEE
Q 036201            8 GFAFVEYVT-KQEAQNALEALS--NTHLYGRHLIFS   40 (112)
Q Consensus         8 GfgFVef~s-~eda~~Ai~~ln--g~~l~gr~L~V~   40 (112)
                      -+|||.|.+ ..+|..|+..||  +..|.|..+++.
T Consensus        56 ~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           56 KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            379999999 899999999995  688889887543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=95.06  E-value=0.041  Score=37.15  Aligned_cols=34  Identities=15%  Similarity=0.168  Sum_probs=30.7

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEe
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV   41 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~   41 (112)
                      |-|+|+|.+...|..|.=+|+|..|.||+|+|.-
T Consensus        63 ~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           63 NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            4499999999999999889999999999998753

>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=93.58  E-value=0.061  Score=35.61  Aligned_cols=37  Identities=16%  Similarity=0.223  Sum_probs=34.3

Q ss_pred             EEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201           10 AFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus        10 gFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ..|.|.+.++|..|-..|+++.++|+.|+|.+++|..
T Consensus        49 irv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq~~~   85 (104)
T 1wey_A           49 VRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLH   85 (104)
T ss_dssp             EEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSS
T ss_pred             EEEEeCChHHHHHHHHHhccceecCceeEEEecCCCC
Confidence            5799999999999999999999999999999998754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	112
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-05
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-05
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-04
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-04
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-04
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.001
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	0.001
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.001
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	0.001
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	0.001
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	0.002
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	0.002
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	0.002
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	0.002
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	0.003
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.003
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	0.003
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	0.003
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.004
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.004

>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 = 47.7 bits (113), Expect = 7e-09
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 1   MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISIIAPTFQVMERA 60
                 RG A+V Y    +A+NA + LS  ++  R+L+    +          FQ M+  
Sbjct: 40  GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN------RAFQKMDTK 93

Query: 61  KEGESLEELRAR 72
           K+ E L+ L+ +
Sbjct: 94  KKEEQLKLLKEK 105

>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 = 40.9 bits (95), Expect = 2e-06
 Identities = 6/45 (13%), Positives = 13/45 (28%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           ++        + +     A +A   L  T   G+ +    A   
Sbjct: 40 FQYFKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTL 84

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 2e-06
 Identities = 22/44 (50%), Positives = 31/44 (70%), Gaps = 1/44 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSN-THLYGRHLIFSVAHDQI 46
          G HRGF FV+++TKQ+A+ A  AL + THLYGR L+   A  ++
Sbjct: 48 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 38.7 bits (90), Expect = 1e-05
 Identities = 13/40 (32%), Positives = 24/40 (60%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          H+GFAFV+YV ++ A+ A+       + G+ L  ++A + 
Sbjct: 49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (90), Expect = 1e-05
 Identities = 8/43 (18%), Positives = 15/43 (34%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
          +   +  G A V +   +EA   ++ L      GR +      
Sbjct: 51 LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWD 93

>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 = 38.5 bits (89), Expect = 1e-05
 Identities = 11/45 (24%), Positives = 17/45 (37%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           +    RG AFV +     A NAL ++     Y + +    A   
Sbjct: 40 SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 84

>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 = 37.7 bits (87), Expect = 2e-05
 Identities = 13/43 (30%), Positives = 19/43 (44%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
                 GF FVEY   ++AQ AL+ L    + G  L   ++ 
Sbjct: 37 AGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISE 79

>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 = 36.5 bits (84), Expect = 6e-05
 Identities = 11/37 (29%), Positives = 17/37 (45%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +G+AF EYV       A+  L+   L  + L+   A
Sbjct: 42 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 78

>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 = 36.4 bits (84), Expect = 7e-05
 Identities = 8/43 (18%), Positives = 20/43 (46%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
          M      G+A+V +    +A+ AL+ ++   + G+ +    + 
Sbjct: 36 MITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ 78

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 36.2 bits (83), Expect = 1e-04
 Identities = 9/45 (20%), Positives = 22/45 (48%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           + G  +G A++E+ ++ +A+  LE      + GR +      ++
Sbjct: 47 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 91

>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 = 35.8 bits (82), Expect = 1e-04
 Identities = 9/39 (23%), Positives = 18/39 (46%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          G   G A V + ++ EA  A+  L++  +  R +   + 
Sbjct: 48 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 2e-04
 Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLY--GRHLIFSVAHDQIISI 49
              N++  A ++Y     AQ+A  +L   ++Y     L    +    +++
Sbjct: 39 TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNV 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 = 35.4 bits (81), Expect = 2e-04
 Identities = 11/42 (26%), Positives = 23/42 (54%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +    R +AFV +  +++A  A++AL+   L G  +  ++A
Sbjct: 38 ERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 79

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 2e-04
 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSN--THLYGRHLIFSVA 42
           +RGFAFVEY + + A  A   L      L+G  +    A
Sbjct: 43 KNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWA 82

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 3e-04
 Identities = 9/43 (20%), Positives = 15/43 (34%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH 43
                  FAFVE+   ++A++A+         G  L      
Sbjct: 47 KNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 89

>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 = 34.5 bits (79), Expect = 3e-04
 Identities = 10/42 (23%), Positives = 18/42 (42%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           + G   G A V +  K +A  A++  +   L GR +   + 
Sbjct: 35 DRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 76

>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 = 34.5 bits (79), Expect = 4e-04
 Identities = 17/41 (41%), Positives = 21/41 (51%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
             G  RG AFV Y  ++EAQ A+ AL+N    G     SV
Sbjct: 42 KLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 82

>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 = 34.5 bits (79), Expect = 4e-04
 Identities = 12/32 (37%), Positives = 20/32 (62%)

Query: 6  HRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
            GF FVEY ++ +A+NA+  ++ T L  R +
Sbjct: 48 ACGFCFVEYYSRADAENAMRYINGTRLDDRII 79

>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 = 34.0 bits (77), Expect = 6e-04
 Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD 44
          ++    + FAF+E+ +  E   A+         G+ L     HD
Sbjct: 42 VQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRRPHD 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.9 bits (77), Expect = 7e-04
 Identities = 11/42 (26%), Positives = 20/42 (47%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             G   G+ FV Y+  ++A+ A+  L+   L  + +  S A
Sbjct: 38 KITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA 79

>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 = 33.8 bits (77), Expect = 8e-04
 Identities = 8/34 (23%), Positives = 15/34 (44%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
              G  FVE+ +  + Q A++ L+      R +
Sbjct: 55 VPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88

>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 = 33.5 bits (76), Expect = 0.001
 Identities = 10/41 (24%), Positives = 18/41 (43%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV 41
             G  RG  F+ +  + EA+ A++ L+     G     +V
Sbjct: 42 QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 82

>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 = 33.6 bits (76), Expect = 0.001
 Identities = 12/42 (28%), Positives = 20/42 (47%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           + G  +G+ F EY  ++ A +A+  L+     GR L    A
Sbjct: 44 RETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA 85

>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 = 33.2 bits (75), Expect = 0.001
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +    RGF FV +    +A++A+ A++   + GR +    A
Sbjct: 41 RETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 82

>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 = 33.0 bits (75), Expect = 0.001
 Identities = 12/42 (28%), Positives = 24/42 (57%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           K G   G+AFV++ ++ ++Q A++ L+   +  + L  S A
Sbjct: 38 YKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA 79

>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 = 33.0 bits (75), Expect = 0.001
 Identities = 8/44 (18%), Positives = 22/44 (50%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          +    +G++FV + T + A +A+ +++ T + G  +      + 
Sbjct: 49 RVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 32.6 bits (74), Expect = 0.002
 Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 1/39 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             RGF FV ++ +      L   S   L  + +   VA
Sbjct: 39 KRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA 76

>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 = 32.7 bits (74), Expect = 0.002
 Identities = 12/42 (28%), Positives = 26/42 (61%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
             G H+G+ FVE++++++A  A++ +    LYG+ +  + A
Sbjct: 45 RVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA 86

>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 = 32.6 bits (74), Expect = 0.002
 Identities = 12/38 (31%), Positives = 17/38 (44%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
            +GF F+   T+  A+ A   L N  L G+ L    A
Sbjct: 42 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 79

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.7 bits (74), Expect = 0.002
 Identities = 8/42 (19%), Positives = 18/42 (42%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
           +    + F FV Y     AQ A+++++   +  + L   + 
Sbjct: 54 KQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 95

>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 = 32.4 bits (73), Expect = 0.003
 Identities = 11/38 (28%), Positives = 22/38 (57%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
          N +G+AF+ + +   +  A+EA++  +L  R +  S A
Sbjct: 39 NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA 76

>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 = 32.4 bits (73), Expect = 0.003
 Identities = 10/41 (24%), Positives = 16/41 (39%)

Query: 2  KFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA 42
               +GFAFV ++  + A  A   +      GR L    +
Sbjct: 45 LTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS 85

>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 = 32.3 bits (73), Expect = 0.003
 Identities = 9/45 (20%), Positives = 22/45 (48%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
           +  ++  + FVE+   ++A  AL A++   + G+ +  + A   
Sbjct: 42 TEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP 86

>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 = 32.4 bits (73), Expect = 0.003
 Identities = 10/43 (23%), Positives = 22/43 (51%)

Query: 5  NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII 47
          N +  A V+     +AQ A+  L+   L+G+ +  +++  Q +
Sbjct: 38 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNV 80

>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 = 32.0 bits (72), Expect = 0.003
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
           +    RGFAFV +    +A+ A E  +   L GR +
Sbjct: 45 QQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 81

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.3 bits (73), Expect = 0.004
 Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 1/34 (2%)

Query: 4  GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL 37
             RGF FV + +  E   A+       + GR +
Sbjct: 59 KRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVV 91

>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 = 31.9 bits (72), Expect = 0.004
 Identities = 12/45 (26%), Positives = 19/45 (42%)

Query: 1  MKFGNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ 45
          +     R  AFV Y   + A  A+  L+ T +    L  ++A  Q
Sbjct: 33 LSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 77

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	112
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.24
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.21
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.18
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.17
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.17
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.16
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.13
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.11
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.11
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.1
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.1
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.09
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.09
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.07
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.07
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.06
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.06
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.06
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.05
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.04
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.04
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.04
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.03
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.02
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.01
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.0
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.0
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.99
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.99
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.98
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.98
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.96
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.95
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.95
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.95
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.93
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.92
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.92
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.89
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.89
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.89
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.88
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.87
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.86
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.86
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	98.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.84
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.84
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.84
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.83
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.83
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.83
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.81
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.81
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.8
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.8
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.79
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.78
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.76
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.72
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.65
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.63
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.61
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.59
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.57
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.56
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.56
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.55
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.53
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.52
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.48
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.45
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.45
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.43
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.42
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.37
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.36
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.3
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.02
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.0
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.24
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	91.86
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	90.96

>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=99.24  E-value=6.7e-12  Score=77.82  Aligned_cols=45  Identities=27%  Similarity=0.496  Sum_probs=41.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|++|+|++|.|+..+
T Consensus        38 g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~k   82 (83)
T d1x5ta1          38 GNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSK   82 (83)
T ss_dssp             CSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCCC
T ss_pred             cccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCcC
Confidence            889999999999999999999999999999999999999886543

>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=99.21  E-value=8.4e-12  Score=78.59  Aligned_cols=45  Identities=33%  Similarity=0.659  Sum_probs=42.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.|++.+
T Consensus        44 ~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~~k   88 (89)
T d2cqba1          44 EKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK   88 (89)
T ss_dssp             CCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCC
T ss_pred             ccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCCC
Confidence            889999999999999999999999999999999999999886543

>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=99.18  E-value=1.6e-11  Score=75.83  Aligned_cols=41  Identities=27%  Similarity=0.521  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.+|.|
T Consensus        41 g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          41 GYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             TEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            78999999999999999999999999999999999998876

>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=99.17  E-value=2e-11  Score=76.81  Aligned_cols=42  Identities=31%  Similarity=0.498  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|+||.++
T Consensus        46 g~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          46 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             cccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            889999999999999999999999999999999999888764

>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=99.17  E-value=2e-11  Score=77.00  Aligned_cols=42  Identities=24%  Similarity=0.381  Sum_probs=40.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|+|.+|.|+
T Consensus        47 ~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          47 GQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             CSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             cccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            789999999999999999999999999999999999998875

>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=99.16  E-value=1.9e-11  Score=75.43  Aligned_cols=42  Identities=24%  Similarity=0.464  Sum_probs=37.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..+.|++|.|.++.|.
T Consensus        40 ~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P~   81 (81)
T d2ghpa1          40 NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL   81 (81)
T ss_dssp             ---CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             ccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCc
Confidence            889999999999999999999999999999999999999883

>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=99.13  E-value=3.1e-11  Score=74.35  Aligned_cols=41  Identities=27%  Similarity=0.545  Sum_probs=39.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.+|.|
T Consensus        41 ~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          41 GQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            78999999999999999999999999999999999999887

>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=99.11  E-value=4.4e-11  Score=74.84  Aligned_cols=42  Identities=24%  Similarity=0.335  Sum_probs=38.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+. |||..|.|+.|.|++|.|+|
T Consensus        45 ~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a~~kP   86 (86)
T d2ghpa3          45 SFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLADKKP   86 (86)
T ss_dssp             -CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEECCCCC
T ss_pred             cccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEcCCCC
Confidence            7899999999999999999995 99999999999999998764

>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=99.11  E-value=5.8e-11  Score=75.60  Aligned_cols=43  Identities=28%  Similarity=0.364  Sum_probs=40.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.||.|+|.+|.+++
T Consensus        55 ~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          55 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             CSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             ccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            7889999999999999999999999999999999999988753

>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=99.10  E-value=4.1e-11  Score=76.06  Aligned_cols=43  Identities=28%  Similarity=0.648  Sum_probs=40.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|+|.+|.|..
T Consensus        48 g~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          48 GQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             CSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             cccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            8899999999999999999999999999999999998887753

>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=99.10  E-value=5.3e-11  Score=75.68  Aligned_cols=42  Identities=52%  Similarity=0.987  Sum_probs=38.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhh-CCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEAL-SNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~l-ng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..| ||..|.|++|.|.+|.+.
T Consensus        48 g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~   90 (94)
T d2cpha1          48 GAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE   90 (94)
T ss_dssp             CSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCC
T ss_pred             CCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCC
Confidence            889999999999999999999998 899999999988877764

>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=99.09  E-value=1e-10  Score=76.15  Aligned_cols=42  Identities=29%  Similarity=0.356  Sum_probs=39.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+.
T Consensus        43 ~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   84 (114)
T d2f9da1          43 PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            678999999999999999999999999999999999888764

>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=99.09  E-value=6.2e-11  Score=76.40  Aligned_cols=42  Identities=19%  Similarity=0.320  Sum_probs=39.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|+|.++.|+
T Consensus        57 g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k   98 (102)
T d2cpza1          57 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK   98 (102)
T ss_dssp             CSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCS
T ss_pred             CCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            789999999999999999999999999999999988888775

>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=99.07  E-value=7.7e-11  Score=72.61  Aligned_cols=44  Identities=27%  Similarity=0.377  Sum_probs=40.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      .+++|||||+|.+.++|..|+..|||..|.|++|+|.++.|+|+
T Consensus        36 ~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P~   79 (79)
T d2bz2a1          36 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM   79 (79)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSCC
T ss_pred             ccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            46789999999999999999999999999999999999988764

>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=99.07  E-value=7e-11  Score=72.89  Aligned_cols=40  Identities=18%  Similarity=0.386  Sum_probs=37.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.||+|+|.+|.
T Consensus        39 g~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          39 RRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             cCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            8899999999999999999999999999999999777664

>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=99.06  E-value=5.4e-11  Score=74.77  Aligned_cols=43  Identities=21%  Similarity=0.444  Sum_probs=39.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.|++
T Consensus        45 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2          45 NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            5689999999999999999999999999999999998887753

>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=99.06  E-value=1.4e-10  Score=71.20  Aligned_cols=40  Identities=25%  Similarity=0.347  Sum_probs=37.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|++|+|.++.
T Consensus        38 g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          38 GRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             cccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            8899999999999999999999999999999999887763

>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=99.06  E-value=9.8e-11  Score=73.39  Aligned_cols=42  Identities=26%  Similarity=0.491  Sum_probs=39.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.|.
T Consensus        44 ~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~   85 (90)
T d1x5sa1          44 QRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS   85 (90)
T ss_dssp             CSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECC
T ss_pred             ccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            889999999999999999999999999999999999888775

>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=99.05  E-value=1.4e-10  Score=74.02  Aligned_cols=43  Identities=23%  Similarity=0.335  Sum_probs=40.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.++.
T Consensus        47 g~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~   89 (99)
T d1whwa_          47 KKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKK   89 (99)
T ss_dssp             CCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCS
T ss_pred             cccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            8899999999999999999999999999999999999888754

>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=99.04  E-value=1.5e-10  Score=73.37  Aligned_cols=41  Identities=29%  Similarity=0.451  Sum_probs=38.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |.++|||||+|.+.++|..|+..|||..|.|++|+|+|+.+
T Consensus        46 ~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~   86 (93)
T d1h2vz_          46 KTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG   86 (93)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESC
T ss_pred             ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            78999999999999999999999999999999998888765

>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=99.04  E-value=8.9e-11  Score=73.34  Aligned_cols=42  Identities=29%  Similarity=0.472  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.+.
T Consensus        40 g~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          40 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             SCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             cccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            899999999999999999999999999999999999888764

>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=99.04  E-value=1.3e-10  Score=72.29  Aligned_cols=43  Identities=26%  Similarity=0.414  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++++|||||+|.+.++|..|+..|||..|.|+.|.|.+|.|..
T Consensus        41 ~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          41 KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            5689999999999999999999999999999999999998753

>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=99.03  E-value=2.5e-10  Score=72.23  Aligned_cols=43  Identities=28%  Similarity=0.471  Sum_probs=40.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|+|.+|.|+.
T Consensus        48 ~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          48 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            4579999999999999999999999999999999999998864

>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=99.02  E-value=1.1e-10  Score=72.36  Aligned_cols=41  Identities=32%  Similarity=0.468  Sum_probs=37.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|.|.++.+
T Consensus        40 ~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1          40 LLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             cccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            35799999999999999999999999999999998887754

>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=99.01  E-value=1.9e-10  Score=73.39  Aligned_cols=42  Identities=31%  Similarity=0.577  Sum_probs=39.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|++|.++
T Consensus        57 g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k   98 (102)
T d2cpxa1          57 GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNK   98 (102)
T ss_dssp             SSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCC
T ss_pred             ccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCc
Confidence            789999999999999999999999999999999988888775

>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=99.00  E-value=2.3e-10  Score=76.92  Aligned_cols=45  Identities=22%  Similarity=0.419  Sum_probs=41.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      |+++|||||+|.+.++|..|+..|||..|.||.|+|.+|.+...+
T Consensus        81 ~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~~  125 (139)
T d1u6fa1          81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQR  125 (139)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCCC
T ss_pred             ccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCCC
Confidence            788999999999999999999999999999999999998775433

>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=99.00  E-value=2.5e-10  Score=73.21  Aligned_cols=43  Identities=30%  Similarity=0.571  Sum_probs=39.1

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      +||||||+|.+.++|..||..|||..|.|++|+|.++.+.+..
T Consensus        49 ~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~~~   91 (98)
T d1wf2a_          49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVN   91 (98)
T ss_dssp             ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSCCCC
T ss_pred             eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            6899999999999999999999999999999999998765433

>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=98.99  E-value=1.9e-10  Score=73.15  Aligned_cols=43  Identities=21%  Similarity=0.474  Sum_probs=40.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.|+.
T Consensus        50 ~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          50 GKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             TEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            6789999999999999999999999999999999999998864

>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=98.99  E-value=3.1e-10  Score=69.41  Aligned_cols=42  Identities=21%  Similarity=0.387  Sum_probs=38.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ++++|||||+|.+.++|..|+..|||..+.|++|+|.++.+.
T Consensus        30 ~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1          30 DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            678999999999999999999999999999999988887654

>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=98.98  E-value=1.8e-10  Score=71.19  Aligned_cols=43  Identities=28%  Similarity=0.380  Sum_probs=39.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCC-eeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNT-HLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~-~l~gr~L~V~~a~~~~   46 (112)
                      +.++|||||+|.+.++|..|++.|||. .+.|+.|+|.+|.|+.
T Consensus        34 ~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1          34 LLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             EEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             ecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            457899999999999999999999995 6999999999998864

>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=98.98  E-value=1.7e-10  Score=74.16  Aligned_cols=41  Identities=29%  Similarity=0.541  Sum_probs=37.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|.++.+
T Consensus        47 g~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_          47 GKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             TEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             eccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            78999999999999999999999999999999996655543

>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=98.96  E-value=7.5e-10  Score=69.48  Aligned_cols=43  Identities=21%  Similarity=0.414  Sum_probs=39.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ...+|||||+|.+.++|..|+..|||..|.|+.|+|.+|.|..
T Consensus        45 ~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          45 TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             CccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            4458999999999999999999999999999999999988754

>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=98.95  E-value=3.4e-10  Score=70.33  Aligned_cols=39  Identities=44%  Similarity=0.622  Sum_probs=35.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|++.|||..+.|  ++|.|.+|
T Consensus        45 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          45 GRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            8899999999999999999999999999987  88977665

>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=98.95  E-value=3.9e-10  Score=71.33  Aligned_cols=40  Identities=23%  Similarity=0.602  Sum_probs=37.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |+++|||||+|.+.++|..|++ |||..|.|+.|.|.+|.+
T Consensus        51 g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          51 GTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             CCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            8899999999999999999996 999999999998887764

>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=98.95  E-value=2.1e-10  Score=74.05  Aligned_cols=41  Identities=24%  Similarity=0.455  Sum_probs=37.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+. |||..|.|+.|.|.++.++
T Consensus        57 g~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          57 RRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             SSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHH
T ss_pred             ccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCC
Confidence            8899999999999999999995 9999999999988776654

>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=98.93  E-value=8e-10  Score=70.45  Aligned_cols=42  Identities=19%  Similarity=0.391  Sum_probs=38.4

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ..||||||+|.+.++|..|+..|||..|.|+.|+|+|+.+.+
T Consensus        52 ~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          52 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             ecceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            358999999999999999999999999999999998887754

>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=98.92  E-value=9.5e-10  Score=69.64  Aligned_cols=42  Identities=21%  Similarity=0.289  Sum_probs=39.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|..||..|||+.|.|+.|+|.+|.+.
T Consensus        50 ~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~~   91 (95)
T d1x4aa1          50 RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG   91 (95)
T ss_dssp             SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccCC
Confidence            567899999999999999999999999999999999888764

>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=98.92  E-value=6.7e-10  Score=69.71  Aligned_cols=42  Identities=24%  Similarity=0.426  Sum_probs=39.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|++|.|.++.+.
T Consensus        37 ~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_          37 DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            568999999999999999999999999999999999988654

>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=98.89  E-value=1.1e-09  Score=67.94  Aligned_cols=39  Identities=23%  Similarity=0.358  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..|.||.|+|.++
T Consensus        48 g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          48 GMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            789999999999999999999999999999999988754

>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=98.89  E-value=1.1e-09  Score=67.56  Aligned_cols=36  Identities=33%  Similarity=0.507  Sum_probs=34.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      |+++|||||+|.+.++|..|+..|||..|.|+.|+|
T Consensus        48 ~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          48 RRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             cccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            789999999999999999999999999999999976

>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=98.89  E-value=1.4e-09  Score=68.50  Aligned_cols=42  Identities=33%  Similarity=0.522  Sum_probs=37.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhC------CCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALS------NTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~ln------g~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|..|+..||      |..|.||.|+|++|.|+
T Consensus        47 ~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          47 EHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR   94 (98)
T ss_dssp             CCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCC
T ss_pred             ccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCC
Confidence            7789999999999999999999987      67789999989888774

>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=98.88  E-value=6.7e-10  Score=69.85  Aligned_cols=41  Identities=27%  Similarity=0.368  Sum_probs=36.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      ++++|||||+|.+.++|..|+..|||..+.|+.|.|.+|.+
T Consensus        43 ~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~   83 (91)
T d1nu4a_          43 LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT   83 (91)
T ss_dssp             HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSS
T ss_pred             ccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCC
Confidence            56789999999999999999999999999999996666554

>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=98.87  E-value=1.1e-09  Score=69.35  Aligned_cols=42  Identities=33%  Similarity=0.521  Sum_probs=37.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCC--CeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSN--THLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng--~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|+..|++  ..+.|+.|.|+||.|.
T Consensus        42 ~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~   85 (96)
T d2disa1          42 MKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPE   85 (96)
T ss_dssp             TTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSS
T ss_pred             ccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCC
Confidence            78999999999999999999999965  5667999999888774

>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=98.87  E-value=9.9e-10  Score=68.33  Aligned_cols=39  Identities=26%  Similarity=0.486  Sum_probs=35.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCe--eEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGR--HLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr--~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..+.|+  +|.|.||
T Consensus        45 g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          45 GVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             ccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            88999999999999999999999999999985  5877664

>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=98.86  E-value=1.2e-09  Score=66.47  Aligned_cols=38  Identities=24%  Similarity=0.449  Sum_probs=34.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|+.|+. +++..|.|+.|.|..|
T Consensus        38 ~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          38 GRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             TBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            8899999999999999999997 7999999999988654

>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=98.86  E-value=1.5e-09  Score=67.65  Aligned_cols=42  Identities=29%  Similarity=0.346  Sum_probs=38.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCee-CCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHL-YGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l-~gr~L~V~~a~~~   45 (112)
                      ++++|||||+|.+.++|..|+..|||..| .|+.|+|+++.++
T Consensus        45 ~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          45 QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            56789999999999999999999999988 5899999988764

>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=98.85  E-value=1.5e-09  Score=70.42  Aligned_cols=39  Identities=18%  Similarity=0.360  Sum_probs=36.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|..|+..|||..+.||+|.|.++
T Consensus        65 ~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          65 DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             CCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            889999999999999999999999999999999988764

>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=98.84  E-value=8.1e-10  Score=67.88  Aligned_cols=38  Identities=26%  Similarity=0.416  Sum_probs=35.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |++||||||+|.+.++|+.|+. +|+..|.||.|.|..|
T Consensus        39 g~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          39 KRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             SSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            8899999999999999999997 6999999999988765

>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=98.84  E-value=2.4e-09  Score=68.65  Aligned_cols=42  Identities=19%  Similarity=0.283  Sum_probs=39.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++||+||+|.+.++|..|+..|||..+.||+|.|.++.+.
T Consensus        54 ~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          54 RHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             TCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSC
T ss_pred             CCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCc
Confidence            467899999999999999999999999999999999998774

>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=98.84  E-value=2e-09  Score=64.78  Aligned_cols=38  Identities=21%  Similarity=0.410  Sum_probs=35.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |.++|||||+|.+.++|..|++ |||..|.||.|.|.+|
T Consensus        38 ~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          38 NRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             TTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             cccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            7899999999999999999997 9999999999988764

>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=98.83  E-value=2.3e-09  Score=68.54  Aligned_cols=43  Identities=21%  Similarity=0.330  Sum_probs=38.2

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      |+++|||||+|.+.++|++|+ .||+..|.||.|+|.+|.+...
T Consensus        54 g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~   96 (104)
T d1wi8a_          54 ERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             TSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             CCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEECCCCCC
Confidence            788999999999999998776 5999999999999999887543

>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=98.83  E-value=2.6e-09  Score=67.01  Aligned_cols=36  Identities=28%  Similarity=0.442  Sum_probs=33.4

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEE
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFS   40 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~   40 (112)
                      .++|||||+|.+.++|..|+..|||..|.||+|+|+
T Consensus        54 ~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          54 GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             CCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            345999999999999999999999999999999885

>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=98.83  E-value=1.4e-09  Score=70.54  Aligned_cols=43  Identities=16%  Similarity=0.170  Sum_probs=39.8

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~   47 (112)
                      +++|||||+|.+.++|..|+..|||..|.|+.|+|.|+.+...
T Consensus        44 k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   86 (104)
T d1weya_          44 KSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI   86 (104)
T ss_dssp             TTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCC
Confidence            5789999999999999999999999999999999999987644

>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=98.83  E-value=2.1e-09  Score=69.09  Aligned_cols=41  Identities=24%  Similarity=0.362  Sum_probs=37.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      |+++|||||+|.+.++|..|++.+|+ .|.||.|.|.++.+.
T Consensus        49 g~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~~   89 (103)
T d2cqda1          49 GKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLG   89 (103)
T ss_dssp             CCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             cccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCCC
Confidence            88999999999999999999999887 699999999888653

>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=98.82  E-value=2.5e-09  Score=69.10  Aligned_cols=41  Identities=24%  Similarity=0.352  Sum_probs=37.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|..|+. ++|..|.|+.|.|.+|.|+
T Consensus        59 ~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          59 KRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             SSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            7899999999999999999996 7999999999999888775

>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=98.81  E-value=2.8e-09  Score=68.48  Aligned_cols=42  Identities=21%  Similarity=0.145  Sum_probs=37.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      ..++|||||+|.+.++|..|+..|||..|.|++|.|.++...
T Consensus        43 ~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          43 PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            467899999999999999999999999999999988777543

>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=98.81  E-value=5.4e-10  Score=71.62  Aligned_cols=42  Identities=10%  Similarity=0.214  Sum_probs=38.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.++|||||+|.+.++|..|+..|||..|.||.+.|.++.|-
T Consensus        56 ~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~Pl   97 (101)
T d1x5oa1          56 GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPL   97 (101)
T ss_dssp             SCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCB
T ss_pred             cccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCCc
Confidence            778999999999999999999999999999999987777664

>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=98.81  E-value=1.8e-09  Score=67.38  Aligned_cols=41  Identities=29%  Similarity=0.418  Sum_probs=38.1

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +++|||||+|.+.++|..|+..|||..|.|+.|+|.+|.+.
T Consensus        42 ~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1          42 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            56899999999999999999999999999999999888764

>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=98.80  E-value=3.3e-09  Score=65.87  Aligned_cols=39  Identities=31%  Similarity=0.420  Sum_probs=35.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+. +++..|.||.|.|..|.
T Consensus        45 g~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          45 KRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            8899999999999999999997 69999999999887663

>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=98.80  E-value=3.7e-09  Score=64.36  Aligned_cols=38  Identities=24%  Similarity=0.393  Sum_probs=34.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      +.++|||||+|.+.+++.+|+. +||..|.||.|.|..|
T Consensus        41 ~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          41 GKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             cccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            7889999999999999988985 8999999999988765

>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=98.80  E-value=1.4e-09  Score=69.71  Aligned_cols=46  Identities=22%  Similarity=0.177  Sum_probs=41.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISII   50 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~   50 (112)
                      |.++|||||+|.+.++|+.|+. ||+..|.||.|.|.++.+.+....
T Consensus        52 g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~~~~~~~~   97 (102)
T d1weza_          52 GRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNSTAGTSGS   97 (102)
T ss_dssp             SCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEECCCCCCCC
T ss_pred             CcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcCCCCCCCC
Confidence            7889999999999999999986 899999999999999888765443

>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=98.79  E-value=1.8e-09  Score=69.01  Aligned_cols=39  Identities=26%  Similarity=0.440  Sum_probs=35.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      |+++|||||+|.+.++|..|+. |||..|.||.|.|.++.
T Consensus        47 g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1          47 GQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            8899999999999999999996 89999999999665543

>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=98.78  E-value=3.4e-09  Score=66.86  Aligned_cols=41  Identities=17%  Similarity=0.394  Sum_probs=36.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      |+|||||||+|.+.++|..|+..  +..|.|+.|.|.++.|+.
T Consensus        47 g~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~~k~   87 (90)
T d2cqga1          47 GHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPNSKQ   87 (90)
T ss_dssp             CSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCCTTC
T ss_pred             cccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCCCCC
Confidence            89999999999999999999985  458999999998887753

>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=98.76  E-value=4e-09  Score=67.63  Aligned_cols=41  Identities=24%  Similarity=0.373  Sum_probs=37.7

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      .++|||||+|.+.++|..|+..|||..|.|++|.|.++.+.
T Consensus        38 ~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1          38 NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             TTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            35799999999999999999999999999999999988654

>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=98.72  E-value=7.7e-09  Score=66.28  Aligned_cols=45  Identities=20%  Similarity=0.290  Sum_probs=40.6

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISI   49 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~   49 (112)
                      ++++|||||+|.+.++|..|+. +|+..|.||.|.|.++.+..+..
T Consensus        54 ~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~~~~~~~   98 (104)
T d1wg5a_          54 GRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVRT   98 (104)
T ss_dssp             SCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEECTTTSCC
T ss_pred             CCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECCHHHhcc
Confidence            7899999999999999999986 89999999999999998876543

>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=98.66  E-value=4.9e-09  Score=65.33  Aligned_cols=40  Identities=23%  Similarity=0.272  Sum_probs=36.3

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeecc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQ   45 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~   45 (112)
                      +.|||||+|.+.++|+.||..|||..|.|+.|.|.++.+.
T Consensus        34 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1          34 RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            4699999999999999999999999999999988776654

>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=98.65  E-value=7.8e-09  Score=65.98  Aligned_cols=41  Identities=24%  Similarity=0.297  Sum_probs=38.2

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ++|||||+|.+.++|..||+.|||..|.|+.|.|.++.+++
T Consensus        49 ~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          49 KDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            57999999999999999999999999999999999987754

>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=98.63  E-value=4.2e-09  Score=63.13  Aligned_cols=34  Identities=24%  Similarity=0.463  Sum_probs=32.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeE
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHL   37 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L   37 (112)
                      +.++|||||+|.+.++|..|+..|||..|.|+.|
T Consensus        37 ~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1          37 NKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             CSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             ccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7899999999999999999999999999999987

>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=98.61  E-value=1.6e-08  Score=62.79  Aligned_cols=37  Identities=16%  Similarity=0.247  Sum_probs=33.7

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEe
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV   41 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~   41 (112)
                      |+++|||||+|.+.++|..|++ ++|..+.|+.|.|.+
T Consensus        44 ~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~   80 (85)
T d1zh5a2          44 KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   80 (85)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEE
T ss_pred             CCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEE
Confidence            7889999999999999999996 799999999996654

>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=98.59  E-value=2.7e-08  Score=61.25  Aligned_cols=39  Identities=28%  Similarity=0.412  Sum_probs=34.2

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeC-CeeEEEEeee
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLY-GRHLIFSVAH   43 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~-gr~L~V~~a~   43 (112)
                      ..+|||||+|.+.++|..|+..|||..|. |+.|+|+||.
T Consensus        43 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          43 NRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             TTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             ccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            35799999999999999999999999885 6899777664

>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=98.57  E-value=1.4e-08  Score=61.94  Aligned_cols=38  Identities=18%  Similarity=0.352  Sum_probs=33.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      |+++|||||+|.+.++|+.|++. ++..|.|+.|.|..|
T Consensus        38 ~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          38 NKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             cccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            88999999999999999999974 777899999988654

>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=98.56  E-value=4.4e-08  Score=61.97  Aligned_cols=43  Identities=26%  Similarity=0.329  Sum_probs=37.7

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeCC--eeEEEEeeecccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLYG--RHLIFSVAHDQII   47 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~g--r~L~V~~a~~~~~   47 (112)
                      +.+|||||+|.+.++|..|+..|||..|.|  ++|+|+||.+.+.
T Consensus        51 ~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~~~   95 (97)
T d1whya_          51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPS   95 (97)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCCC
T ss_pred             ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCCCC
Confidence            468999999999999999999999999986  5898888887543

>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=98.56  E-value=2.5e-08  Score=64.18  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=37.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeC--CeeEEEEeeeccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLY--GRHLIFSVAHDQI   46 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~--gr~L~V~~a~~~~   46 (112)
                      .+++|||||+|.+.++|..|+..|||..|.  ++.|.|.++.+..
T Consensus        42 ~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1          42 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             ETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             eCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            356899999999999999999999999884  7889898887754

>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=98.55  E-value=1.1e-08  Score=66.54  Aligned_cols=40  Identities=20%  Similarity=0.266  Sum_probs=35.4

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |.++|||||+|.+.++|..|+. |||..|.||.|.|..+.+
T Consensus        57 g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          57 GKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             SSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             cceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcCh
Confidence            8899999999999999999986 899999999997655543

>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=98.53  E-value=9.5e-08  Score=59.19  Aligned_cols=42  Identities=17%  Similarity=0.266  Sum_probs=36.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhh--CCCeeCCeeEEEEeeeccc
Q 036201            5 NHRGFAFVEYVTKQEAQNALEAL--SNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~l--ng~~l~gr~L~V~~a~~~~   46 (112)
                      +++|||||+|.+.++|..|+..+  ++..+.|+.|+|.|+..+.
T Consensus        42 ~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          42 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            46899999999999999999865  6789999999998887654

>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=98.52  E-value=2.7e-08  Score=61.93  Aligned_cols=43  Identities=28%  Similarity=0.281  Sum_probs=37.5

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k   48 (112)
                      +.++|||||+|.+.++|+.|+.  ++..|.|++|.|.++.|+...
T Consensus        39 ~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          39 KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCCC
T ss_pred             eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCCC
Confidence            5678999999999999999985  788999999999999886443

>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=98.48  E-value=6e-08  Score=62.27  Aligned_cols=41  Identities=20%  Similarity=0.323  Sum_probs=37.6

Q ss_pred             CcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccc
Q 036201            6 HRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQI   46 (112)
Q Consensus         6 srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~   46 (112)
                      ..|++||+|.+.++|..|+..|||..+.||.|.|.++.+..
T Consensus        57 ~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~~~~   97 (104)
T d1o0pa_          57 GCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDS   97 (104)
T ss_dssp             TCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEECHHH
T ss_pred             CceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcCHHH
Confidence            46999999999999999999999999999999999887643

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=3.8e-09  Score=65.95  Aligned_cols=37  Identities=22%  Similarity=0.445  Sum_probs=34.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEe
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSV   41 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~   41 (112)
                      ++++|||||+|.+.++|+.|+. |||..|.|+.|+|..
T Consensus        45 ~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_          45 NQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIRR   81 (90)
T ss_dssp             ETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCBC
T ss_pred             CCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEECC
Confidence            6789999999999999999985 999999999998864

>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=98.45  E-value=1.1e-07  Score=60.55  Aligned_cols=41  Identities=17%  Similarity=0.272  Sum_probs=36.1

Q ss_pred             CCCcceEEEEeCCHHHHHHHHH--hhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALE--ALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~--~lng~~l~gr~L~V~~a~~   44 (112)
                      .+++|||||+|.+.++|..|+.  .+++..|.|+.|+|.+|..
T Consensus        52 ~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~   94 (99)
T d1x4fa1          52 MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK   94 (99)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECS
T ss_pred             eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCC
Confidence            3568999999999999999998  5788899999998888754

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=9e-08  Score=65.34  Aligned_cols=40  Identities=23%  Similarity=0.362  Sum_probs=36.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~   44 (112)
                      |.++|||||+|.+.++|..|+. +++..|.|+.|.|.+|.|
T Consensus       136 ~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         136 GKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             CccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            7889999999999999999997 799999999997776655

>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=98.42  E-value=2.3e-07  Score=57.92  Aligned_cols=40  Identities=23%  Similarity=0.412  Sum_probs=35.5

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhh--CCCeeCCeeEEEEeeec
Q 036201            5 NHRGFAFVEYVTKQEAQNALEAL--SNTHLYGRHLIFSVAHD   44 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~l--ng~~l~gr~L~V~~a~~   44 (112)
                      ..++||||+|.+.++|..|+..|  ++..+.|++|+|+||.+
T Consensus        43 ~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~   84 (89)
T d1x4da1          43 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK   84 (89)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECC
T ss_pred             ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCC
Confidence            45789999999999999999966  67889999999988865

>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=98.37  E-value=3.2e-07  Score=55.44  Aligned_cols=38  Identities=18%  Similarity=0.180  Sum_probs=33.3

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      +.++|||||+|.+.++|..|+. +|+..|.|+.|.|..+
T Consensus        37 ~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          37 KKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             TSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             cccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            3456899999999999999995 8999999999988754

>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=98.36  E-value=2.7e-07  Score=58.84  Aligned_cols=45  Identities=16%  Similarity=0.228  Sum_probs=38.0

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhh--CCCeeCCeeEEEEeeeccccc
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEAL--SNTHLYGRHLIFSVAHDQIIS   48 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~l--ng~~l~gr~L~V~~a~~~~~k   48 (112)
                      .+++|||||+|.+.++|..|+..|  ++..+.|++|+|.|+......
T Consensus        48 ~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~~~~   94 (104)
T d1wexa_          48 MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT   94 (104)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSCC
T ss_pred             EecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCCccC
Confidence            357899999999999999999987  566788999999998765433

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.30  E-value=3e-07  Score=56.84  Aligned_cols=40  Identities=18%  Similarity=0.193  Sum_probs=33.9

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCee-EEEEeeec
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRH-LIFSVAHD   44 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~-L~V~~a~~   44 (112)
                      ++++|||||+|.+.++|+.|+. +||..|.|+. |.|..+.+
T Consensus        36 ~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1          36 SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            5778999999999999999996 9999999985 44655543

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.02  E-value=4e-06  Score=53.32  Aligned_cols=29  Identities=21%  Similarity=0.453  Sum_probs=26.6

Q ss_pred             CCcceEEEEeCCHHHHHHHHHhhCCCeeC
Q 036201            5 NHRGFAFVEYVTKQEAQNALEALSNTHLY   33 (112)
Q Consensus         5 ~srGfgFVef~s~eda~~Ai~~lng~~l~   33 (112)
                      ..+|||||+|.+.++|..|+..|||..+.
T Consensus        54 ~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          54 PNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             TTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             cCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            46899999999999999999999998873

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.00  E-value=3.8e-06  Score=54.22  Aligned_cols=35  Identities=17%  Similarity=0.096  Sum_probs=30.3

Q ss_pred             CCcceEEEEeCCH-HHHHHHHHhhCCCeeCCeeEEE
Q 036201            5 NHRGFAFVEYVTK-QEAQNALEALSNTHLYGRHLIF   39 (112)
Q Consensus         5 ~srGfgFVef~s~-eda~~Ai~~lng~~l~gr~L~V   39 (112)
                      +.+|||||.|.++ ++|..|+..||+..|.++.+.|
T Consensus        45 ~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_          45 RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            4589999999995 6788999999999999888844

>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=97.24  E-value=0.00034  Score=46.83  Aligned_cols=69  Identities=25%  Similarity=0.263  Sum_probs=48.8

Q ss_pred             CCCcceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeeeccccccc---cCccc-----chhcccchhHHHHHHHHH
Q 036201            4 GNHRGFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAHDQIISII---APTFQ-----VMERAKEGESLEELRART   73 (112)
Q Consensus         4 g~srGfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~~~~~k~~---~~~~~-----~~~~a~~~~~~~~~~~~~   73 (112)
                      |.++|||||+|.+.++|..|+.. ++..+.++.+.+....+......   .....     .+++.-++++|.++....
T Consensus        45 ~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~  121 (183)
T d1u1qa_          45 KRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY  121 (183)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGG
T ss_pred             CCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccC
Confidence            78899999999999999999875 66678899888877766443311   11111     466667777777766554

>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=91.86  E-value=0.19  Score=29.67  Aligned_cols=35  Identities=23%  Similarity=0.289  Sum_probs=32.7

Q ss_pred             eEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEeee
Q 036201            9 FAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVAH   43 (112)
Q Consensus         9 fgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a~   43 (112)
                      .|-|...+..+|..|+..|+...|.+++|.|+++.
T Consensus        37 ~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          37 KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            58899999999999999999999999999998874

>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=90.96  E-value=0.12  Score=32.11  Aligned_cols=34  Identities=21%  Similarity=0.360  Sum_probs=29.3

Q ss_pred             ceEEEEeCCHHHHHHHHHhhCCCeeCCeeEEEEee
Q 036201            8 GFAFVEYVTKQEAQNALEALSNTHLYGRHLIFSVA   42 (112)
Q Consensus         8 GfgFVef~s~eda~~Ai~~lng~~l~gr~L~V~~a   42 (112)
                      +--+|+|.+-+.|-+|+. ++|..++|++|+|..-
T Consensus        59 d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          59 GQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGP   92 (95)
T ss_dssp             TEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECC
T ss_pred             CeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecC
Confidence            456899999999999986 8999999999988643