Psyllid ID: psy3346

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------8
Protein Sequence
MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV
Secondary Structure (PSIPRED)
ccccccHHcccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEcccccccccccEEEEEEccHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcccccccEEEEEcccccccHHHHHHHHHHHcccEEEEccccccccccccEEEEEEEccHHHHHcc
Coil and Loop (DISEMBL)
mgseattvkrkssnvakqtgskilvrnipfqakQSEVEELFKAFGELkfvrlpkkmvgsglhrgfgfVEFITKNEAKRV
Flexible Loop (DISEMBL)
mgseattvkrkssnvakqtgskilvrnipfqaKQSEVEELFKAFGELKFVRLPKKmvgsglhrgfgfvefitkneakrv
Low Complexity Region (SEG)
MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV
Disordered region (IsUnstruct)
**********************ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT*******
Disordered Region (DISOPRED)
************************VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE****
Disordered Region (DISEMBL)
*****************QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV
Disordered Region (DISPRO)
*****************QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE****
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV
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	79	2.2.26 [Sep-21-2011]
Q8R3C6	952	Probable RNA-binding prot	yes	N/A	0.924	0.076	0.68	2e-22
Q9Y4C8	960	Probable RNA-binding prot	yes	N/A	0.924	0.076	0.666	3e-22
Q54PB2	895	Multiple RNA-binding doma	yes	N/A	0.734	0.064	0.516	9e-12
P0CR16	769	Multiple RNA-binding doma	yes	N/A	0.797	0.081	0.477	7e-11
P0CR17	769	Multiple RNA-binding doma	N/A	N/A	0.797	0.081	0.477	7e-11
O13620	833	Multiple RNA-binding doma	yes	N/A	0.860	0.081	0.444	2e-10
Q5BGA9	819	Multiple RNA-binding doma	yes	N/A	0.936	0.090	0.410	8e-10
Q4WJT7	825	Multiple RNA-binding doma	yes	N/A	0.848	0.081	0.416	1e-09
Q6CEW9	828	Multiple RNA-binding doma	yes	N/A	0.848	0.080	0.420	2e-09
Q06106	887	Multiple RNA-binding doma	yes	N/A	0.886	0.078	0.473	2e-09

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

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 808 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 867

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+FITK +AK+ 
Sbjct: 868 FGFVDFITKQDAKKA 882

Plays a role in embryo pre-implantation development.
Mus musculus (taxid: 10090)

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

 Score =  103 bits (257), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 816 AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRG 875

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+F+TK +AKR 
Sbjct: 876 FGFVDFLTKQDAKRA 890

Plays a role in embryo pre-implantation development.

Homo sapiens (taxid: 9606)

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

 Score = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 46/60 (76%), Gaps = 2/60 (3%)

Query: 20  GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
            SKI+++N+PF++   E+ +LF A+GE++ VR+PKK   +G HRGFGFVEF+T+ EAK  
Sbjct: 794 SSKIIIKNLPFESTIKEIRKLFTAYGEIQSVRIPKK--PNGGHRGFGFVEFLTEEEAKNA 851

Dictyostelium discoideum (taxid: 44689)

>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 = 65.9 bits (159), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 32/67 (47%), Positives = 45/67 (67%), Gaps = 4/67 (5%)

Query: 17  KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFIT 72
           K   +K+LV+N+PF+A + +V ELF A+G+LK +RLP+K V    G+   RGF F+EF T
Sbjct: 636 KTKSTKVLVKNLPFEATKKDVRELFSAYGQLKSLRLPRKAVPTSTGAQSTRGFAFLEFTT 695

Query: 73  KNEAKRV 79
             EA R 
Sbjct: 696 HTEAARA 702

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 = 65.9 bits (159), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 32/67 (47%), Positives = 45/67 (67%), Gaps = 4/67 (5%)

Query: 17  KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFIT 72
           K   +K+LV+N+PF+A + +V ELF A+G+LK +RLP+K V    G+   RGF F+EF T
Sbjct: 636 KTKSTKVLVKNLPFEATKKDVRELFSAYGQLKSLRLPRKAVPTSTGAQSTRGFAFLEFTT 695

Query: 73  KNEAKRV 79
             EA R 
Sbjct: 696 HTEAARA 702

Involved in pre-rRNA processing.

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

>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 = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/72 (44%), Positives = 49/72 (68%), Gaps = 4/72 (5%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A  V+++ S  +K  G+KIL++N+PF+A + +V+ L  A+G+L+ VR+PKK   S   RG
Sbjct: 707 AAEVRKQDS--SKPKGTKILIKNLPFEATKKDVQSLLGAYGQLRSVRVPKKFDRSA--RG 762

Query: 65  FGFVEFITKNEA 76
           F F EF+T  EA
Sbjct: 763 FAFAEFVTAREA 774

Involved in pre-rRNA processing.

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

>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 = 62.4 bits (150), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%), Gaps = 4/78 (5%)

Query: 2   GSEATTVKRKSSNVAKQTG--SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 59
           G +A   +RK     K     +KI+++N+PFQA + +V  LF A+G+L+ VR+PKK   S
Sbjct: 676 GMDAAEERRKEDTAKKIAARRTKIIIKNLPFQATKKDVRSLFGAYGQLRSVRVPKKFDRS 735

Query: 60  GLHRGFGFVEFITKNEAK 77
              RGFGF +F++  EA+
Sbjct: 736 A--RGFGFADFVSAREAE 751

Involved in pre-rRNA processing.

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

>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 = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/72 (41%), Positives = 49/72 (68%), Gaps = 5/72 (6%)

Query: 9   KRKSSNVAKQTG---SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF 65
           +R+  + AK+     +KI+++N+PFQA + +V  LF A+G+L+ VR+PKK   S   RGF
Sbjct: 687 ERRREDTAKKIAARRTKIIIKNLPFQATKKDVRSLFGAYGQLRSVRVPKKFDRSA--RGF 744

Query: 66  GFVEFITKNEAK 77
           GF +F++  EA+
Sbjct: 745 GFADFVSAREAE 756

Involved in pre-rRNA processing.

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

>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 = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 11  KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
           +++   K   SKIL++N+PF+A + +V++LF AFG LK VR+PKK   +   RGF F E+
Sbjct: 693 ETTETKKAIDSKILIKNLPFEATKKDVQKLFGAFGSLKTVRVPKKF--NSESRGFAFAEY 750

Query: 71  ITKNEAKRV 79
           ++  EA+  
Sbjct: 751 VSAKEAEHA 759

Involved in pre-rRNA processing.

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

>sp|Q06106|MRD1_YEAST Multiple RNA-binding domain-containing protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MRD1 PE=1 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/76 (47%), Positives = 52/76 (68%), Gaps = 6/76 (7%)

Query: 2   GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
            S++   K KS+   K++G KI+V+N+PF+A + +V ELF +FG+LK VR+PKK   S  
Sbjct: 748 ASQSGNTKTKSN---KKSG-KIIVKNLPFEATRKDVFELFNSFGQLKSVRVPKKFDKSA- 802

Query: 62  HRGFGFVEFITKNEAK 77
            RGF FVEF+   EA+
Sbjct: 803 -RGFAFVEFLLPKEAE 817

Involved in pre-rRNA processing. Required for maintaining steady-state levels of 40S ribosomal subunit. Required for the initial processing of pre-rRNA at the A0 to A2 sites, leading to the processing of the 23S pre-rRNA intermediate to the 18S rRNA.

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

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	79
345490259	904	PREDICTED: probable RNA-binding protein	0.962	0.084	0.645	3e-22
392352553	955	PREDICTED: probable RNA-binding protein	0.924	0.076	0.68	8e-21
30794154	952	probable RNA-binding protein 19 [Mus mus	0.924	0.076	0.68	8e-21
392332679	846	PREDICTED: probable RNA-binding protein	0.924	0.086	0.68	8e-21
12835985	590	unnamed protein product [Mus musculus]	0.949	0.127	0.68	1e-20
345790896	970	PREDICTED: probable RNA-binding protein	0.924	0.075	0.666	1e-20
168278697	960	RNA binding motif protein 19 [synthetic	0.924	0.076	0.666	1e-20
40788328	973	KIAA0682 protein [Homo sapiens]	0.924	0.075	0.666	1e-20
5912081	960	hypothetical protein [Homo sapiens]	0.924	0.076	0.666	1e-20
13279134	960	RBM19 protein [Homo sapiens] gi|13544005	0.924	0.076	0.666	1e-20

>gi|345490259|ref|XP_001605134.2| PREDICTED: probable RNA-binding protein 19-like [Nasonia vitripennis]

 Score =  108 bits (271), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 51/79 (64%), Positives = 62/79 (78%)

Query: 1   MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
           + ++  T  +K+S + +QTG+KILVRN+PFQA   EV+ELFKAFGE+K VRLPKKMVG  
Sbjct: 761 LQTDVITTAKKTSKITEQTGTKILVRNVPFQANADEVKELFKAFGEIKSVRLPKKMVGEE 820

Query: 61  LHRGFGFVEFITKNEAKRV 79
            HRGFGFVEF TK EAKR 
Sbjct: 821 KHRGFGFVEFYTKKEAKRA 839

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|392352553|ref|XP_003751242.1| PREDICTED: probable RNA-binding protein 19 [Rattus norvegicus]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 811 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 870

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+FITK +AK+ 
Sbjct: 871 FGFVDFITKQDAKKA 885

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|30794154|ref|NP_083038.1| probable RNA-binding protein 19 [Mus musculus] gi|73621449|sp|Q8R3C6.1|RBM19_MOUSE RecName: Full=Probable RNA-binding protein 19; AltName: Full=RNA-binding motif protein 19 gi|19343654|gb|AAH25619.1| RNA binding motif protein 19 [Mus musculus] gi|21707580|gb|AAH34010.1| RNA binding motif protein 19 [Mus musculus] gi|148687830|gb|EDL19777.1| RNA binding motif protein 19 [Mus musculus]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 808 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 867

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+FITK +AK+ 
Sbjct: 868 FGFVDFITKQDAKKA 882

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|392332679|ref|XP_003752658.1| PREDICTED: probable RNA-binding protein 19 [Rattus norvegicus]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 702 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 761

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+FITK +AK+ 
Sbjct: 762 FGFVDFITKQDAKKA 776

Source: Rattus norvegicus

Species: Rattus norvegicus

Genus: Rattus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|12835985|dbj|BAB23448.1| unnamed protein product [Mus musculus]

 Score =  103 bits (258), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 51/75 (68%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 446 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 505

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+FITK +AK+ 
Sbjct: 506 FGFVDFITKQDAKKA 520

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|345790896|ref|XP_543410.3| PREDICTED: probable RNA-binding protein 19 [Canis lupus familiaris]

 Score =  103 bits (258), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 57/75 (76%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T  RK     KQT SKILVRNIPFQA + E++ELF  FGELK VRLPKKM G+G HRG
Sbjct: 818 ALTSTRKKQVPRKQTTSKILVRNIPFQADKREIQELFSTFGELKTVRLPKKMTGTGTHRG 877

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+F+TK +AKR 
Sbjct: 878 FGFVDFLTKQDAKRA 892

Source: Canis lupus familiaris

Species: Canis lupus

Genus: Canis

Family: Canidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|168278697|dbj|BAG11228.1| RNA binding motif protein 19 [synthetic construct]

 Score =  103 bits (258), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 816 AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRG 875

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+F+TK +AKR 
Sbjct: 876 FGFVDFLTKQDAKRA 890

Source: synthetic construct

Species: synthetic construct

Genus: N/A

Family: N/A

Order: N/A

Class: N/A

Phylum: N/A

>gi|40788328|dbj|BAA31657.2| KIAA0682 protein [Homo sapiens]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 829 AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRG 888

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+F+TK +AKR 
Sbjct: 889 FGFVDFLTKQDAKRA 903

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|5912081|emb|CAB55987.1| hypothetical protein [Homo sapiens]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 816 AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRG 875

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+F+TK +AKR 
Sbjct: 876 FGFVDFLTKQDAKRA 890

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|13279134|gb|AAH04289.1| RBM19 protein [Homo sapiens] gi|13544005|gb|AAH06137.1| RBM19 protein [Homo sapiens] gi|190689379|gb|ACE86464.1| RNA binding motif protein 19 protein [synthetic construct] gi|190690741|gb|ACE87145.1| RNA binding motif protein 19 protein [synthetic construct]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/75 (66%), Positives = 56/75 (74%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct: 816 AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRG 875

Query: 65  FGFVEFITKNEAKRV 79
           FGFV+F+TK +AKR 
Sbjct: 876 FGFVDFLTKQDAKRA 890

Source: Homo sapiens

Species: Homo sapiens

Genus: Homo

Family: Hominidae

Order: Primates

Class: Mammalia

Phylum: Chordata

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	79
MGI|MGI:1921361	952	Rbm19 "RNA binding motif prote	0.936	0.077	0.689	1.6e-20
UNIPROTKB|Q9Y4C8	960	RBM19 "Probable RNA-binding pr	0.936	0.077	0.675	2.1e-20
UNIPROTKB|E2RRF5	968	RBM19 "Uncharacterized protein	0.936	0.076	0.675	2.7e-20
UNIPROTKB|F1RKD1	965	RBM19 "Uncharacterized protein	0.936	0.076	0.675	3.5e-20
UNIPROTKB|F1P1R2	621	RBM19 "Uncharacterized protein	0.936	0.119	0.648	1.5e-19
UNIPROTKB|F1NEC5	945	RBM19 "Uncharacterized protein	0.936	0.078	0.648	3.1e-19
ZFIN|ZDB-GENE-031125-3	927	rbm19 "RNA binding motif prote	0.949	0.080	0.618	7.4e-18
FB|FBgn0036018	918	CG3335 [Drosophila melanogaste	0.886	0.076	0.591	1.1e-16
UNIPROTKB|F1N0L5	920	RBM19 "Uncharacterized protein	0.873	0.075	0.565	2.1e-15
DICTYBASE|DDB_G0284663	895	mrd1 "RNA-binding region RNP-1	0.696	0.061	0.543	5.2e-12

MGI|MGI:1921361 Rbm19 "RNA binding motif protein 19" [Mus musculus (taxid:10090)]

 Score = 254 (94.5 bits), Expect = 1.6e-20, P = 1.6e-20
 Identities = 51/74 (68%), Positives = 56/74 (75%)

Query:     5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
             A T  RK     KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct:   808 ALTSTRKKQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 867

Query:    65 FGFVEFITKNEAKR 78
             FGFV+FITK +AK+
Sbjct:   868 FGFVDFITKQDAKK 881

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005694 "chromosome" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO;IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0007275 "multicellular organismal development" evidence=IEA

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

UNIPROTKB|Q9Y4C8 RBM19 "Probable RNA-binding protein 19" [Homo sapiens (taxid:9606)]

 Score = 253 (94.1 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 50/74 (67%), Positives = 56/74 (75%)

Query:     5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
             A T+ RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct:   816 AVTLARKKQVPRKQTTSKILVRNIPFQAHSREIRELFSTFGELKTVRLPKKMTGTGTHRG 875

Query:    65 FGFVEFITKNEAKR 78
             FGFV+F+TK +AKR
Sbjct:   876 FGFVDFLTKQDAKR 889

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISS

GO:0005730 "nucleolus" evidence=ISS;IDA

GO:0005737 "cytoplasm" evidence=ISS;IDA

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

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|E2RRF5 RBM19 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 252 (93.8 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 50/74 (67%), Positives = 57/74 (77%)

Query:     5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
             A T  RK     KQT SKILVRNIPFQA + E++ELF  FGELK VRLPKKM G+G HRG
Sbjct:   816 ALTSTRKKQVPRKQTTSKILVRNIPFQADKREIQELFSTFGELKTVRLPKKMTGTGTHRG 875

Query:    65 FGFVEFITKNEAKR 78
             FGFV+F+TK +AKR
Sbjct:   876 FGFVDFLTKQDAKR 889

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 251 (93.4 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 50/74 (67%), Positives = 54/74 (72%)

Query:     5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
             A T  RK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct:   821 APTATRKKQVARKQTTSKILVRNIPFQADSREIRELFSTFGELKTVRLPKKMTGTGTHRG 880

Query:    65 FGFVEFITKNEAKR 78
             FGFV+F TK +AKR
Sbjct:   881 FGFVDFFTKQDAKR 894

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

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

 Score = 242 (90.2 bits), Expect = 1.5e-19, P = 1.5e-19
 Identities = 48/74 (64%), Positives = 54/74 (72%)

Query:     5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
             A    RK   V KQ  SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct:   479 AVKSSRKKQTVKKQKTSKILVRNIPFQATVREIRELFSTFGELKTVRLPKKMAGTGSHRG 538

Query:    65 FGFVEFITKNEAKR 78
             FGFV+F+TK +AK+
Sbjct:   539 FGFVDFLTKQDAKK 552

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

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

 Score = 242 (90.2 bits), Expect = 3.1e-19, P = 3.1e-19
 Identities = 48/74 (64%), Positives = 54/74 (72%)

Query:     5 ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
             A    RK   V KQ  SKILVRNIPFQA   E+ ELF  FGELK VRLPKKM G+G HRG
Sbjct:   803 AVKSSRKKQTVKKQKTSKILVRNIPFQATVREIRELFSTFGELKTVRLPKKMAGTGSHRG 862

Query:    65 FGFVEFITKNEAKR 78
             FGFV+F+TK +AK+
Sbjct:   863 FGFVDFLTKQDAKK 876

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

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

 Score = 229 (85.7 bits), Expect = 7.4e-18, P = 7.4e-18
 Identities = 47/76 (61%), Positives = 54/76 (71%)

Query:     3 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 62
             S     KRK     KQT SKILVRNIPFQA   E+ ELF  FGELK VRLPKK +G G H
Sbjct:   787 SGVAQAKRKKQTARKQTTSKILVRNIPFQATVKELRELFCTFGELKTVRLPKKGIG-GSH 845

Query:    63 RGFGFVEFITKNEAKR 78
             RGFGF++F+TK +AK+
Sbjct:   846 RGFGFIDFLTKQDAKK 861

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

FB|FBgn0036018 CG3335 [Drosophila melanogaster (taxid:7227)]

 Score = 218 (81.8 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 42/71 (59%), Positives = 57/71 (80%)

Query:     9 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGF 67
             +R+ ++  KQTG+KILVRNIPFQA+  EV ++FKAFGEL+ +R+PKK   G   HRGFGF
Sbjct:   773 QRRLASQKKQTGTKILVRNIPFQAQYREVRDIFKAFGELRSLRIPKKATTGEDAHRGFGF 832

Query:    68 VEFITKNEAKR 78
             V++++K EAKR
Sbjct:   833 VDYMSKAEAKR 843

GO:0004386 "helicase activity" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1N0L5 RBM19 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 206 (77.6 bits), Expect = 2.1e-15, P = 2.1e-15
 Identities = 39/69 (56%), Positives = 50/69 (72%)

Query:    10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
             R   +  +QT +KI VR  PFQ    E++E+F  FGELK VRLPKK+ G+G HRGFGFV+
Sbjct:   781 RHKHSPRRQTDTKIWVRVCPFQGDSRELKEIFNTFGELKTVRLPKKLTGTGTHRGFGFVD 840

Query:    70 FITKNEAKR 78
             F+TK +AKR
Sbjct:   841 FLTKQDAKR 849

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

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

 Score = 169 (64.5 bits), Expect = 5.2e-12, Sum P(2) = 5.2e-12
 Identities = 31/57 (54%), Positives = 45/57 (78%)

Query:    21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
             SKI+++N+PF++   E+ +LF A+GE++ VR+PKK  G   HRGFGFVEF+T+ EAK
Sbjct:   795 SKIIIKNLPFESTIKEIRKLFTAYGEIQSVRIPKKPNGG--HRGFGFVEFLTEEEAK 849

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

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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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8R3C6	RBM19_MOUSE	No assigned EC number	0.68	0.9240	0.0766	yes	N/A
Q6CQR6	MRD1_KLULA	No assigned EC number	0.5357	0.6835	0.0615	yes	N/A
Q54PB2	MRD1_DICDI	No assigned EC number	0.5166	0.7341	0.0648	yes	N/A
Q6FXP4	MRD1_CANGA	No assigned EC number	0.5081	0.7468	0.0685	yes	N/A
Q9Y4C8	RBM19_HUMAN	No assigned EC number	0.6666	0.9240	0.0760	yes	N/A
Q75A83	MRD1_ASHGO	No assigned EC number	0.5283	0.6455	0.0608	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	79
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-30
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	6e-23
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	2e-14
smart00360	73	smart00360, RRM, RNA recognition motif	1e-12
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-10
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-08
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-07
cd12569	72	cd12569, RRM4_RBM19, RNA recognition motif 4 in RN	7e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	9e-07
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-06
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	2e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-06
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	7e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	8e-06
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	3e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-05
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	5e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	6e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	9e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-04
cd12568	72	cd12568, RRM3_MRD1, RNA recognition motif 3 in yea	1e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	3e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	5e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	7e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	7e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	9e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	0.001
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.001
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.001
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.002
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	0.002
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.002
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.002
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.002
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.003
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.003
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.003
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.003
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.004
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.004
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.004
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.004

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

 Score =  101 bits (253), Expect = 3e-30
 Identities = 43/58 (74%), Positives = 48/58 (82%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          SKILVRNIPF+A   E+ ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +AKR
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKR 58

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|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 = 82.7 bits (205), Expect = 6e-23
 Identities = 34/57 (59%), Positives = 45/57 (78%), Gaps = 2/57 (3%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          +K++VRN+PF+A + E+ ELF  FG++K VRLPKK  GS  HRGF FVEF+TK EA+
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGS--HRGFAFVEFVTKQEAQ 55

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

 Score = 61.0 bits (148), Expect = 2e-14
 Identities = 30/56 (53%), Positives = 40/56 (71%), Gaps = 2/56 (3%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          +KILV+N+PF+A + +V  LF ++G+LK VR+PKK   S   RGF FVEF T  EA
Sbjct: 1  TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA--RGFAFVEFSTAKEA 54

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 = 56.8 bits (138), Expect = 1e-12
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           + V N+P    + E+ ELF  FG+++ VRL +    +G  +GF FVEF ++ +A++ 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKE-TGKSKGFAFVEFESEEDAEKA 57

Length = 73

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

 Score = 52.3 bits (126), Expect = 6e-11
 Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 2/59 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK--MVGSGLHRGFGFVEFITKNEAKR 78
          +I VRN+ F+  + ++  +F  FGE++ +R+PKK       L+ GF FV F   + A+ 
Sbjct: 2  EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

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

 Score = 51.2 bits (123), Expect = 2e-10
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + V N+P    + ++ ELF  FGE++ VR+ +   G    +GF FVEF +  +A++ 
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGK--SKGFAFVEFESPEDAEKA 55

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

 Score = 50.7 bits (122), Expect = 2e-10
 Identities = 20/55 (36%), Positives = 38/55 (69%), Gaps = 2/55 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          +++VRN+PF+  ++++++LF  FG +  V +P+K    G  +GF FV+F +K +A
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP--DGKKKGFAFVQFTSKADA 53

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

 Score = 50.3 bits (121), Expect = 5e-10
 Identities = 23/57 (40%), Positives = 38/57 (66%), Gaps = 1/57 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + +RN+PF A + E++ELF  FGE+K+ R+ K  + +G  +G  FV+F TK  A++ 
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKL-TGHSKGTAFVKFKTKESAQKC 58

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 47.2 bits (113), Expect = 5e-09
 Identities = 16/56 (28%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + V N+P    + ++++LF  FG ++ +R+ +    +G  +GF FVEF  + +A++
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD--ETGRSKGFAFVEFEDEEDAEK 54

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. 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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 46.2 bits (110), Expect = 2e-08
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + V N+ + A+Q ++EE FK  GE+  VR+ +   G    +GFG VEF T+  A++
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRS--KGFGHVEFATEEGAQK 55

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

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

 Score = 45.7 bits (109), Expect = 2e-08
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           + V N+P+   + ++++LF  FGE+   R+      +G  RGFGFVE  T  EA   
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRE-TGRSRGFGFVEMETAEEANAA 57

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 45.6 bits (109), Expect = 2e-08
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + VRN+P    + ++ E F  +G+++ VRL +        RGF FVEF +  +A+  
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN---KDRPRGFAFVEFASPEDAEAA 54

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

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

 Score = 45.3 bits (108), Expect = 3e-08
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          + V  +  +  +  +   F  FG++K +++P     +  HRGF FVEF    +A 
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYE-TQKHRGFAFVEFEEPEDAA 54

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

 Score = 43.9 bits (104), Expect = 1e-07
 Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          + V N+ F A +  + E F  +GE+  VRLP     SG  +GFG+VEF ++  A+
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDP-DSGRPKGFGYVEFSSQEAAQ 54

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

 Score = 43.0 bits (102), Expect = 2e-07
 Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 5/58 (8%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + VRN+P+     ++EE F   G +K  FV   K   GS   RGFG+V F  + +AKR
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDK---GSKKCRGFGYVTFALEEDAKR 56

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

 Score = 41.9 bits (99), Expect = 6e-07
 Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 5/57 (8%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEA 76
          ++ VRN+PF   + E+ ELF+AFGE+  V LP  K+   +   +GF FV F+    A
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKE---TKRSKGFAFVSFMFPEHA 54

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

>gnl|CDD|241013 cd12569, RRM4_RBM19, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 42.0 bits (99), Expect = 7e-07
 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 7/56 (12%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          ILV+N+P     +E+ ELF  FG L  V LP   +          VEF+  +EAK 
Sbjct: 3  ILVKNLPAGTLTAELRELFSKFGSLGRVLLPPAGIT-------AIVEFLEPSEAKL 51

This subgroup corresponds to the RRM4 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 = 72

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

 Score = 41.6 bits (98), Expect = 9e-07
 Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 6/61 (9%)

Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNE 75
          +TG ++ VRN+P+  K+ ++E+LF  FGEL  V +   KK   SG  +GF +V F+   +
Sbjct: 1  ETG-RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKK---SGKSKGFAYVLFLDPED 56

Query: 76 A 76
          A
Sbjct: 57 A 57

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

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

 Score = 41.6 bits (98), Expect = 1e-06
 Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + V  +P  A    ++ +F  +G + +V LP +   +G  +GF F+EF T  EA++ 
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLP-RYKHTGDIKGFAFIEFETPEEAQKA 57

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

 Score = 41.2 bits (97), Expect = 1e-06
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          K+ V  +PF   + E+E+LFK  G +K VRL      SG  +G  +VE+  ++ A +
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR--SGKPKGLAYVEYENESSASQ 58

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

>gnl|CDD|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 40.7 bits (96), Expect = 2e-06
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 7/56 (12%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          ILV+N+PF   + E+ ELF+ FG L  + LP         R    VEF+  ++A++
Sbjct: 3  ILVKNLPFGTTEEELRELFEKFGSLGRLLLPPS-------RTIALVEFLEPSDARK 51

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 40.3 bits (95), Expect = 4e-06
 Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          +I V ++     + +++ +F+AFG++K   L      +G H+G+GF+E+     A+
Sbjct: 2  RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPE-TGKHKGYGFIEYENPQSAQ 56

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

 Score = 40.3 bits (95), Expect = 4e-06
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV----GSGLHRGFGFVEFITKNEAKR 78
          + V+N+ F+  +  +++ F+  G ++ V + KK      G  L  G+GFVEF +K  A++
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 79 V 79
           
Sbjct: 63 A 63

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

 Score = 39.8 bits (94), Expect = 5e-06
 Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          I V N+   A + ++ ELF+ FG +  V L K    +G  RGF FV F T+ +A+R 
Sbjct: 2  IRVTNLSEDADEDDLRELFRPFGPISRVYLAKDK-ETGQSRGFAFVTFHTREDAERA 57

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

 Score = 39.6 bits (93), Expect = 5e-06
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          + V N+ +   + E+ +LF   GE+  VRL K   G    +G+ +VEF  +   +
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGK--SKGYAYVEFENEESVQ 54

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

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

 Score = 40.3 bits (94), Expect = 5e-06
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
             + VRN+P+ A +  +   F  FG +++   P     +G  +G GFV F  +    
Sbjct: 1  DFTLFVRNLPYDATEESLAPHFSKFGSVRYAL-PVIDKSTGRAKGTGFVCFKDQYTYN 57

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

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

 Score = 39.3 bits (92), Expect = 7e-06
 Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           ++V  +P++  + ++++ F  FGEL  V++ KK   +G  +GFGFV F    +  +V
Sbjct: 1  DLIVLGLPWKTTEQDLKDYFSTFGELLMVQV-KKDPKTGQSKGFGFVRFADYEDQVKV 57

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

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

 Score = 39.2 bits (92), Expect = 7e-06
 Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 5/56 (8%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNE 75
          K+ V N+P+     E++E F  FG++K   +P  K+   +GL +G+GFV F +++ 
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKE---TGLSKGYGFVSFSSRDG 53

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

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 39.2 bits (92), Expect = 8e-06
 Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          S+++V+N+P   K+ ++ +LF+AFG +  V+L  K    G  R FGFV + T+ EA+
Sbjct: 1  SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQL--KYTKDGKFRKFGFVGYKTEEEAQ 55

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

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 39.1 bits (92), Expect = 9e-06
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G+K+ V  +  +  + E+E LF  FG ++ V L K    +G  RGFGFV F +  +A  
Sbjct: 1  GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPE-TGESRGFGFVTFESVEDADA 58

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

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

 Score = 38.8 bits (91), Expect = 1e-05
 Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          V  +P    Q E+E LF  +G +   R+    V  GL RG GF+ F  + EA+R
Sbjct: 5  VSGLPKTMTQQELEALFSPYGRIITSRILCDNVT-GLSRGVGFIRFDKRIEAER 57

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

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

 Score = 38.4 bits (90), Expect = 2e-05
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          V N+ ++    ++  +F+ +GE+  V +P+    +   RGF FV F  K +A
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDR-YTRESRGFAFVRFYDKRDA 53

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

 Score = 40.3 bits (93), Expect = 2e-05
 Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 7   TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 66
           +   KS   +K+  + + V N+P+   + ++ ELFK FG +K VRL +    +G  RGF 
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRE-TGKSRGFA 160

Query: 67  FVEFITKNEAKRV 79
           FVEF ++  A++ 
Sbjct: 161 FVEFESEESAEKA 173

Length = 306

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

 Score = 38.3 bits (90), Expect = 2e-05
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G ++ V  IP    + E+  LF+  G +  +RL   M  SGL+RG+ FV +  K  A+R
Sbjct: 1  GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRL--MMDFSGLNRGYAFVTYTNKEAAQR 57

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

 Score = 38.3 bits (90), Expect = 2e-05
 Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          + V N+  +  +  + ELF   G +  V +PK  V +  H+G+GFVEF+++ +A
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRV-TQAHQGYGFVEFLSEEDA 53

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

 Score = 38.3 bits (89), Expect = 2e-05
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + VRN+ F   Q ++ + F     +K   V    +   +G  RG+GFV F    +A+ 
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPE---TGESRGYGFVTFAMLEDAQE 56

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

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

 Score = 38.3 bits (90), Expect = 2e-05
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          V N P    QS++ +LF+ +GE+  +R P         R F +V+F +   A  
Sbjct: 5  VTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNK--TRRFCYVQFTSPESAAA 56

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

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

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 22  KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
           K+ V N+ F   + E+ ++F+ FG+++ V+L +     G  +GFGF++F    EAK
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPET-GRSKGFGFIQFHDAEEAK 242

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

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

 Score = 38.0 bits (89), Expect = 3e-05
 Identities = 17/54 (31%), Positives = 34/54 (62%), Gaps = 1/54 (1%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          V N+ F   + ++  +F+ FGE++FV+L +    +G  +G+GF++F    +AK+
Sbjct: 3  VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDP-ETGRSKGYGFIQFADAEDAKK 55

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

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.7 bits (88), Expect = 3e-05
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          I++R +P    + ++     + G E K VRL ++   +G  RGF FVEF++  EA R
Sbjct: 5  IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRK-TTGASRGFAFVEFMSLEEATR 60

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, 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. Both, RBM5 and RBM10, 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 = 81

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

 Score = 37.5 bits (88), Expect = 3e-05
 Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 7/56 (12%)

Query: 24 LVRNIPFQAKQSEVEELFKAFGELKFVRLP-KKMVGSGLHRGFGFVEFITKNEAKR 78
          L RN+     +  ++E+F  +G +K V LP  + V   L RG+ +VEF +  +A++
Sbjct: 6  LTRNV----NKDHLKEIFSNYGTVKDVDLPIDREVN--LPRGYAYVEFESPEDAEK 55

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

 Score = 39.5 bits (92), Expect = 3e-05
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           R SS+  K  G+ + V  +P    Q E+E +F  FG++   R+    V +GL +G GF+ 
Sbjct: 81  RPSSDSIK--GANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV-TGLSKGVGFIR 137

Query: 70  FITKNEAKR 78
           F  ++EA R
Sbjct: 138 FDKRDEADR 146

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

>gnl|CDD|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 = 37.6 bits (88), Expect = 3e-05
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          KI +  +P    + +V+EL ++FG+LK   L K    +GL +G+ F E++  +  
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKD-SATGLSKGYAFCEYLDPSVT 55

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

 Score = 37.6 bits (88), Expect = 4e-05
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          +KI V  +P+      + + F  FGE++   V   ++   +G  RG+GFV F  K  A+R
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQ---TGKSRGYGFVTFKDKESAER 57

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 37.4 bits (87), Expect = 4e-05
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          ++ V NIPF+ +  ++ ++F  FG +  V +     GS   +GFGFV F    +A R
Sbjct: 2  RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS---KGFGFVTFANSADADR 55

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

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

 Score = 37.6 bits (88), Expect = 4e-05
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          + V N+P +    +  EL   FG ++   L       G  +G+GFVE+ +K  A
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSEST-GESKGYGFVEYASKASA 54

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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 37.4 bits (87), Expect = 5e-05
 Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 27 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          N+P+   + +++E F+    +  VRLP++    G  RGFG+ EF
Sbjct: 8  NLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEF 50

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 39.0 bits (91), Expect = 5e-05
 Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 9   KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
           + +     K  G  + V+N+       ++ ELF   GE+   ++   +   G+ RGFGFV
Sbjct: 274 ELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV--MLDEKGVSRGFGFV 331

Query: 69  EFITKNEAKR 78
            F    EA R
Sbjct: 332 CFSNPEEANR 341

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

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

 Score = 37.6 bits (88), Expect = 5e-05
 Identities = 15/56 (26%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + V  +  Q  +  + E+F  +G+++ +RL + +V +G  +G+ FVE+  + +A R
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIV-TGFSKGYAFVEYEHERDALR 60

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

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

 Score = 37.4 bits (86), Expect = 6e-05
 Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++   +A+R
Sbjct: 2  TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVNAKDAER 58

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

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

 Score = 36.8 bits (85), Expect = 9e-05
 Identities = 14/48 (29%), Positives = 30/48 (62%), Gaps = 3/48 (6%)

Query: 22 KILVRNIPFQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
          K+++RN+P+  K+   ++++F  +G+++   +P+K    G   GF FV
Sbjct: 2  KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRK--RGGKLCGFAFV 47

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

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

 Score = 36.5 bits (85), Expect = 1e-04
 Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 6/48 (12%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          + VRNI    +  E+  LF+ FG++      + +  +  HRGF  V +
Sbjct: 4  LFVRNINSNVEDEELRALFEQFGDI------RTLYTACKHRGFIMVSY 45

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|241012 cd12568, RRM3_MRD1, RNA recognition motif 3 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.2 bits (84), Expect = 1e-04
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 7/56 (12%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          ILV+N P+     E+ +LF+  G+L  V +P     +G       VEF    +A+ 
Sbjct: 3  ILVKNFPYGTTAEELRDLFEPHGKLTRVLMPP----AGT---IAIVEFANPQQARL 51

This subgroup corresponds to the RRM3 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 = 72

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

 Score = 36.4 bits (85), Expect = 1e-04
 Identities = 14/61 (22%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + +++R +     + ++ +   A   +    VRL +  + +G  RGF FVEF +  +A +
Sbjct: 3  NTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKL-TGTSRGFAFVEFPSLEDATQ 61

Query: 79 V 79
           
Sbjct: 62 W 62

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

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 22  KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
           +I + N+P    + +++EL ++FG+LK   L K  + +GL +G+ F E+
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKD-IATGLSKGYAFCEY 344

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

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

 Score = 36.2 bits (84), Expect = 1e-04
 Identities = 15/58 (25%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + ++V  +P    Q E+  LF+A G ++  ++ +  + +G   G+GFV+++ +N+A++
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRI-TGQSLGYGFVDYVDENDAQK 57

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

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

 Score = 36.0 bits (84), Expect = 1e-04
 Identities = 17/57 (29%), Positives = 33/57 (57%), Gaps = 10/57 (17%)

Query: 21 SKILVRNIP-FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          S++ V N+   +  + ++EE+F  +G         K++G  LH+G+GFV+F  + +A
Sbjct: 1  SRVFVGNLNTDKVSKEDLEEIFSKYG---------KILGISLHKGYGFVQFDNEEDA 48

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

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

 Score = 35.8 bits (83), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 9/49 (18%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          ++ +  +P++A++ +VE  FK +G ++ +          L  GFGFVEF
Sbjct: 1  RVYIGRLPYRARERDVERFFKGYGRIREIN---------LKNGFGFVEF 40

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

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

 Score = 35.8 bits (83), Expect = 2e-04
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 11/62 (17%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLP-----KKMVGSGLHRGFGFVEFITKNEA 76
          ++ +RN+ +   + ++E+LF  +G L  V LP     KK       +GF FV ++    A
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKP------KGFAFVTYMIPEHA 57

Query: 77 KR 78
           +
Sbjct: 58 VK 59

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

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 35.7 bits (83), Expect = 2e-04
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          + V NIP+ A + ++ E+F   G +   RL      +G  +G+GF EF
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRD-TGKPKGYGFCEF 47

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

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

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          S+I+V+N+P    +  + E F++ GE+  V++ +     G  R FGFV F ++ +A++
Sbjct: 1  SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT--RDGKSRRFGFVGFKSEEDAQQ 56

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

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 35.3 bits (81), Expect = 3e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G ++ V  IP    + E+  +F++ G +  +RL   M   G +RG+ FV +  K+EAKR
Sbjct: 1  GCEVFVGKIPRDVYEDELVPVFESVGRIYEMRL--MMDFDGKNRGYAFVMYTQKHEAKR 57

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 18/59 (30%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          ++I V  IP    + E+ + F  FG +K V++      +G+ +G+GFV F T+ +A+++
Sbjct: 3  NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR--AGVSKGYGFVTFETQEDAEKI 59

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

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

 Score = 34.7 bits (80), Expect = 5e-04
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
           ++ V +I F+  +  + + F  FG +K + +    V +  H+GF FVE+
Sbjct: 1  CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPV-TMKHKGFAFVEY 49

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

 Score = 34.5 bits (79), Expect = 7e-04
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 5/56 (8%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + N+P    Q + EEL + FG L+  F+   +    +G  +G+GFVE++ K+ A R
Sbjct: 4  IANLPPTYTQQQFEELVRPFGNLERCFLVYSET---TGHSKGYGFVEYMKKDSAAR 56

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

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

 Score = 34.3 bits (79), Expect = 7e-04
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          ++ V N+P    + E++E FK FG +  VR+  K  G G    FGFV F
Sbjct: 5  QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKG-GGGRLPNFGFVVF 52

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

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

 Score = 34.2 bits (79), Expect = 7e-04
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          I VRN+PF     ++++LF+  G +  +R   K    G  +GFG V F +  +A+R
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNV--LRADVKTDNDGRSKGFGTVLFESPEDAQR 54

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

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 34.5 bits (79), Expect = 7e-04
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          V N+P      E EEL +A+G ++   L    V +G  +G+GFVE++ K+ A +
Sbjct: 4  VTNLPISFTLEEFEELVRAYGNIERCFLVYSEV-TGHSKGYGFVEYMKKDSASK 56

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 34.2 bits (78), Expect = 9e-04
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          G++I V  IP    + E+  LF+  G +  +RL    + +GL+RG+ FV F TK  A+
Sbjct: 1  GTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPL-TGLNRGYAFVTFCTKEAAQ 57

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           R+++ + K T   + V+N+     + ++ ELF  FGE+          GSG  RGF FV 
Sbjct: 170 REAAPLKKFT--NLYVKNLDPSVNEDKLRELFAKFGEI--TSAAVMKDGSGRSRGFAFVN 225

Query: 70  FITKNEAKR 78
           F    +A +
Sbjct: 226 FEKHEDAAK 234

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

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 34.0 bits (78), Expect = 0.001
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 9/58 (15%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG--FGFVEFITKNEAK 77
          +I V N+P   +  ++E+LF  +G ++ + L  +       RG  F FVEF    +A+
Sbjct: 1  RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNR-------RGPPFAFVEFEDPRDAE 51

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 13  SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 72
           S V    G ++ V  IP    + E+  LF+  G +  +RL   M  SG +RG+ FV F  
Sbjct: 51  SGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRL--MMDFSGQNRGYAFVTFCG 108

Query: 73  KNEAKR 78
           K EAK 
Sbjct: 109 KEEAKE 114

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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 33.5 bits (77), Expect = 0.001
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          +I V N+P   ++ ++E+LF  +G +K + L  +  G      F FVEF
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGP----PFAFVEF 45

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEA 76
          ++ + ++V  +P    Q E+  LF + GE++  +L + K+ G  L  G+GFV ++   +A
Sbjct: 1  ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSL--GYGFVNYVRPEDA 58

Query: 77 KR 78
          ++
Sbjct: 59 EK 60

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

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 33.5 bits (77), Expect = 0.002
 Identities = 8/28 (28%), Positives = 15/28 (53%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELK 48
           KI + NIP   +  +++ L   +G +K
Sbjct: 1  RKIQISNIPPHVRWEDLDSLLSTYGTVK 28

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 33.2 bits (76), Expect = 0.002
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 22 KILVRNIPFQAKQSEVEELFKA-FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          ++ + NIP+  K  ++++LF+   GE+ +V L K     G  RG G VEF  K   ++
Sbjct: 1  RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD--EEGKSRGCGVVEFKDKESVQK 56

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

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

 Score = 32.9 bits (76), Expect = 0.002
 Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 7/54 (12%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRL---PKKMVGSGLHRGFGFVEFITK 73
          + V N+PF  ++ E+ + F+  G+++ VR+    K    +G+ +GFG+V F TK
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRK----TGIGKGFGYVLFKTK 51

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

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

 Score = 34.7 bits (79), Expect = 0.002
 Identities = 15/49 (30%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 22  KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
           +I V ++     +++++ +F+AFGE+   +L +   G G H+G+GF+E+
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRG-HKGYGFIEY 253

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|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 33.0 bits (75), Expect = 0.002
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          ++ V N+P    +SE++E F +FG +  +R+  K VG  L   FGFV F      +R+
Sbjct: 7  QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKL-PNFGFVVFDDSEPVQRI 63

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 32.9 bits (75), Expect = 0.003
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G ++ V  IP    + E+  LF+  G++   RL   M  SG +RG+ FV + TK EA+ 
Sbjct: 1  GCEVFVGKIPRDMYEDELVPLFERAGKIYEFRL--MMEFSGENRGYAFVMYTTKEEAQL 57

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

 Score = 32.6 bits (75), Expect = 0.003
 Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 7/58 (12%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           ++ V N+P    + E +ELF  +GE+  V L K+       +GFGF+   T+  A++
Sbjct: 2  CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-------KGFGFIRLDTRTNAEK 52

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

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

 Score = 32.5 bits (75), Expect = 0.003
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 8/57 (14%)

Query: 21 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          +KIL ++N+P +  +  +E LF  F   K VRL  +       RG  FVEF T+ +A
Sbjct: 2  NKILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-------RGIAFVEFETEEQA 51

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

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

 Score = 32.7 bits (74), Expect = 0.003
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          + + V  +P    Q E+E+LF  +G +   R+    V +G+ RG GF+ F  + EA+
Sbjct: 2  ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQV-TGISRGVGFIRFDKRIEAE 57

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 32.4 bits (74), Expect = 0.003
 Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 9/46 (19%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          VR  P    +S + E+F  +G +K V++            F FVEF
Sbjct: 4  VRPFPPDTSESAIREIFSPYGAVKEVKMIS---------NFAFVEF 40

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

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

 Score = 32.6 bits (74), Expect = 0.004
 Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          + + V N+P Q  + E+ ++F+A+G +    L +    +GL RG  FV +  + EA+
Sbjct: 1  TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKS-TGLPRGVAFVRYDKREEAQ 56

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

 Score = 32.5 bits (75), Expect = 0.004
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 13/61 (21%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR------GFGFVEFITKNEA 76
          + V N+ F   + ++ ELF   G++K + +       GL R      GF FVE+ T+ +A
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIM-------GLDRFTKTPCGFCFVEYYTREDA 53

Query: 77 K 77
          +
Sbjct: 54 E 54

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

 Score = 32.2 bits (74), Expect = 0.004
 Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + + ++P    + E+ + F  FG +  +RL +    +G  +G+ FVEF +   AK V
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSK-KTGKSKGYAFVEFESPEVAKIV 57

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

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

 Score = 32.2 bits (74), Expect = 0.004
 Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 37 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          +   F   GE+  V++  +   +G   G+GFVEF T   A++ 
Sbjct: 16 IYSAFAECGEVTSVKI-IRNKQTGKSAGYGFVEFATHEAAEQA 57

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	79
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.78
KOG0149|consensus	247		99.77
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
KOG0122|consensus	270		99.68
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.65
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.65
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.64
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.63
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.63
KOG0121|consensus	153		99.63
PLN03120	260	nucleic acid binding protein; Provisional	99.62
KOG0113|consensus	335		99.62
PLN03121	243	nucleic acid binding protein; Provisional	99.6
KOG0125|consensus	376		99.6
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.6
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.59
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.57
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.54
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.53
KOG0144|consensus	510		99.53
KOG0117|consensus	506		99.53
KOG0127|consensus	678		99.52
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.52
smart00362	72	RRM_2 RNA recognition motif.	99.52
KOG0114|consensus	124		99.51
KOG0148|consensus	321		99.51
KOG0107|consensus	195		99.49
KOG0126|consensus	219		99.48
KOG0131|consensus	203		99.47
smart00360	71	RRM RNA recognition motif.	99.47
PLN03213	759	repressor of silencing 3; Provisional	99.45
KOG4207|consensus	256		99.44
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.44
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.43
KOG0130|consensus	170		99.43
KOG0148|consensus	321		99.42
KOG0144|consensus	510		99.42
KOG0105|consensus	241		99.39
KOG0145|consensus	360		99.38
KOG0108|consensus	435		99.36
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.35
KOG0111|consensus	298		99.34
KOG0124|consensus	544		99.3
KOG4205|consensus	311		99.28
KOG0127|consensus	678		99.27
KOG0146|consensus	371		99.26
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.26
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.26
KOG0146|consensus	371		99.25
KOG0415|consensus	479		99.24
KOG0145|consensus	360		99.24
KOG0147|consensus	549		99.24
KOG4212|consensus	608		99.2
KOG0123|consensus	369		99.18
KOG0117|consensus	506		99.17
KOG0110|consensus	725		99.14
KOG4208|consensus	214		99.13
KOG0124|consensus	544		99.11
smart00361	70	RRM_1 RNA recognition motif.	99.09
KOG0116|consensus	419		99.07
KOG4205|consensus	311		99.02
KOG0153|consensus	377		99.0
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.97
KOG0123|consensus	369		98.95
KOG0132|consensus	894		98.93
KOG0109|consensus	346		98.93
KOG4211|consensus	510		98.91
KOG4206|consensus	221		98.88
KOG0533|consensus	243		98.85
KOG0131|consensus	203		98.82
KOG4661|consensus	940		98.8
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.78
KOG0110|consensus	725		98.76
KOG4660|consensus	549		98.75
KOG4211|consensus	510		98.72
KOG4209|consensus	231		98.71
KOG4212|consensus	608		98.7
KOG1548|consensus	382		98.58
KOG0106|consensus	216		98.58
KOG0226|consensus	290		98.55
KOG4454|consensus	267		98.54
KOG1457|consensus	284		98.53
KOG0109|consensus	346		98.47
KOG0151|consensus	877		98.47
KOG1457|consensus	284		98.45
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.42
KOG0147|consensus	549		98.3
KOG4849|consensus	498		98.2
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.2
KOG0120|consensus	500		98.08
KOG4210|consensus	285		98.01
KOG1190|consensus	492		98.0
KOG4206|consensus	221		97.9
KOG0129|consensus	520		97.83
KOG1995|consensus	351		97.81
KOG0129|consensus	520		97.77
KOG1365|consensus	508		97.76
KOG2314|consensus	698		97.74
KOG1365|consensus	508		97.71
KOG1855|consensus	484		97.5
KOG3152|consensus	278		97.48
KOG0128|consensus	881		97.48
KOG4307|consensus	944		97.47
KOG0105|consensus	241		97.44
KOG0128|consensus	881		97.34
KOG0115|consensus	275		97.32
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.3
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.3
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.29
KOG4676|consensus	479		97.23
KOG0106|consensus	216		97.08
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.0
KOG1456|consensus	494		96.92
KOG4307|consensus	944		96.89
KOG0112|consensus	975		96.57
KOG0112|consensus	975		96.43
KOG1190|consensus	492		96.43
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.42
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.36
KOG2193|consensus	584		95.66
KOG0120|consensus	500		95.19
KOG1548|consensus	382		94.61
KOG1456|consensus	494		94.5
KOG2416|consensus	718		94.42
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.25
KOG2591|consensus	684		94.01
KOG2068|consensus	327		93.86
KOG4410|consensus	396		92.37
KOG4210|consensus	285		92.32
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	91.95
KOG4660|consensus	549		91.79
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	90.74
KOG1996|consensus	378		90.58
KOG2891|consensus	445		90.55
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	90.48
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	89.62
PF15513	62	DUF4651: Domain of unknown function (DUF4651)	89.36
KOG2202|consensus	260		88.3
KOG2253|consensus	668		88.01
KOG4285|consensus	350		86.94
KOG4008|consensus	261		86.82
KOG0804|consensus	493		86.26
KOG4483|consensus	528		84.42
KOG2135|consensus	526		84.24
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	84.08
KOG4676|consensus	479		81.97

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

Probab=99.78  E-value=1.3e-18  Score=97.03  Aligned_cols=62  Identities=21%  Similarity=0.492  Sum_probs=57.4

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++ .+++++|||||+|.+.++|++|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~kGfaFV~F~~~e~A~~A   92 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDR-ETGRSRGFGFVNFNDEGAATAA   92 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecC-CCCCcceEEEEEECCHHHHHHH
Confidence            3457899999999999999999999999999999999987 7899999999999999999875

>KOG0149|consensus

Probab=99.77  E-value=1.1e-18  Score=102.30  Aligned_cols=59  Identities=25%  Similarity=0.514  Sum_probs=56.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      -++|||++|+|.+..+.|+++|++||+|.+..++.|+ .+|+++||+||+|.+.++|.+|
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~-~t~rskGyGfVTf~d~~aa~rA   70 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDK-NTGRSKGYGFVTFRDAEAATRA   70 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEecc-CCccccceeeEEeecHHHHHHH
Confidence            4689999999999999999999999999999999998 9999999999999999999875

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.72  E-value=3.3e-17  Score=102.04  Aligned_cols=64  Identities=22%  Similarity=0.541  Sum_probs=58.8

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+++++++|+++|+.||.|..|+++.++ .+++++|||||+|.++++|++|
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~-~tg~srGyaFVeF~~~e~A~~A  165 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY-KTGYSFGYAFVDFGSEADSQRA  165 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCccCcEEEEEEccHHHHHHH
Confidence            345568999999999999999999999999999999999987 7899999999999999999875

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=2.6e-17  Score=102.05  Aligned_cols=60  Identities=25%  Similarity=0.596  Sum_probs=56.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++||.|..|+++.++ .+|+++|||||+|.+.++|++|
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~-~~g~s~g~afV~f~~~~~A~~A   61 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK-VTGQSLGYGFVNYVRPEDAEKA   61 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcC-CCCccceEEEEEECcHHHHHHH
Confidence            36799999999999999999999999999999999987 7899999999999999999875

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.72  E-value=3.5e-17  Score=80.59  Aligned_cols=55  Identities=27%  Similarity=0.688  Sum_probs=51.5

Q ss_pred             EEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        23 l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |||+|||+.+++++|+++|++||.+..+.+..+  .++..+++|||+|.+.++|++|
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~--~~~~~~~~a~V~F~~~~~a~~a   55 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN--SSGKSKGYAFVEFESEEDAEKA   55 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE--TTSSEEEEEEEEESSHHHHHHH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc--ccccccceEEEEEcCHHHHHHH
Confidence            799999999999999999999999999999887  6788999999999999999864

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=4.6e-17  Score=100.92  Aligned_cols=60  Identities=25%  Similarity=0.485  Sum_probs=55.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.+|||+|||+.+++++|.++|++||.|.+++++.++ .++.++|||||+|.+.++|.+|
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~-~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDL-TTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcC-CCCCccceEEEEECCHHHHHHH
Confidence            34579999999999999999999999999999999996 7999999999999999998765

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

>KOG0122|consensus

Probab=99.68  E-value=1.3e-16  Score=94.13  Aligned_cols=63  Identities=30%  Similarity=0.640  Sum_probs=58.7

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+..+|.|.||+.++++.+|+++|.+||.|..+.|..++ .+|.++|||||.|.+.++|.+|
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK-~TG~~kGFAFVtF~sRddA~rA  247 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDK-ETGLSKGFAFVTFESRDDAARA  247 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEcc-ccCcccceEEEEEecHHHHHHH
Confidence            34467889999999999999999999999999999999998 9999999999999999999875

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.65  E-value=6.4e-16  Score=76.44  Aligned_cols=55  Identities=36%  Similarity=0.715  Sum_probs=49.0

Q ss_pred             EEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        23 l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |||+|||+++++++|+++|..+|.|..+.+..++ . +..+|+|||+|.+.++|.+|
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~-~-~~~~~~a~v~f~~~~~a~~a   55 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNK-D-GQSRGFAFVEFSSEEDAKRA   55 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEEST-T-SSEEEEEEEEESSHHHHHHH
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeee-c-cccCCEEEEEeCCHHHHHHH
Confidence            7999999999999999999999999999999885 4 88999999999999999764

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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.65  E-value=7.3e-16  Score=96.10  Aligned_cols=60  Identities=22%  Similarity=0.486  Sum_probs=56.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++ .+++++|||||+|.+.++|++|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~-~tg~~kG~aFV~F~~~e~A~~A  251 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDK-LTGTPRGVAFVRFNKREEAQEA  251 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecC-CCCccceEEEEEECCHHHHHHH
Confidence            46789999999999999999999999999999999886 7899999999999999999875

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

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

Probab=99.64  E-value=7.2e-16  Score=101.24  Aligned_cols=61  Identities=25%  Similarity=0.533  Sum_probs=57.1

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|.+||.|.+++++.++ .+++++|||||+|.+.++|++|
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~-~TgkskGfAFVeF~s~e~A~~A  165 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP-ATGKHKGFAFVEYEVPEAAQLA  165 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecC-CCCCcCCeEEEEeCcHHHHHHH
Confidence            456899999999999999999999999999999999987 8899999999999999999865

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.

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

Probab=99.63  E-value=1.3e-15  Score=99.75  Aligned_cols=60  Identities=35%  Similarity=0.527  Sum_probs=56.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+++|||+|||+++++++|+++|++||.|..++|+.+  .+++++|||||+|.+.++|++|
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D--~sG~sRGfaFV~F~~~e~A~~A  115 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD--FSGQNRGYAFVTFCGKEEAKEA  115 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC--CCCCccceEEEEeCCHHHHHHH
Confidence            45799999999999999999999999999999999999  7899999999999999999875

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=99.63  E-value=1.8e-15  Score=96.67  Aligned_cols=62  Identities=19%  Similarity=0.407  Sum_probs=57.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++ .++.++|||||+|.+.++|++|
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~-~~~~skg~afVeF~~~e~A~~A  147 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR-NSRRSKGVAYVEFYDVESVIKA  147 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCcceEEEEEECCHHHHHHH
Confidence            3456899999999999999999999999999999999987 7899999999999999999865

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

>KOG0121|consensus

Probab=99.63  E-value=5.3e-16  Score=84.19  Aligned_cols=62  Identities=21%  Similarity=0.420  Sum_probs=56.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+||++.++|+.|.++|+++|.|..|.+-.++ .+..+.|||||+|.+.++|+.|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr-~kktpCGFCFVeyy~~~dA~~A   94 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDR-FKKTPCGFCFVEYYSRDDAEDA   94 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEecccc-CCcCccceEEEEEecchhHHHH
Confidence            3457999999999999999999999999999999998887 7777899999999999998764

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.62  E-value=1.9e-15  Score=90.48  Aligned_cols=56  Identities=18%  Similarity=0.408  Sum_probs=50.7

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|+.||.|.++.++.++    ..+|||||+|.++++|+.|
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~----~~~GfAFVtF~d~eaAe~A   59 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN----ERSQIAYVTFKDPQGAETA   59 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC----CCCCEEEEEeCcHHHHHHH
Confidence            5799999999999999999999999999999998873    2469999999999998764

>KOG0113|consensus

Probab=99.62  E-value=1.9e-15  Score=91.35  Aligned_cols=61  Identities=20%  Similarity=0.495  Sum_probs=56.0

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..+-+||||+-|+++++|..|+..|+.||.|..|+|+.++ .+|+++|||||+|+...+...
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~-vTgkskGYAFIeye~erdm~~  158 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDK-VTGKSKGYAFIEYEHERDMKA  158 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeec-ccCCccceEEEEeccHHHHHH
Confidence            3456899999999999999999999999999999999998 899999999999998877554

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.60  E-value=4.2e-15  Score=88.06  Aligned_cols=58  Identities=19%  Similarity=0.299  Sum_probs=51.6

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.+|||+||++.+++++|+++|+.||.|.+|+|+.+    +...++|||+|.++++++.|
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D----~et~gfAfVtF~d~~aaetA   60 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS----GEYACTAYVTFKDAYALETA   60 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC----CCcceEEEEEECCHHHHHHH
Confidence            35789999999999999999999999999999999887    34458999999999998754

>KOG0125|consensus

Probab=99.60  E-value=2.1e-15  Score=92.16  Aligned_cols=63  Identities=29%  Similarity=0.536  Sum_probs=55.9

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......+++|+|.|||+...+-||+.+|++||.|.+|.++.+  . ..++||+||+|+++++|++|
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--E-RGSKGFGFVTmen~~dadRA  152 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--E-RGSKGFGFVTMENPADADRA  152 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--c-CCCCccceEEecChhhHHHH
Confidence            344566789999999999999999999999999999999887  3 34789999999999999875

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

Probab=99.60  E-value=3.6e-15  Score=97.48  Aligned_cols=57  Identities=25%  Similarity=0.480  Sum_probs=54.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+++++++|+++|++||.|.+|++.+++ .+++++|||||+|.+.++|++|
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~-~t~~s~G~afV~F~~~~~A~~A   58 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDS-VTRRSLGYGYVNFQNPADAERA   58 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcceEEEEEECCHHHHHHH
Confidence            79999999999999999999999999999999986 7789999999999999999875

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

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

Probab=99.59  E-value=5.5e-15  Score=97.18  Aligned_cols=60  Identities=22%  Similarity=0.469  Sum_probs=55.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|+.||.|.++++..++ .+++++|||||+|.+.++|.+|
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~-~tgksKGfGFVeFe~~e~A~kA  262 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP-TGRGHKGYGFIEYNNLQSQSEA  262 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecC-CCCCcCCeEEEEECCHHHHHHH
Confidence            35799999999999999999999999999999999987 7788999999999999998764

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.

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

Probab=99.57  E-value=1.6e-14  Score=93.27  Aligned_cols=61  Identities=26%  Similarity=0.605  Sum_probs=55.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.++ .+|.++|||||+|.+.++|..|
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~A  353 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDI-ATGLSKGYAFCEYKDPSVTDVA  353 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-CCCCcCeEEEEEECCHHHHHHH
Confidence            346799999999999999999999999999999998886 7899999999999999998764

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=99.54  E-value=2.6e-14  Score=93.49  Aligned_cols=61  Identities=33%  Similarity=0.583  Sum_probs=56.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+||++.+++++|+++|++||.|.+++++.+  .+|.++|||||+|.+.++|.+|
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d--~~g~~~g~gfV~f~~~~~A~~A  342 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD--EKGVSRGFGFVCFSNPEEANRA  342 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC--CCCCcCCeEEEEeCCHHHHHHH
Confidence            345678999999999999999999999999999999998  7899999999999999999875

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

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

Probab=99.53  E-value=3.5e-14  Score=90.75  Aligned_cols=59  Identities=32%  Similarity=0.640  Sum_probs=55.0

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||..+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|.+|
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~-~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDP-ETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCccceEEEEEECCHHHHHHH
Confidence            5899999999999999999999999999999999886 6789999999999999998764

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.

>KOG0144|consensus

Probab=99.53  E-value=2.1e-14  Score=90.46  Aligned_cols=62  Identities=29%  Similarity=0.551  Sum_probs=57.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+.-++||+.+|..++|.+|+++|++||.|.+|.+++|+ .++.++|||||.|.+.++|.+|
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk-~t~~s~gcCFv~~~trk~a~~a   92 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDK-STGQSKGCCFVKYYTRKEADEA   92 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeeccc-ccCcccceEEEEeccHHHHHHH
Confidence            3445689999999999999999999999999999999998 8999999999999999998764

>KOG0117|consensus

Probab=99.53  E-value=3.1e-14  Score=89.92  Aligned_cols=62  Identities=34%  Similarity=0.523  Sum_probs=58.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++.|||+.||.++.|++|..+|++.|+|-.++|+.++ .+|.++|||||+|.+.++|++|
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~-~sG~nRGYAFVtf~~Ke~Aq~A  141 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDP-FSGDNRGYAFVTFCTKEEAQEA  141 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecc-cCCCCcceEEEEeecHHHHHHH
Confidence            3668999999999999999999999999999999999998 8999999999999999999875

>KOG0127|consensus

Probab=99.52  E-value=4.2e-14  Score=91.25  Aligned_cols=61  Identities=34%  Similarity=0.675  Sum_probs=56.9

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.+|||+|||+++++++|.+.|++||.|.+..++.++ .++.++|.|||.|.+..++.+|
T Consensus       290 ~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k-~T~~skGtAFv~Fkt~~~~~~c  350 (678)
T KOG0127|consen  290 TEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDK-DTGHSKGTAFVKFKTQIAAQNC  350 (678)
T ss_pred             cccceEEEecCCccccHHHHHHHHHhhccceeEEEEecc-CCCCcccceEEEeccHHHHHHH
Confidence            446899999999999999999999999999999999998 9999999999999999988765

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

Probab=99.52  E-value=6.2e-14  Score=82.79  Aligned_cols=59  Identities=37%  Similarity=0.747  Sum_probs=55.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|.+||.+..+.+..++ .++.++|||||+|.+.+++..|
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~-~~~~~~g~~~v~f~~~~~~~~a  173 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR-ETGKSRGFAFVEFESEESAEKA  173 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc-ccCccCceEEEEecCHHHHHHH
Confidence            6999999999999999999999999999999999987 7899999999999999998764

>smart00362 RRM_2 RNA recognition motif

Probab=99.52  E-value=9.3e-14  Score=67.72  Aligned_cols=55  Identities=35%  Similarity=0.765  Sum_probs=49.8

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||..+++++|+++|.+||.+..+.+..+  . +.++|+|||+|.+.++|++|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~--~-~~~~~~~~v~f~~~~~a~~a   55 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKD--T-GKSKGFAFVEFESEEDAEKA   55 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecC--C-CCCCceEEEEeCCHHHHHHH
Confidence            5899999999999999999999999999988876  3 77889999999999998754

>KOG0114|consensus

Probab=99.51  E-value=8.2e-14  Score=73.33  Aligned_cols=61  Identities=25%  Similarity=0.521  Sum_probs=52.7

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+....+-|||.|||+++|.+++.++|.+||.|..+++-..+    ..+|.|||.|++..+|.+|
T Consensus        13 lppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k----~TrGTAFVVYedi~dAk~A   73 (124)
T KOG0114|consen   13 LPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK----ETRGTAFVVYEDIFDAKKA   73 (124)
T ss_pred             CChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc----CcCceEEEEehHhhhHHHH
Confidence            334457889999999999999999999999999999987653    4579999999999998765

>KOG0148|consensus

Probab=99.51  E-value=3e-14  Score=85.49  Aligned_cols=66  Identities=24%  Similarity=0.509  Sum_probs=60.1

Q ss_pred             CcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        13 ~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+....+..+||+-|...++.++|++.|.+||+|..+++++|. .+++++||+||.|.+.++|++|
T Consensus        55 sk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~-~T~KsKGYgFVSf~~k~dAEnA  120 (321)
T KOG0148|consen   55 SKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM-NTGKSKGYGFVSFPNKEDAENA  120 (321)
T ss_pred             CCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecc-cCCcccceeEEeccchHHHHHH
Confidence            33444557899999999999999999999999999999999998 8999999999999999999875

>KOG0107|consensus

Probab=99.49  E-value=6.5e-14  Score=79.47  Aligned_cols=56  Identities=30%  Similarity=0.544  Sum_probs=49.6

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .-.++|||+||+..+++.+|+..|..||.+..+.+-..      +.|||||+|+++.+|+.|
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn------PPGfAFVEFed~RDA~DA   63 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN------PPGFAFVEFEDPRDAEDA   63 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec------CCCceEEeccCcccHHHH
Confidence            44789999999999999999999999999998877554      369999999999998865

>KOG0126|consensus

Probab=99.48  E-value=7.7e-15  Score=83.80  Aligned_cols=57  Identities=18%  Similarity=0.495  Sum_probs=52.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHH
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE   75 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~   75 (79)
                      .+..-|||+|||++.|+.+|.-+|++||.|..|.|++|+ .+|+++||||+.|++..+
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk-~TGKSKGFaFLcYEDQRS   89 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDK-KTGKSKGFAFLCYEDQRS   89 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecC-CCCcccceEEEEecCccc
Confidence            345689999999999999999999999999999999998 999999999999988654

>KOG0131|consensus

Probab=99.47  E-value=8.8e-14  Score=79.35  Aligned_cols=62  Identities=26%  Similarity=0.454  Sum_probs=57.4

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ....+.+|||+||+..++++.|.++|-+.|+|..++++.++ .+..++||||++|.++++|+-
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDr-v~~~~qGygF~Ef~~eedadY   66 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDR-VTQKHQGYGFAEFRTEEDADY   66 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhh-hcccccceeEEEEechhhhHH
Confidence            34567899999999999999999999999999999999998 888899999999999999874

>smart00360 RRM RNA recognition motif

Probab=99.47  E-value=2.4e-13  Score=66.00  Aligned_cols=54  Identities=37%  Similarity=0.727  Sum_probs=48.7

Q ss_pred             EeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        25 v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |+|||..+++++|+++|.+||.+..+.+..++ .++.++|+|||+|.+.++|.+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~-~~~~~~~~a~v~f~~~~~a~~a   54 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDK-DTGKSKGFAFVEFESEEDAEKA   54 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCC-CCCCCCceEEEEeCCHHHHHHH
Confidence            57999999999999999999999999988875 5688899999999999998764

>PLN03213 repressor of silencing 3; Provisional

Probab=99.45  E-value=3.3e-13  Score=86.74  Aligned_cols=52  Identities=17%  Similarity=0.448  Sum_probs=46.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCH
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK   73 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~   73 (79)
                      .....+||||||++.+++++|+..|..||.|..+.|++   .+|  +|||||+|.+.
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR---ETG--RGFAFVEMssd   58 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR---TKG--RSFAYIDFSPS   58 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec---ccC--CceEEEEecCC
Confidence            34568999999999999999999999999999999994   466  89999999986

>KOG4207|consensus

Probab=99.44  E-value=2.1e-13  Score=79.33  Aligned_cols=65  Identities=22%  Similarity=0.450  Sum_probs=58.3

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +++....+.|.|-||.+.++.++|+.+|++||.|-.|.|+.++ .++.++|||||-|....+|+.|
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr-~Tr~sRgFaFVrf~~k~daedA   71 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDR-YTRQSRGFAFVRFHDKRDAEDA   71 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceeccccc-ccccccceeEEEeeecchHHHH
Confidence            3444556789999999999999999999999999999999998 8999999999999988887764

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.44  E-value=8.7e-13  Score=64.53  Aligned_cols=56  Identities=30%  Similarity=0.652  Sum_probs=50.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|+|+|||+.+++++|+++|..+|.|..+.+..+  ..+..+|+|||+|.+.++|..|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~--~~~~~~~~~~v~f~s~~~a~~a   56 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRD--KDTKSKGFAFVEFEDEEDAEKA   56 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeC--CCCCcceEEEEEECCHHHHHHH
Confidence            4899999999999999999999999999999877  3447789999999999998754

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).

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

Probab=99.43  E-value=4.3e-13  Score=86.72  Aligned_cols=53  Identities=25%  Similarity=0.429  Sum_probs=48.5

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|++||.|.++.++.+       +|||||+|.+.++|++|
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-------k~~afVef~~~e~A~~A   54 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-------KRQALVEFEDEESAKAC   54 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-------CCEEEEEeCchHHHHHH
Confidence            468999999999999999999999999999988765       38999999999999875

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).

>KOG0130|consensus

Probab=99.43  E-value=2.4e-13  Score=74.59  Aligned_cols=67  Identities=24%  Similarity=0.427  Sum_probs=60.8

Q ss_pred             cCcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        12 ~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+....++..|||.++...++++++...|..||+|++++|..++ .+|-.+|||.|+|++.+.|++|
T Consensus        64 pgPqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDR-RtGy~KGYaLvEYet~keAq~A  130 (170)
T KOG0130|consen   64 PGPQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDR-RTGYVKGYALVEYETLKEAQAA  130 (170)
T ss_pred             CCCccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeecccc-ccccccceeeeehHhHHHHHHH
Confidence            334556678999999999999999999999999999999999998 8999999999999999998865

>KOG0148|consensus

Probab=99.42  E-value=5e-13  Score=80.29  Aligned_cols=56  Identities=29%  Similarity=0.469  Sum_probs=51.7

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++++||++|++.-++++++++.|++||.|.+|++..++       ||+||.|.+.|+|..|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q-------GYaFVrF~tkEaAahA  216 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ-------GYAFVRFETKEAAAHA  216 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc-------ceEEEEecchhhHHHH
Confidence            4668999999999999999999999999999999998884       9999999999998764

>KOG0144|consensus

Probab=99.42  E-value=8.1e-14  Score=87.85  Aligned_cols=60  Identities=32%  Similarity=0.495  Sum_probs=55.3

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+.|+..++|.+++++|.+||.|++|.+.++  ..+.+||||||.|.+.+-|..|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd--~~~~sRGcaFV~fstke~A~~A  181 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD--PDGLSRGCAFVKFSTKEMAVAA  181 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheec--ccccccceeEEEEehHHHHHHH
Confidence            34789999999999999999999999999999999999  7999999999999999877643

>KOG0105|consensus

Probab=99.39  E-value=7.4e-13  Score=76.10  Aligned_cols=58  Identities=28%  Similarity=0.528  Sum_probs=50.6

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||.++.+.+|+.+|-+||.|..|.|...+    ...+||||+|+++.+|+.|
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~----g~ppfafVeFEd~RDAeDA   61 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP----GPPPFAFVEFEDPRDAEDA   61 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC----CCCCeeEEEecCccchhhh
Confidence            457899999999999999999999999999999885542    3458999999999998765

>KOG0145|consensus

Probab=99.38  E-value=9e-13  Score=79.14  Aligned_cols=61  Identities=25%  Similarity=0.580  Sum_probs=56.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.|.|.-||...++++++.+|...|+|++|++++|+ .+|++.||+||.|..+++|++|
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK-itGqSLGYGFVNYv~p~DAe~A   99 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK-ITGQSLGYGFVNYVRPKDAEKA   99 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeecc-ccccccccceeeecChHHHHHH
Confidence            345678888899999999999999999999999999999 9999999999999999999875

>KOG0108|consensus

Probab=99.36  E-value=1.3e-12  Score=83.38  Aligned_cols=58  Identities=31%  Similarity=0.615  Sum_probs=55.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+||+|+|+++++++|..+|+..|.|.+++++.|+ .+|+.+||||++|.+.+++..|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~-~tG~~~G~~f~~~~~~~~~~~a   76 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDR-ETGKPKGFGFCEFTDEETAERA   76 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccc-cCCCcCceeeEecCchhhHHHH
Confidence            899999999999999999999999999999999999 9999999999999999988754

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

Probab=99.35  E-value=4.7e-12  Score=81.95  Aligned_cols=56  Identities=18%  Similarity=0.325  Sum_probs=50.2

Q ss_pred             CCCCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+ .+++++|+++|++||.|..++++.++      +|+|||+|.+.++|+.|
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~------~g~afV~f~~~~~A~~A  329 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK------KETALIEMADPYQAQLA  329 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC------CCEEEEEECCHHHHHHH
Confidence            3567999999998 69999999999999999999988762      59999999999999865

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).

>KOG0111|consensus

Probab=99.34  E-value=5.4e-13  Score=78.43  Aligned_cols=62  Identities=27%  Similarity=0.508  Sum_probs=57.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||++|..++++.-|...|-+||.|..|.++.|. .+++++||+||+|...|+|..|
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDy-esqkHRgFgFVefe~aEDAaaA   68 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDY-ESQKHRGFGFVEFEEAEDAAAA   68 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccch-hcccccceeEEEeeccchhHHH
Confidence            3457899999999999999999999999999999999997 8999999999999999988654

>KOG0124|consensus

Probab=99.30  E-value=1.2e-12  Score=81.63  Aligned_cols=58  Identities=26%  Similarity=0.564  Sum_probs=55.1

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      -|++||+.+.++..++.|+..|.+||+|+++.+.+|+ .+++++|||||+|+-+|.|+-
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp-~T~kHKgFAFVEYEvPEaAqL  170 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP-ATGKHKGFAFVEYEVPEAAQL  170 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeeccccc-ccccccceEEEEEeCcHHHHH
Confidence            5899999999999999999999999999999999998 999999999999999998764

>KOG4205|consensus

Probab=99.28  E-value=6.2e-12  Score=77.48  Aligned_cols=59  Identities=25%  Similarity=0.551  Sum_probs=54.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      +.+++||++|+|+++++.|+..|.+||.|..+.+++++ .+++++||+||+|.+.+.+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~-~t~rsrgFgfv~f~~~~~v~~   63 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDP-STGRSRGFGFVTFATPEGVDA   63 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccC-CCCCcccccceecCCCcchhe
Confidence            78999999999999999999999999999999999998 889999999999997766543

>KOG0127|consensus

Probab=99.27  E-value=7.3e-12  Score=81.14  Aligned_cols=60  Identities=32%  Similarity=0.677  Sum_probs=55.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.||||++||++++.++|.++|+.+|+|..+.++.++ .++.++||+||+|.-.+++++|
T Consensus         4 ~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~-gs~~~RGfgfVtFam~ED~qrA   63 (678)
T KOG0127|consen    4 SGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNK-GSSEKRGFGFVTFAMEEDVQRA   63 (678)
T ss_pred             CCceEEEecCCCccchhHHHHhhhcccCcceeEEecCC-CcccccCccceeeehHhHHHHH
Confidence            45899999999999999999999999999999999887 7888999999999999998764

>KOG0146|consensus

Probab=99.26  E-value=4.4e-12  Score=76.49  Aligned_cols=61  Identities=25%  Similarity=0.446  Sum_probs=55.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++++|||+.|...-+|++++.+|.+||.|.+|.+.+.  ..|.++||+||.|.+..+|+.|
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg--~dg~sKGCAFVKf~s~~eAqaA   76 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRG--PDGNSKGCAFVKFSSHAEAQAA   76 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecC--CCCCCCCceEEEeccchHHHHH
Confidence            346899999999999999999999999999999999998  7899999999999999888753

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

Probab=99.26  E-value=2.3e-11  Score=80.08  Aligned_cols=52  Identities=25%  Similarity=0.461  Sum_probs=46.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhc--CCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAF--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++|  |.|..|.++         ++||||+|.+.++|++|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~---------rgfAFVeF~s~e~A~kA  285 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI---------RDYAFVHFEDREDAVKA  285 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee---------cCeEEEEeCCHHHHHHH
Confidence            35789999999999999999999999  999988653         36999999999999875

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

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

Probab=99.26  E-value=3.4e-11  Score=77.95  Aligned_cols=56  Identities=23%  Similarity=0.399  Sum_probs=44.0

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcC------------CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFG------------ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g------------~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|.++|..++            .|..+.+       +..+|||||+|.+.++|..|
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-------~~~kg~afVeF~~~e~A~~A  239 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-------NKEKNFAFLEFRTVEEATFA  239 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-------CCCCCEEEEEeCCHHHHhhh
Confidence            34568999999999999999999998752            2333322       34579999999999999875

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

>KOG0146|consensus

Probab=99.25  E-value=1.3e-11  Score=74.49  Aligned_cols=64  Identities=19%  Similarity=0.387  Sum_probs=59.0

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+++|.|||-.||.+..+.+|..+|-+||.|.+.++..|+ .++.+++|+||.|.++.+++.|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDR-ATNQSKCFGFVSfDNp~SaQaA  343 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDR-ATNQSKCFGFVSFDNPASAQAA  343 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehh-ccccccceeeEecCCchhHHHH
Confidence            456789999999999999999999999999999999988888 9999999999999999988754

>KOG0415|consensus

Probab=99.24  E-value=1.3e-11  Score=76.75  Aligned_cols=62  Identities=18%  Similarity=0.361  Sum_probs=58.0

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++...|||..|.+-++.++|.-+|+.||.|.+|.++++. .+|.+..||||+|.+.+++++|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~-ktgdsLqyaFiEFen~escE~A  297 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDR-KTGDSLQYAFIEFENKESCEQA  297 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecc-cccchhheeeeeecchhhHHHH
Confidence            4556899999999999999999999999999999999998 8999999999999999999875

>KOG0145|consensus

Probab=99.24  E-value=7.7e-12  Score=75.21  Aligned_cols=63  Identities=29%  Similarity=0.525  Sum_probs=56.4

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +...+..|||.+||...+..+|+.+|++||.|-.-++..|. .+|.++|.+||.|...++|+.|
T Consensus       123 ~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dq-vtg~srGVgFiRFDKr~EAe~A  185 (360)
T KOG0145|consen  123 DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQ-VTGLSRGVGFIRFDKRIEAEEA  185 (360)
T ss_pred             hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhc-ccceecceeEEEecchhHHHHH
Confidence            34557899999999999999999999999998888887777 7899999999999999998764

>KOG0147|consensus

Probab=99.24  E-value=4.9e-12  Score=81.53  Aligned_cols=57  Identities=30%  Similarity=0.722  Sum_probs=53.4

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .|||+||.+.+++++|+.+|++||.|..|.++.+. .+|.++||+|++|.+.++|.+|
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~-~tG~skgfGfi~f~~~~~ar~a  336 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDS-ETGRSKGFGFITFVNKEDARKA  336 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeecccc-ccccccCcceEEEecHHHHHHH
Confidence            39999999999999999999999999999999985 5999999999999999998764

>KOG4212|consensus

Probab=99.20  E-value=6.4e-11  Score=75.39  Aligned_cols=58  Identities=26%  Similarity=0.550  Sum_probs=53.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHh-HhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELF-KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f-~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.+||.|||+++.+.+|+.+| ++-|+|++|.|..|  .+|+++|||.|+|+++|.+++|
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D--~~GK~rGcavVEFk~~E~~qKa  102 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD--ESGKARGCAVVEFKDPENVQKA  102 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc--cCCCcCCceEEEeeCHHHHHHH
Confidence            4669999999999999999999 46799999999999  7999999999999999998875

>KOG0123|consensus

Probab=99.18  E-value=7.8e-11  Score=74.30  Aligned_cols=58  Identities=21%  Similarity=0.511  Sum_probs=52.0

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++..+||.||+++++..+|..+|+.||.|.+|++..+  ..| ++|| ||.|++.++|.+|
T Consensus        74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~--~~g-~kg~-FV~f~~e~~a~~a  131 (369)
T KOG0123|consen   74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATD--ENG-SKGY-FVQFESEESAKKA  131 (369)
T ss_pred             cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc--CCC-ceee-EEEeCCHHHHHHH
Confidence            34455999999999999999999999999999999998  566 8999 9999999999864

>KOG0117|consensus

Probab=99.17  E-value=9.8e-11  Score=74.40  Aligned_cols=62  Identities=26%  Similarity=0.341  Sum_probs=51.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCC-eeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ....++|||+|||.+.+++++++.+++.++ |..|.+..++....++||||||+|.++..|.-
T Consensus       161 Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~  223 (506)
T KOG0117|consen  161 SVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAM  223 (506)
T ss_pred             eeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHH
Confidence            356799999999999999999999999874 67777766543567899999999999987753

>KOG0110|consensus

Probab=99.14  E-value=4.1e-11  Score=79.23  Aligned_cols=61  Identities=66%  Similarity=1.119  Sum_probs=55.1

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++.|+|.|||+..+..+++.+|..||.+.+++++... ..+.++|||||+|-++.+|.+|
T Consensus       611 k~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~-~k~a~rGF~Fv~f~t~~ea~nA  671 (725)
T KOG0110|consen  611 KKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKI-GKGAHRGFGFVDFLTPREAKNA  671 (725)
T ss_pred             cccceeeeeccchHHHHHHHHHHHhcccceeeeccchhh-cchhhccceeeeccCcHHHHHH
Confidence            337899999999999999999999999999999998864 6778899999999999998765

>KOG4208|consensus

Probab=99.13  E-value=2e-10  Score=66.73  Aligned_cols=59  Identities=29%  Similarity=0.524  Sum_probs=52.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhc-CCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAF-GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ...-+|+..+|....+.++..+|.++ |.+...++-+++ .||.++|||||+|++++.|.-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnk-rTGNSKgYAFVEFEs~eVA~I  107 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNK-RTGNSKGYAFVEFESEEVAKI  107 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeeccc-ccCCcCceEEEEeccHHHHHH
Confidence            34568899999999999999999998 678888887887 899999999999999998864

>KOG0124|consensus

Probab=99.11  E-value=2.2e-10  Score=71.75  Aligned_cols=57  Identities=23%  Similarity=0.490  Sum_probs=51.5

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      -.+|||..+.++.++++|+.+|+.||+|.+|.+-+.+ ..+.++||+|++|.+..+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~p-t~~~HkGyGfiEy~n~qs~~  266 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAP-TGRGHKGYGFIEYNNLQSQS  266 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccC-CCCCccceeeEEeccccchH
Confidence            4689999999999999999999999999999999986 67779999999998876543

>smart00361 RRM_1 RNA recognition motif

Probab=99.09  E-value=3.2e-10  Score=56.16  Aligned_cols=45  Identities=22%  Similarity=0.355  Sum_probs=36.9

Q ss_pred             HHHHHHHhH----hcCCeeEEE-eecccCCC--CCcceEEEEEecCHHHHhcC
Q psy3346          34 QSEVEELFK----AFGELKFVR-LPKKMVGS--GLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        34 ~~~l~~~f~----~~g~i~~~~-~~~~~~~~--~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +++|+++|+    +||.|.++. ++.++ .+  +.++||+||+|.+.++|.+|
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~-~~~~~~~rG~~fV~f~~~~dA~~A   53 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDN-VGYENHKRGNVYITFERSEDAARA   53 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCC-CCCCCCCcEEEEEEECCHHHHHHH
Confidence            467888888    999999985 55554 44  88999999999999999865

>KOG0116|consensus

Probab=99.07  E-value=3.5e-10  Score=72.15  Aligned_cols=61  Identities=34%  Similarity=0.562  Sum_probs=49.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+|||.|||.+++..+|+++|.+||.|+...+.... ..++..+||||+|.+.++++.|
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~-~~~~~~~fgFV~f~~~~~~~~~  346 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRS-PGGKNPCFGFVEFENAAAVQNA  346 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEec-cCCCcCceEEEEEeecchhhhh
Confidence            335669999999999999999999999999998875542 2345459999999998887653

>KOG4205|consensus

Probab=99.02  E-value=7.6e-10  Score=68.38  Aligned_cols=58  Identities=26%  Similarity=0.521  Sum_probs=53.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..++||++||..+++.+++++|.+||.|..+.++.|. .+.+++||+||.|.+.+++++
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~-~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDK-TTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecc-cccccccceeeEeccccccce
Confidence            5589999999999999999999999999999999887 889999999999999988765

>KOG0153|consensus

Probab=99.00  E-value=8e-10  Score=68.47  Aligned_cols=59  Identities=17%  Similarity=0.416  Sum_probs=51.3

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++.+..-.+|||++|-..+++.+|+..|.+||+|.++.+...+       ++|||+|.+.++|+.|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~-------~CAFv~ftTR~aAE~A  280 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK-------GCAFVTFTTREAAEKA  280 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc-------ccceeeehhhHHHHHH
Confidence            3445556899999999999999999999999999999887653       7999999999998865

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

Probab=98.97  E-value=5.6e-09  Score=54.78  Aligned_cols=56  Identities=25%  Similarity=0.519  Sum_probs=48.3

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhc--CCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAF--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      +||.|+|||...+.++|.+++...  |....+.|+.|. .++.+.|||||.|.+++.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf-~~~~N~GYAFVNf~~~~~~~   59 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDF-KNKCNLGYAFVNFTSPQAAI   59 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeec-cCCCceEEEEEEcCCHHHHH
Confidence            689999999999999999998543  566777888886 78889999999999998875

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

>KOG0123|consensus

Probab=98.95  E-value=1.6e-09  Score=68.42  Aligned_cols=61  Identities=30%  Similarity=0.613  Sum_probs=56.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......|||.||+..++.+.|+.+|+.+|.|.++++..+  ..+.++||+||.|.+.++|.+|
T Consensus       267 ~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~--~~g~skG~gfV~fs~~eeA~~A  327 (369)
T KOG0123|consen  267 SLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVD--ENGKSKGFGFVEFSSPEEAKKA  327 (369)
T ss_pred             cccccccccccCccccchhHHHHHHhcccceeeEEEEec--cCCCccceEEEEcCCHHHHHHH
Confidence            556789999999999999999999999999999999998  7899999999999999998764

>KOG0132|consensus

Probab=98.93  E-value=1.7e-09  Score=72.54  Aligned_cols=53  Identities=25%  Similarity=0.584  Sum_probs=48.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+||||+.|+..+++.+|..+|+.||.|.+|.++..       +|||||......+|.+|
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-------R~cAfI~M~~RqdA~ka  473 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-------RGCAFIKMVRRQDAEKA  473 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-------CceeEEEEeehhHHHHH
Confidence            489999999999999999999999999999988665       59999999999999875

>KOG0109|consensus

Probab=98.93  E-value=1.1e-09  Score=66.76  Aligned_cols=48  Identities=29%  Similarity=0.596  Sum_probs=41.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      .+|||+|||..+++.+|+.+|++||+|.+|.++.+         ||||..++...++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN---------YgFVHiEdktaae   50 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN---------YGFVHIEDKTAAE   50 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc---------cceEEeecccccH
Confidence            57999999999999999999999999999998775         6777777665554

>KOG4211|consensus

Probab=98.91  E-value=5e-09  Score=67.34  Aligned_cols=59  Identities=22%  Similarity=0.562  Sum_probs=51.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......|-+.+|||++|+++|..+|+.++ |..+.+++   .+|+..|-|||+|.+.+++++|
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r---~~Gr~sGeA~Ve~~seedv~~A   65 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR---RNGRPSGEAYVEFTSEEDVEKA   65 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec---cCCCcCcceEEEeechHHHHHH
Confidence            45567888999999999999999999996 88866665   4799999999999999998765

>KOG4206|consensus

Probab=98.88  E-value=8.5e-09  Score=60.68  Aligned_cols=55  Identities=25%  Similarity=0.405  Sum_probs=46.5

Q ss_pred             CCeEEEeCCCCCCCHHHHHH----HhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..||||.||+..+..++|+.    +|++||.|..|....    +.+.+|-|||.|.+.+.|-.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k----t~KmRGQA~VvFk~~~~As~   67 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK----TPKMRGQAFVVFKETEAASA   67 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC----CCCccCceEEEecChhHHHH
Confidence            33999999999999998877    999999998886644    46788999999999887654

>KOG0533|consensus

Probab=98.85  E-value=9.2e-09  Score=61.70  Aligned_cols=59  Identities=32%  Similarity=0.541  Sum_probs=53.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+|+|.|||+.+.+++|+++|..||.+..+.+..+  ..|.+.|.|-|.|...++|++|
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~--~~G~s~Gta~v~~~r~~DA~~a  140 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD--RAGRSLGTADVSFNRRDDAERA  140 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC--CCCCCCccceeeecchHhHHHH
Confidence            3478999999999999999999999998899989898  6999999999999999888753

>KOG0131|consensus

Probab=98.82  E-value=5.3e-09  Score=60.07  Aligned_cols=62  Identities=21%  Similarity=0.449  Sum_probs=51.7

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..-+..+||+||.+.+++..|...|+.||.+.. -.+.++. .+|.++||+|+.|.+.+.+.+|
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~-~tg~~~~~g~i~~~sfeasd~a  155 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP-DTGNPKGFGFINYASFEASDAA  155 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccc-cCCCCCCCeEEechhHHHHHHH
Confidence            344578999999999999999999999998654 3566665 7789999999999999887653

>KOG4661|consensus

Probab=98.80  E-value=1.1e-08  Score=67.42  Aligned_cols=60  Identities=22%  Similarity=0.416  Sum_probs=53.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++.|||.+|+..+...+|+.+|++||.|...+++.+. .+...++|+||++.+.++|.+|
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNa-RsPGaRCYGfVTMSts~eAtkC  463 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNA-RSPGARCYGFVTMSTSAEATKC  463 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecC-CCCCcceeEEEEecchHHHHHH
Confidence            46899999999999999999999999999988888775 5666789999999999988765

>PF13893 RRM_5: RNA recognition motif

Probab=98.78  E-value=1.4e-08  Score=48.07  Aligned_cols=37  Identities=43%  Similarity=0.802  Sum_probs=30.9

Q ss_pred             HHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          37 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        37 l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |.++|++||.|..+.+..+  .    +++|||+|.+.++|+.|
T Consensus         1 L~~~f~~fG~V~~i~~~~~--~----~~~a~V~f~~~~~A~~a   37 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKK--K----RGFAFVEFASVEDAQKA   37 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETT--S----TTEEEEEESSHHHHHHH
T ss_pred             ChHHhCCcccEEEEEEEeC--C----CCEEEEEECCHHHHHHH
Confidence            6789999999999988665  2    58999999999999864

(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 ....

>KOG0110|consensus

Probab=98.76  E-value=1.5e-08  Score=67.49  Aligned_cols=60  Identities=32%  Similarity=0.561  Sum_probs=49.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCC--CCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS--GLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||.||+++++.+++...|...|.|.++.|...+...  --+.|||||+|.++++|++|
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a  576 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAA  576 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHH
Confidence            4559999999999999999999999999999886653111  12459999999999998865

>KOG4660|consensus

Probab=98.75  E-value=1.7e-08  Score=65.61  Aligned_cols=59  Identities=27%  Similarity=0.472  Sum_probs=50.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+..+|+|-|||..+++++|+.+|+.||+|..++.      +-..+|.+||+|.+..+|++|
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~------t~~~~~~~~v~FyDvR~A~~A  128 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE------TPNKRGIVFVEFYDVRDAERA  128 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc------ccccCceEEEEEeehHhHHHH
Confidence            34556789999999999999999999999999999654      334579999999999998875

>KOG4211|consensus

Probab=98.72  E-value=6.1e-08  Score=62.50  Aligned_cols=60  Identities=22%  Similarity=0.430  Sum_probs=50.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....|.+++||+.|++++|.++|+..--+.. +.++.+  ..+++.|-|||.|++.+.|++|
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d--~rgR~tGEAfVqF~sqe~ae~A  161 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD--QRGRPTGEAFVQFESQESAEIA  161 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc--CCCCcccceEEEecCHHHHHHH
Confidence            45678999999999999999999988754444 556777  5788889999999999999875

>KOG4209|consensus

Probab=98.71  E-value=1.8e-08  Score=60.22  Aligned_cols=64  Identities=23%  Similarity=0.416  Sum_probs=56.8

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+...+||+|+.+.++.+++...|+.||.+..+.++.++ ..+.++||+||+|.+.+.++.+
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~-~~~~~k~~~yvef~~~~~~~~a  159 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDK-FRGHPKGFAYVEFSSYELVEEA  159 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccc-cCCCcceeEEEecccHhhhHHH
Confidence            445678899999999999999999999999999999999887 7778999999999999887653

>KOG4212|consensus

Probab=98.70  E-value=2.3e-08  Score=64.07  Aligned_cols=58  Identities=24%  Similarity=0.585  Sum_probs=49.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+..|+|+|+|||+++|+..|+.-|..||.+.+..++.    .|+++|  .|.|.++++|++|
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime----~GkskG--VVrF~s~edAEra  589 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME----NGKSKG--VVRFFSPEDAERA  589 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc----cCCccc--eEEecCHHHHHHH
Confidence            345578899999999999999999999999999888743    477776  8999999999875

>KOG1548|consensus

Probab=98.58  E-value=1.8e-07  Score=58.27  Aligned_cols=58  Identities=17%  Similarity=0.356  Sum_probs=49.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCee--------EEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELK--------FVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      .++.|||.|||.++|.+++.++|++||-|.        .|+|.++  ..|..+|-|.+.|...++++-
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd--~~G~lKGDaLc~y~K~ESVeL  198 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD--NQGKLKGDALCCYIKRESVEL  198 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec--CCCCccCceEEEeecccHHHH
Confidence            357799999999999999999999999774        3777777  679999999999988887653

>KOG0106|consensus

Probab=98.58  E-value=7e-08  Score=57.00  Aligned_cols=50  Identities=30%  Similarity=0.747  Sum_probs=43.7

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+||++||+.+.+.+|..+|..||.+..+.+..         ||+||+|.+..+|+.|
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~---------gf~fv~fed~rda~Da   51 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN---------GFGFVEFEDPRDADDA   51 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec---------ccceeccCchhhhhcc
Confidence            4689999999999999999999999988876533         7889999999988764

>KOG0226|consensus

Probab=98.55  E-value=1e-07  Score=57.30  Aligned_cols=62  Identities=18%  Similarity=0.397  Sum_probs=55.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++.+||.+-|-.+++++.|-..|.+|-.....++++++ .+|+++||+||.|.++.++.+|
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk-RTgKSkgygfVSf~~pad~~rA  248 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK-RTGKSKGYGFVSFRDPADYVRA  248 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccc-cccccccceeeeecCHHHHHHH
Confidence            4557899999999999999999999999887788888888 8999999999999999987543

>KOG4454|consensus

Probab=98.54  E-value=3.8e-08  Score=58.14  Aligned_cols=58  Identities=22%  Similarity=0.351  Sum_probs=50.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ....++|||.|+...++++.|.++|-+-|+|.++.|+.+  ..+..+ ||||.|+++.++.
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~--~d~~~k-Fa~v~f~~E~sv~   63 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSG--QDQEQK-FAYVFFPNENSVQ   63 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCC--ccCCCc-eeeeecccccchh
Confidence            456789999999999999999999999999999999888  455555 9999999877654

>KOG1457|consensus

Probab=98.53  E-value=3.5e-07  Score=54.39  Aligned_cols=63  Identities=19%  Similarity=0.263  Sum_probs=49.0

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...-+||||.+||.++...+|..+|..|-..+...+..........+.+||++|.+..+|.+|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aa   93 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAA   93 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHH
Confidence            344799999999999999999999999976666666443202233568999999999998754

>KOG0109|consensus

Probab=98.47  E-value=1.5e-07  Score=57.66  Aligned_cols=52  Identities=23%  Similarity=0.402  Sum_probs=46.0

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ...++++|+||.+.++..+|+..|.+||.+.+|.++.         +|+||.|.-.++|..
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk---------dy~fvh~d~~eda~~  127 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK---------DYAFVHFDRAEDAVE  127 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeec---------ceeEEEEeeccchHH
Confidence            3467899999999999999999999999999998866         589999998887754

>KOG0151|consensus

Probab=98.47  E-value=2e-07  Score=62.61  Aligned_cols=63  Identities=22%  Similarity=0.358  Sum_probs=51.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccC--CCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~--~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++..+.+|++||++.+++..|...|..||++..++++..+.  .....+-|+||.|-+..+|++|
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era  235 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERA  235 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHH
Confidence            34567899999999999999999999999999988776531  1233456899999999988764

>KOG1457|consensus

Probab=98.45  E-value=1.4e-07  Score=55.97  Aligned_cols=59  Identities=14%  Similarity=0.359  Sum_probs=46.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      .....+.+|||.||..++++++|+.+|+.|.....+++...   .|  ...||++|+..+.|..
T Consensus       205 ~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~---~g--~~vaf~~~~~~~~at~  263 (284)
T KOG1457|consen  205 SGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR---GG--MPVAFADFEEIEQATD  263 (284)
T ss_pred             ccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC---CC--cceEeecHHHHHHHHH
Confidence            34456789999999999999999999999987666665432   22  3679999998888764

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.42  E-value=6.6e-07  Score=47.67  Aligned_cols=53  Identities=23%  Similarity=0.467  Sum_probs=33.1

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++.|+|.+++..++.++|+..|++||.|.+|.+....       .-|||.|.+++.|+.|
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-------~~g~VRf~~~~~A~~a   53 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-------TEGYVRFKTPEAAQKA   53 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--------SEEEEEESS---HHHH
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-------CEEEEEECCcchHHHH
Confidence            3578899999999999999999999999999886652       4689999999888653

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

>KOG0147|consensus

Probab=98.30  E-value=1.6e-07  Score=61.17  Aligned_cols=63  Identities=17%  Similarity=0.363  Sum_probs=55.3

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ...+.+.+++|+--|+..++..+|.++|+.+|.|..++++.++ .++.++|.+||+|.+.+++.
T Consensus       173 ~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr-~s~rskgi~Yvef~D~~sVp  235 (549)
T KOG0147|consen  173 SPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDR-NSRRSKGIAYVEFCDEQSVP  235 (549)
T ss_pred             CchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccc-cchhhcceeEEEEecccchh
Confidence            3445567889999999999999999999999999999999998 88999999999999877653

>KOG4849|consensus

Probab=98.20  E-value=1.3e-06  Score=54.92  Aligned_cols=59  Identities=10%  Similarity=0.234  Sum_probs=48.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcC--CeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      .....+||+||-|.+|+++|.+.+...|  .+..+++..++ .+|+++|||.+...+..+++
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR-~NGQSKG~AL~~~~SdAa~K  138 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENR-TNGQSKGYALLVLNSDAAVK  138 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcc-cCCcccceEEEEecchHHHH
Confidence            3456799999999999999999988776  46677777777 89999999999987765543

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

Probab=98.20  E-value=1.2e-05  Score=37.75  Aligned_cols=51  Identities=22%  Similarity=0.464  Sum_probs=40.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.|-|.+.+++..+. +...|..||+|..+.+...       .-+.|+.|.+..+|++|
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~-------~~~~~l~y~~~~~ae~A   52 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES-------TNWMYLKYKSRKDAEKA   52 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC-------CcEEEEEECCHHHHHhh
Confidence            457788888776644 5558889999999877532       36899999999999886

>KOG0120|consensus

Probab=98.08  E-value=5.7e-06  Score=54.15  Aligned_cols=59  Identities=32%  Similarity=0.597  Sum_probs=52.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHH
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA   76 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a   76 (79)
                      ......+||++||...++..+++++..||.+....++.+. .+|-++||||.+|-++...
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~-~~g~skg~af~ey~dpsvt  344 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS-ATGNSKGFAFCEYCDPSVT  344 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc-ccccccceeeeeeeCCcch
Confidence            3456789999999999999999999999999999998887 7789999999999876554

>KOG4210|consensus

Probab=98.01  E-value=2.6e-06  Score=52.50  Aligned_cols=57  Identities=33%  Similarity=0.605  Sum_probs=50.5

Q ss_pred             CCeEE-EeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          20 GSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        20 ~~~l~-v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ..++| +++|+..++.++|+..|..+|.|..++++.++ .++..+|++|+.|.......
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~-~s~~~kg~a~~~~~~~~~~~  241 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDE-ESGDSKGFAYVDFSAGNSKK  241 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCC-CccchhhhhhhhhhhchhHH
Confidence            34555 99999999999999999999999999999887 89999999999998877654

>KOG1190|consensus

Probab=98.00  E-value=7.6e-06  Score=52.33  Aligned_cols=52  Identities=21%  Similarity=0.367  Sum_probs=44.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ..+.+.++|||++++|+++..++.+||.|..+.+...+       --||++|.+.++|-
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGk-------nQAflem~d~~sAv   78 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGK-------NQAFLEMADEESAV   78 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeeccc-------hhhhhhhcchhhhh
Confidence            56789999999999999999999999999998876652       26899999988874

>KOG4206|consensus

Probab=97.90  E-value=4.6e-05  Score=45.20  Aligned_cols=55  Identities=27%  Similarity=0.529  Sum_probs=46.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      -.....+|+.|||.+++.+.+..+|.+|.....++++...      .+.|||+|.+...+.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~------~~iAfve~~~d~~a~  197 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR------SGIAFVEFLSDRQAS  197 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC------CceeEEecchhhhhH
Confidence            3456789999999999999999999999989999887652      488999998876643

>KOG0129|consensus

Probab=97.83  E-value=8.1e-05  Score=48.74  Aligned_cols=58  Identities=22%  Similarity=0.498  Sum_probs=43.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeeccc--CCCCCcce---EEEEEecCHHHHh
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM--VGSGLHRG---FGFVEFITKNEAK   77 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~--~~~~~~~g---~~fv~f~~~~~a~   77 (79)
                      -.++|||++||++++|+.|...|..||.+ .+.++...  ...--++|   |+|+.|+++.++.
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~  320 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQ  320 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHH
Confidence            35789999999999999999999999964 55666321  01112345   9999999988764

>KOG1995|consensus

Probab=97.81  E-value=4.3e-05  Score=47.97  Aligned_cols=62  Identities=19%  Similarity=0.291  Sum_probs=53.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCee--------EEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELK--------FVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....-+|||.+||..+++.++..+|.+||.|.        .|.+..++ .++..+|-|.|.|.++..|+.|
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dk-eT~~~KGeatvS~~D~~~akaa  132 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDK-ETGAPKGEATVSYEDPPAAKAA  132 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccc-cccCcCCceeeeecChhhhhhh
Confidence            45567999999999999999999999999774        35566676 8999999999999999988765

>KOG0129|consensus

Probab=97.77  E-value=0.0001  Score=48.34  Aligned_cols=61  Identities=16%  Similarity=0.298  Sum_probs=51.4

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhH-hcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFK-AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      -+..+|||||+||.-++..+|-.+|. -||.|..+-|=.|+ .-+-++|-|-|+|.+..+-.+
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~-k~KYPkGaGRVtFsnqqsYi~  428 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDP-KLKYPKGAGRVTFSNQQAYIK  428 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCc-ccCCCCCcceeeecccHHHHH
Confidence            34568999999999999999999997 69999999887775 566688999999998776443

>KOG1365|consensus

Probab=97.76  E-value=0.00011  Score=46.94  Aligned_cols=60  Identities=25%  Similarity=0.377  Sum_probs=46.9

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHh-c---CCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKA-F---GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~-~---g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.-.|..++||+++++.++.++|.+ |   |....+.++..  ..|+..|-|||.|..+++|+.|
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r--pdgrpTGdAFvlfa~ee~aq~a  222 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR--PDGRPTGDAFVLFACEEDAQFA  222 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC--CCCCcccceEEEecCHHHHHHH
Confidence            33456778899999999999999963 2   23455655555  6889999999999999998764

>KOG2314|consensus

Probab=97.74  E-value=0.00014  Score=48.42  Aligned_cols=61  Identities=21%  Similarity=0.395  Sum_probs=49.6

Q ss_pred             CCCCCeEEEeCCCCCCCH------HHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQ------SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~------~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.-...|+|.|+|.--..      .-|.++|+++|++....++.+  ..|..+||.|++|.+..+|+.|
T Consensus        55 eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~--e~ggtkG~lf~E~~~~~~A~~a  121 (698)
T KOG2314|consen   55 EGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPID--EEGGTKGYLFVEYASMRDAKKA  121 (698)
T ss_pred             CCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccC--ccCCeeeEEEEEecChhhHHHH
Confidence            355678999999875332      346788999999999999988  5677999999999999998764

>KOG1365|consensus

Probab=97.71  E-value=3.5e-05  Score=49.19  Aligned_cols=58  Identities=19%  Similarity=0.488  Sum_probs=48.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCC-eeE--EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGE-LKF--VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~--~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...|.+++||++.+.++|..+|..|-. |..  ++++.+  ..|+..|-|||.|.+.++|..|
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N--~qGrPSGeAFIqm~nae~a~aa  340 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN--GQGRPSGEAFIQMRNAERARAA  340 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc--CCCCcChhhhhhhhhhHHHHHH
Confidence            567899999999999999999998852 433  778777  7899999999999999987653

>KOG1855|consensus

Probab=97.50  E-value=0.00011  Score=47.29  Aligned_cols=62  Identities=19%  Similarity=0.390  Sum_probs=48.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecc---c-CCCCCc--------ceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK---M-VGSGLH--------RGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~---~-~~~~~~--------~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|.+.|||.+-.-+-|.++|+.+|.|..|++...   + ...+..        +-+|+|+|...+.|.+|
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA  302 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA  302 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH
Confidence            45789999999999988999999999999999987433   1 022222        45789999999888765

>KOG3152|consensus

Probab=97.48  E-value=4e-05  Score=46.40  Aligned_cols=59  Identities=32%  Similarity=0.442  Sum_probs=44.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCC--------CCcce----EEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS--------GLHRG----FGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~--------~~~~g----~~fv~f~~~~~a~~   78 (79)
                      ..-.||+++||+......|+++|..||.|-.|.|.... .+        |.+..    -|+|+|.+...|.+
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~-~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~  143 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPED-DSKRAARKRKGGNYKKLYSEGWVEFISKRVAKR  143 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchh-hHHHHHHhhcCCCccccchhHHHHHHHHHHHHH
Confidence            34579999999999999999999999999999885432 22        22222    26788887776653

>KOG0128|consensus

Probab=97.48  E-value=7.3e-05  Score=51.41  Aligned_cols=57  Identities=25%  Similarity=0.397  Sum_probs=51.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ...++|.|.|+..|.+.++.++..+|.+.+.+++..  ..|+++|.+||.|.++.++.+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~--r~gkpkg~a~v~y~~ea~~s~  792 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV--RAGKPKGKARVDYNTEADASR  792 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhh--hccccccceeccCCCcchhhh
Confidence            467999999999999999999999999999988887  689999999999999887754

>KOG4307|consensus

Probab=97.47  E-value=0.00035  Score=47.68  Aligned_cols=57  Identities=23%  Similarity=0.476  Sum_probs=48.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCe-eEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.|-+.|+|++++-++|.++|..|-.+ .+|.+.+.  ..|...|-|-|.|++.++|.+|
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n--d~G~pTGe~mvAfes~~eAr~A  925 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN--DDGVPTGECMVAFESQEEARRA  925 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec--CCCCcccceeEeecCHHHHHhh
Confidence            478899999999999999999998644 34566565  7899999999999999999875

>KOG0105|consensus

Probab=97.44  E-value=0.00095  Score=39.11  Aligned_cols=56  Identities=18%  Similarity=0.497  Sum_probs=47.0

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ++.......+.|.+||++.++.+|+.....-|.+....+..+        |++.|+|-..++-+
T Consensus       109 ppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD--------g~GvV~~~r~eDMk  164 (241)
T KOG0105|consen  109 PPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD--------GVGVVEYLRKEDMK  164 (241)
T ss_pred             CcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc--------cceeeeeeehhhHH
Confidence            344566788999999999999999999999999988887777        67889988877643

>KOG0128|consensus

Probab=97.34  E-value=9.4e-06  Score=55.57  Aligned_cols=59  Identities=24%  Similarity=0.372  Sum_probs=49.7

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      -.++|+.||+..+.+.+|...|.++|.+..+++.... ..++.+|+||++|..++++.+|
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~-n~~~~rG~~Y~~F~~~~~~~aa  725 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHK-NEKRFRGKAYVEFLKPEHAGAA  725 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHh-hccccccceeeEeecCCchhhh
Confidence            4678999999999999999999999988777665332 5788999999999999887654

>KOG0115|consensus

Probab=97.32  E-value=0.00015  Score=43.94  Aligned_cols=56  Identities=25%  Similarity=0.371  Sum_probs=48.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..|||.||+.-++.+.+.+-|+.||.|..-.+..|  ..++..+-++|.|...-.+.+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD--~r~k~t~eg~v~~~~k~~a~~   87 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD--DRGKPTREGIVEFAKKPNARK   87 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec--ccccccccchhhhhcchhHHH
Confidence            67999999999999999999999999988777777  678888889999987666544

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

Probab=97.30  E-value=0.0012  Score=33.82  Aligned_cols=49  Identities=24%  Similarity=0.449  Sum_probs=34.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ....+++ .|.+....+|.++|++||.| .|.++.+        .-|||.....+.|..
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~d--------TSAfV~l~~r~~~~~   57 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWIND--------TSAFVALHNRDQAKV   57 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECT--------TEEEEEECCCHHHHH
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcC--------CcEEEEeecHHHHHH
Confidence            3455555 99999999999999999975 5666666        358999988887653

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>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=97.30  E-value=0.00096  Score=34.28  Aligned_cols=48  Identities=25%  Similarity=0.374  Sum_probs=31.2

Q ss_pred             CeEEEeCCCCCCCHHHH----HHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEV----EELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l----~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..|+|.|||...+...+    ++++..|| .|..+           ..+.|++.|.+++.|.+|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----------~~~tAilrF~~~~~A~RA   55 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----------SGGTAILRFPNQEFAERA   55 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------------TT-EEEEESSHHHHHHH
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----------eCCEEEEEeCCHHHHHHH
Confidence            46899999999987665    55555776 34443           126799999999999875

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.29  E-value=0.00048  Score=43.56  Aligned_cols=61  Identities=25%  Similarity=0.392  Sum_probs=42.5

Q ss_pred             CCCeEEEeCCCCCCCHHHH------HHHhHhcCCeeEEEeecccCCCCCcceE--EEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEV------EELFKAFGELKFVRLPKKMVGSGLHRGF--GFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l------~~~f~~~g~i~~~~~~~~~~~~~~~~g~--~fv~f~~~~~a~~a   79 (79)
                      +..-+||-+||+.+..+++      .++|.+||.|..|.+-..........+.  .||+|.+.++|.+|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarc  181 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARC  181 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHH
Confidence            3456899999999877662      5889999999998764431011112232  39999999998764

>KOG4676|consensus

Probab=97.23  E-value=0.00039  Score=44.59  Aligned_cols=58  Identities=21%  Similarity=0.288  Sum_probs=46.0

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeeccc--CCCCCcceEEEEEecCHHHHh
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM--VGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~--~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ...|-|.||.+.++.++++.+|...|.|..+.|....  ..-......|||.|.+...+.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~   66 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVT   66 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCccee
Confidence            3489999999999999999999999999999885432  122334578999998877654

>KOG0106|consensus

Probab=97.08  E-value=0.00054  Score=40.79  Aligned_cols=54  Identities=31%  Similarity=0.652  Sum_probs=44.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.+.+.|++..+.+.+|...|.++|.+....+         ..+++||+|...+++.+|
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~---------~~~~~~v~Fs~~~da~ra  149 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA---------RRNFAFVEFSEQEDAKRA  149 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh---------hccccceeehhhhhhhhc
Confidence            455789999999999999999999999998743322         357899999999998764

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.00  E-value=0.0022  Score=33.91  Aligned_cols=60  Identities=13%  Similarity=0.118  Sum_probs=36.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEE-eecccC-----CCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVR-LPKKMV-----GSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~-~~~~~~-----~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+-|.|-+.|+. ....+.+.|++||.|.+.. +..+..     .......+-.|.|.++.+|++|
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rA   70 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRA   70 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHH
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHH
Confidence            3556778889888 5566788899999987664 111100     0112346899999999999875

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG1456|consensus

Probab=96.92  E-value=0.0048  Score=39.66  Aligned_cols=56  Identities=20%  Similarity=0.310  Sum_probs=45.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....-.+.|++|-..+++.+|.+-++.||.|..+..+..       +.-+.|+|++.+.|.+|
T Consensus        28 ~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~-------~r~alvefedi~~akn~   83 (494)
T KOG1456|consen   28 PNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH-------KRQALVEFEDIEGAKNC   83 (494)
T ss_pred             CCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc-------cceeeeeeccccchhhh
Confidence            344567999999999999999999999999988866443       25688999988877654

>KOG4307|consensus

Probab=96.89  E-value=0.00094  Score=45.71  Aligned_cols=60  Identities=18%  Similarity=0.243  Sum_probs=48.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ...+..|||..||..+++.++.++|...-.|++ |.|...  .++..++.|||.|..++++..
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~--P~~~~~~~afv~F~~~~a~~~  491 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL--PTDLLRPAAFVAFIHPTAPLT  491 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccC--Ccccccchhhheeccccccch
Confidence            455789999999999999999999987666655 666555  688889999999998776554

>KOG0112|consensus

Probab=96.57  E-value=0.00058  Score=47.52  Aligned_cols=58  Identities=14%  Similarity=0.289  Sum_probs=46.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHH
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA   76 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a   76 (79)
                      .....+||++||+..+++.+++..|..+|.+..|.+-..+  -+.-..|+||.|.+...+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~--~~~esa~~f~~~~n~dmt  426 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH--IKTESAYAFVSLLNTDMT  426 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC--CCcccchhhhhhhccccC
Confidence            4557899999999999999999999999999999886652  344456888888765543

>KOG0112|consensus

Probab=96.43  E-value=0.0041  Score=43.59  Aligned_cols=56  Identities=9%  Similarity=0.291  Sum_probs=46.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.+++++|..++....+...|..||.|..|.+-..       ..|+||.|++...++.|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-------q~yayi~yes~~~aq~a  507 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-------QPYAYIQYESPPAAQAA  507 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-------CcceeeecccCccchhh
Confidence            345678999999999999999999999999999877443       37999999998877653

>KOG1190|consensus

Probab=96.43  E-value=0.0087  Score=38.86  Aligned_cols=55  Identities=16%  Similarity=0.190  Sum_probs=41.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      +..++.+.|+|.+++++++++.|..-|...+....     -++.+.++.+.+.+.|+|-.
T Consensus       413 psatlHlsnip~svsee~lk~~f~~~g~~vkafkf-----f~kd~kmal~q~~sveeA~~  467 (492)
T KOG1190|consen  413 PSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF-----FQKDRKMALPQLESVEEAIQ  467 (492)
T ss_pred             chhheeeccCCcccchhHHHHhhhcCCceEEeeee-----cCCCcceeecccCChhHhhh
Confidence            34589999999999999999999887765443321     23345789999999988754

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.42  E-value=0.034  Score=26.92  Aligned_cols=52  Identities=12%  Similarity=0.140  Sum_probs=39.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhc---CCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~---g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+..|+|.++.. .+.++++.+|..|   .....+.++.|        .-|-|.|.+.+.|.+|
T Consensus         4 rpeavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdD--------tScNvvf~d~~~A~~A   58 (62)
T PF10309_consen    4 RPEAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDD--------TSCNVVFKDEETAARA   58 (62)
T ss_pred             eeceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecC--------CcEEEEECCHHHHHHH
Confidence            456799999854 6778899999888   13567888887        2367889999998765

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=96.36  E-value=0.0051  Score=35.60  Aligned_cols=61  Identities=11%  Similarity=0.182  Sum_probs=32.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHh-cCCe---eEEEeeccc-CCCCCcceEEEEEecCHHHHh
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKA-FGEL---KFVRLPKKM-VGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~-~g~i---~~~~~~~~~-~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ..+..+|.|++||+..+++++.+.+.+ ++.-   ..+.-.... ........-|||.|.+.+++.
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~   69 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLL   69 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHH
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHH
Confidence            345679999999999999998886665 5543   333311111 011112356999999987753

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG2193|consensus

Probab=95.66  E-value=0.011  Score=38.75  Aligned_cols=51  Identities=24%  Similarity=0.300  Sum_probs=36.7

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+|++||.+.++..++..+|..-- ....-.|+.        .||+||.+.+...|.+|
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k--------~gyafvd~pdq~wa~ka   53 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK--------SGYAFVDCPDQQWANKA   53 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee--------cceeeccCCchhhhhhh
Confidence            4689999999999999999996431 111222333        28999999988877543

>KOG0120|consensus

Probab=95.19  E-value=0.039  Score=36.81  Aligned_cols=44  Identities=25%  Similarity=0.404  Sum_probs=30.9

Q ss_pred             HHHHHhHhcCCeeEEEeecc-cC-CCCCcceEEEEEecCHHHHhcC
Q psy3346          36 EVEELFKAFGELKFVRLPKK-MV-GSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        36 ~l~~~f~~~g~i~~~~~~~~-~~-~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +++.-+.+||.|..|.+++. .. ...-..|-.||+|.+.+++++|
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA  470 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRA  470 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHH
Confidence            34455567899999988776 20 1222346789999999998875

>KOG1548|consensus

Probab=94.61  E-value=0.08  Score=33.84  Aligned_cols=60  Identities=17%  Similarity=0.313  Sum_probs=43.1

Q ss_pred             ccCCCCCeEEEeCCCC----CCC-------HHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPF----QAK-------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~----~~~-------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|.+.|+=.    ..+       .++|.+-..+||.|.++.+.-.     .+.|.+-|.|.+.++|+.|
T Consensus       260 sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~-----hPdGvvtV~f~n~eeA~~c  330 (382)
T KOG1548|consen  260 SKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR-----HPDGVVTVSFRNNEEADQC  330 (382)
T ss_pred             ccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc-----CCCceeEEEeCChHHHHHH
Confidence            3445678899998721    223       2456677889999999876432     3568899999999998764

>KOG1456|consensus

Probab=94.50  E-value=0.23  Score=32.29  Aligned_cols=59  Identities=19%  Similarity=0.273  Sum_probs=47.9

Q ss_pred             ccCCCCCeEEEeCCCCCC-CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+++.+.|-+|.-.. .-+.|..+|-.||.|..|+++..+      .|.|.|++.+..+.++|
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk------~gtamVemgd~~aver~  341 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK------PGTAMVEMGDAYAVERA  341 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc------cceeEEEcCcHHHHHHH
Confidence            345667899999998764 556789999999999999998874      47799999998887764

>KOG2416|consensus

Probab=94.42  E-value=0.039  Score=37.52  Aligned_cols=56  Identities=14%  Similarity=0.188  Sum_probs=41.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHh-cCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKA-FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ........|||.||-.-.|...|++++.. +|.|... |+-      +-+..|||.|.+.++|-
T Consensus       439 sR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmD------kIKShCyV~yss~eEA~  495 (718)
T KOG2416|consen  439 SRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMD------KIKSHCYVSYSSVEEAA  495 (718)
T ss_pred             CCCCccceEeeecccccchHHHHHHHHhhccCchHHH-HHH------HhhcceeEecccHHHHH
Confidence            33445678999999999999999999985 5555554 322      23567999999988874

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.25  E-value=0.22  Score=28.28  Aligned_cols=54  Identities=24%  Similarity=0.231  Sum_probs=36.5

Q ss_pred             CCCCCeEEEeCCCCCC----CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          17 KQTGSKILVRNIPFQA----KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~----~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      +..-.+|.|+=|....    +-..+...++.||+|.++.+--        +.-|.|.|.+..+|=+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--------rqsavVvF~d~~SAC~  140 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--------RQSAVVVFKDITSACK  140 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--------CceEEEEehhhHHHHH
Confidence            4556778787555444    3345666678899999986422        2458999998887643

>KOG2591|consensus

Probab=94.01  E-value=0.19  Score=34.14  Aligned_cols=54  Identities=17%  Similarity=0.313  Sum_probs=41.9

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhH--hcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFK--AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~--~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...|.+.++-||..+-.++++.+|+  .|-.+.+|.+-.+.       + =||+|++..+|+.|
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------n-WyITfesd~DAQqA  228 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------N-WYITFESDTDAQQA  228 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------c-eEEEeecchhHHHH
Confidence            3456788889999999999999995  47777777764431       2 38999999999865

>KOG2068|consensus

Probab=93.86  E-value=0.034  Score=35.15  Aligned_cols=61  Identities=16%  Similarity=0.296  Sum_probs=41.4

Q ss_pred             CCCeEEEeCCCCCCCHHHH---HHHhHhcCCeeEEEeecccCCCCC--cceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMVGSGL--HRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l---~~~f~~~g~i~~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~~a   79 (79)
                      +..-+|+.+|+.....+.+   .+.|.+||.|..+..-.++.....  ...-++|+|...++|..|
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rc  141 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRC  141 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhH
Confidence            3456888899988766654   467888999999877665310111  112379999998887654

>KOG4410|consensus

Probab=92.37  E-value=0.48  Score=29.86  Aligned_cols=49  Identities=12%  Similarity=0.143  Sum_probs=36.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCe-eEEEeecccCCCCCcceEEEEEecCHHH
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNE   75 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~~g~~fv~f~~~~~   75 (79)
                      ...|+++|||.++.-.+|+..+.+.+.+ .++.|.       .+.|-||..|.+...
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswk-------g~~~k~flh~~~~~~  379 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWK-------GHFGKCFLHFGNRKG  379 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCCceeEeee-------cCCcceeEecCCccC
Confidence            4679999999999999999999887642 333331       245779999977543

>KOG4210|consensus

Probab=92.32  E-value=0.051  Score=33.82  Aligned_cols=59  Identities=19%  Similarity=0.068  Sum_probs=46.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..++.|++++.+.+.+.+...++...|......+.... ....++|++++.|...+.+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~-~~~~sk~~~s~~f~~ks~~~~  145 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLE-DSLSSKGGLSVHFAGKSQFFA  145 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhc-cccccccceeeccccHHHHHH
Confidence            46789999999999998888888888866555554433 567788999999999887654

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=91.95  E-value=0.61  Score=22.84  Aligned_cols=39  Identities=15%  Similarity=0.342  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          31 QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        31 ~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++-.+++..|..|+ ...|.  .+  .+    | =||.|.+..+|++|
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~--~d--~t----G-fYIvF~~~~Ea~rC   49 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIR--DD--RT----G-FYIVFNDSKEAERC   49 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEE--ec--CC----E-EEEEECChHHHHHH
Confidence            467788999999996 45544  33  12    3 37999999999875

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

>KOG4660|consensus

Probab=91.79  E-value=0.21  Score=33.68  Aligned_cols=55  Identities=16%  Similarity=0.350  Sum_probs=32.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhH-hcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          22 KILVRNIPFQAKQSEVEELFK-AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ++.|.|+|...|...|.+... ..|.-..+.|+.|- .+..+.|||||.|-+++++.
T Consensus       390 t~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF-~nkcNvGYAFINm~sp~ai~  445 (549)
T KOG4660|consen  390 TLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDF-KNKCNVGYAFINMTSPEAII  445 (549)
T ss_pred             hhHhhccCchhhHHhhhhhhccccCccceEEecccc-ccccccceeEEeecCHHHHH
Confidence            344444444444433333321 23444556666664 56668899999999988764

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=90.74  E-value=0.78  Score=28.90  Aligned_cols=61  Identities=13%  Similarity=0.177  Sum_probs=43.7

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeeccc------CCCCCcceEEEEEecCHHHH
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKM------VGSGLHRGFGFVEFITKNEA   76 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~------~~~~~~~g~~fv~f~~~~~a   76 (79)
                      +....+.|.+.|+..+++--.+..-|.+||+|+++.++.+.      ....+......+.|-+.+.+
T Consensus        11 D~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~C   77 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREIC   77 (309)
T ss_pred             ccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHH
Confidence            34456778899999999888888889999999999987652      01222234556777666654

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG1996|consensus

Probab=90.58  E-value=0.75  Score=29.13  Aligned_cols=44  Identities=20%  Similarity=0.153  Sum_probs=31.2

Q ss_pred             HHHHHHhHhcCCeeEEEeecccCCCCCcc-eEEEEEecCHHHHhcC
Q psy3346          35 SEVEELFKAFGELKFVRLPKKMVGSGLHR-GFGFVEFITKNEAKRV   79 (79)
Q Consensus        35 ~~l~~~f~~~g~i~~~~~~~~~~~~~~~~-g~~fv~f~~~~~a~~a   79 (79)
                      +++++-+++||.|..|.+...+ ...... ---||+|...++|.+|
T Consensus       301 de~keEceKyg~V~~viifeip-~~p~deavRiFveF~r~e~aiKA  345 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIP-SQPEDEAVRIFVEFERVESAIKA  345 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecC-CCccchhheeeeeeccHHHHHHH
Confidence            4677888999999988776654 222222 2369999999988764

>KOG2891|consensus

Probab=90.55  E-value=0.61  Score=29.39  Aligned_cols=54  Identities=26%  Similarity=0.468  Sum_probs=36.7

Q ss_pred             CCCCCeEEEeCCCCC------------CCHHHHHHHhHhcCCeeEEEeec-cc---CCCCCcceEEEEEe
Q psy3346          17 KQTGSKILVRNIPFQ------------AKQSEVEELFKAFGELKFVRLPK-KM---VGSGLHRGFGFVEF   70 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~------------~~~~~l~~~f~~~g~i~~~~~~~-~~---~~~~~~~g~~fv~f   70 (79)
                      ...+.+||+.+||-.            .+++.|+..|..||.|..+.++. ++   ..+|+..|..|-.|
T Consensus       146 gerpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gf  215 (445)
T KOG2891|consen  146 GERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGF  215 (445)
T ss_pred             CCCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeecc
Confidence            345678888888753            46778999999999999988853 22   13555545444333

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=90.48  E-value=1.7  Score=23.40  Aligned_cols=56  Identities=13%  Similarity=0.167  Sum_probs=35.7

Q ss_pred             CCeEEEeCCCCC-CCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQ-AKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~-~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      .+.+.+--.|+. ++.+.|..+..++- .|..++++++.   ..++-.+.+.|.+.++|+.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~---~pnrymVLikF~~~~~Ad~   69 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG---TPNRYMVLIKFRDQESADE   69 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC---CCceEEEEEEECCHHHHHH
Confidence            344444444554 45555655555553 57788888872   2356778999999998863

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

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=89.62  E-value=1  Score=24.46  Aligned_cols=49  Identities=29%  Similarity=0.362  Sum_probs=25.4

Q ss_pred             CeEEEeCCCCC---------CCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCH
Q psy3346          21 SKILVRNIPFQ---------AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK   73 (79)
Q Consensus        21 ~~l~v~nl~~~---------~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~   73 (79)
                      -++.|.|++.+         .+.+.|++.|..|.++. ++...++   ..+.|++.|.|.+.
T Consensus         9 wmgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~k-v~~l~~~---~gh~g~aiv~F~~~   66 (116)
T PF03468_consen    9 WMGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLK-VKPLYGK---QGHTGFAIVEFNKD   66 (116)
T ss_dssp             -EEEEE----EE-TTS-EE---SHHHHHHHHH---SE-EEEEEET---TEEEEEEEEE--SS
T ss_pred             CEEEEEcCccccCCCCceeccCHHHHHHHHHhcCCce-eEECcCC---CCCcEEEEEEECCC
Confidence            34566677554         34578999999998764 4444442   35789999999764

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>PF15513 DUF4651: Domain of unknown function (DUF4651)

Probab=89.36  E-value=1.5  Score=21.21  Aligned_cols=18  Identities=22%  Similarity=0.654  Sum_probs=14.9

Q ss_pred             HHHHHHhHhcCCeeEEEe
Q psy3346          35 SEVEELFKAFGELKFVRL   52 (79)
Q Consensus        35 ~~l~~~f~~~g~i~~~~~   52 (79)
                      .+|+++|+..|.|.-+.+
T Consensus         9 ~~iR~~fs~lG~I~vLYv   26 (62)
T PF15513_consen    9 AEIRQFFSQLGEIAVLYV   26 (62)
T ss_pred             HHHHHHHHhcCcEEEEEE
Confidence            578999999999876654

>KOG2202|consensus

Probab=88.30  E-value=0.12  Score=31.76  Aligned_cols=35  Identities=17%  Similarity=0.300  Sum_probs=25.9

Q ss_pred             hcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          43 AFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        43 ~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +||+|..+.+-.+  ......|=+||.|...++|++|
T Consensus        92 kygEiee~~Vc~N--l~~hl~GNVYV~f~~Ee~ae~a  126 (260)
T KOG2202|consen   92 KYGEIEELNVCDN--LGDHLVGNVYVKFRSEEDAEAA  126 (260)
T ss_pred             Hhhhhhhhhhhcc--cchhhhhhhhhhcccHHHHHHH
Confidence            8899988754333  3334568899999999999875

>KOG2253|consensus

Probab=88.01  E-value=0.34  Score=33.39  Aligned_cols=53  Identities=19%  Similarity=0.295  Sum_probs=40.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      ...+...++||+|+...+..+-++.++..||-|.++.  +.        -|||..|..+....
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~k--r~--------~fgf~~f~~~~~~~   87 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWK--RD--------KFGFCEFLKHIGDL   87 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhh--hh--------hhcccchhhHHHHH
Confidence            3445678999999999999999999999999775542  22        27888887766543

>KOG4285|consensus

Probab=86.94  E-value=1.4  Score=28.07  Aligned_cols=52  Identities=17%  Similarity=0.196  Sum_probs=36.0

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.=|-|-++|+... ..|...|.+||.|.+...       +.+--|-+|.|.+..+|++|
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~-------~~ngNwMhirYssr~~A~KA  248 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVT-------PSNGNWMHIRYSSRTHAQKA  248 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeec-------CCCCceEEEEecchhHHHHh
Confidence            34455556776644 456778999999866532       23345889999999998875

>KOG4008|consensus

Probab=86.82  E-value=0.87  Score=27.87  Aligned_cols=36  Identities=8%  Similarity=0.311  Sum_probs=29.6

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEE
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVR   51 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~   51 (79)
                      ...+..++|+.|+|..++++.|..+.+++|-+..+.
T Consensus        36 ~~~eKd~lfl~Nvp~~~tee~lkr~vsqlg~vq~~~   71 (261)
T KOG4008|consen   36 NSNEKDCLFLVNVPLLSTEEHLKRFVSQLGHVQELL   71 (261)
T ss_pred             ccccccceeeecccccccHHHHHHHHHHhhhhhhee
Confidence            345678999999999999999999999998654443

>KOG0804|consensus

Probab=86.26  E-value=5.5  Score=26.77  Aligned_cols=55  Identities=11%  Similarity=0.235  Sum_probs=44.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHh
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK   77 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~   77 (79)
                      .+.|.|-.+|...+-.+|..|...+- .|..++++++.  .+ ++-...+.|.+.++|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~p-nrymvLIkFr~q~da~  129 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MP-NRYMVLIKFRDQADAD  129 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CC-ceEEEEEEeccchhHH
Confidence            78899999999999999999998764 58899998872  22 3455789999998875

>KOG4483|consensus

Probab=84.42  E-value=3  Score=27.64  Aligned_cols=51  Identities=12%  Similarity=0.169  Sum_probs=39.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCC-eeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ...|-|-++|.....++|...|..|+. --.|.|+.+        -.+|..|.+...|..
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDd--------thalaVFss~~~Aae  442 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDD--------THALAVFSSVNRAAE  442 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEeec--------ceeEEeecchHHHHH
Confidence            467888899999999999999999863 456677766        457888888777654

>KOG2135|consensus

Probab=84.24  E-value=0.8  Score=30.65  Aligned_cols=52  Identities=23%  Similarity=0.382  Sum_probs=36.8

Q ss_pred             CCCCeEEEeCCCCCC-CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHH
Q psy3346          18 QTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA   76 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a   76 (79)
                      .+.+.+-+.-.|+.. +..+|...|.+||.|..|.+-..       --.|.|+|.+..+|
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-------~~~a~vTF~t~aea  422 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-------SLHAVVTFKTRAEA  422 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc-------hhhheeeeeccccc
Confidence            445666666666664 56789999999999999876433       13467888777665

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

Probab=84.08  E-value=2.5  Score=24.00  Aligned_cols=53  Identities=19%  Similarity=0.246  Sum_probs=31.9

Q ss_pred             CCCCeEEEeCCCC------CCCH---HHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPF------QAKQ---SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~------~~~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..-||.|.-+.+      ...+   .+|.+.|..||.+.-+++..+         .-+|+|.+-++|.+|
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~---------~mwVTF~dg~sALaa   86 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD---------TMWVTFRDGQSALAA   86 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT---------CEEEEESSCHHHHHH
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC---------eEEEEECccHHHHHH
Confidence            4456666664441      1222   357778888998777766554         368999988887654

; PDB: 1UFW_A 2DNR_A.

>KOG4676|consensus

Probab=81.97  E-value=0.14  Score=33.43  Aligned_cols=47  Identities=17%  Similarity=0.104  Sum_probs=35.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT   72 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~   72 (79)
                      +++++++|+..+...++.+.|..+|.+...++-.     +....+|-++|..
T Consensus       152 Rt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as-----k~~s~~c~~sf~~  198 (479)
T KOG4676|consen  152 RTREVQSLISAAILPESGESFERKGEVSYAHTAS-----KSRSSSCSHSFRK  198 (479)
T ss_pred             hhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc-----cCCCcchhhhHhh
Confidence            7899999999999999999999999987766633     3333455566643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	79
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		1e-22
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		8e-05
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		2e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		4e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		6e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-04

>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 =  101 bits (251), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 47/63 (74%), Positives = 52/63 (82%)
Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +A
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 77 KRV 79
          K+ 
Sbjct: 72 KKA 74

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G+ ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++T  +A+R
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 76

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          A Q  S ++V  +P++  + +++E F  FGE+  V++ KK + +G  +GFGFV F
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHSKGFGFVRF 64

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++T  +A+R
Sbjct: 5  TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 61

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++T  +A+R
Sbjct: 3  TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 59

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 39.3 bits (90), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + ++V  +P    Q E+  LF + GE++  +L +  V +G   G+GFV ++T  +A+R
Sbjct: 3  TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAER 59

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-13
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-13
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-13
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	8e-13
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	9e-13
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	8e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-11
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-11
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-11
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-11
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	7e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-11
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-10
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-08
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-10
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-10
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-10
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	5e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-10
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	8e-10
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-09
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-09
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-09
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-09
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-09
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-09
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	6e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-09
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	8e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	8e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-08
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-08
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	5e-08
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-08
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	9e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	7e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-07
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-07
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-06
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-06
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-06
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-06
2div_A	99	TRNA selenocysteine associated protein; structural	6e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	9e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-05
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-05
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	7e-05
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-04
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-04
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-04
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	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 = 86.2 bits (214), Expect = 4e-24
 Identities = 47/70 (67%), Positives = 52/70 (74%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
                  KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRGFGFV
Sbjct: 4  GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63

Query: 69 EFITKNEAKR 78
          +FITK +AK+
Sbjct: 64 DFITKQDAKK 73

>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 = 63.5 bits (155), Expect = 2e-14
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 8   VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
           V    S V   +  K+ +  +P      +V+EL  +FG LK   L K    +GL +G+ F
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAF 160

Query: 68  VEFITKNEAKR 78
            E++  N   +
Sbjct: 161 CEYVDINVTDQ 171

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

 Score = 46.9 bits (112), Expect = 4e-08
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 77
          ++ V NIPF   +  + + F A   L  +      P   V     + F F+EF + +E  
Sbjct: 6  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 78 R 78
          +
Sbjct: 66 Q 66

>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 = 61.0 bits (149), Expect = 2e-14
 Identities = 13/58 (22%), Positives = 33/58 (56%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          +K+ +  +     +  + E+F  +G++K + +P + +   L +G+ +VEF   +EA++
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

>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 = 60.4 bits (147), Expect = 5e-14
 Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 9  KRKSSNVAK--QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 66
             SS +      G  + +RN+ F +++  + E+ + FG+LK+VR+      +   +G  
Sbjct: 2  SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-TEHSKGCA 60

Query: 67 FVEFITKNEAKR 78
          F +F+T+  A++
Sbjct: 61 FAQFMTQEAAQK 72

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

 Score = 59.2 bits (144), Expect = 1e-13
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            K+ +  +PF   + E+EE+ KA G +K +RL      +G  +G  +VE+  +++A +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR--AGKPKGLAYVEYENESQASQ 73

>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 = 58.8 bits (143), Expect = 2e-13
 Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           ++ VRN+ + + + ++E+LF A+G L  +  P   + +   +GF FV F+    A +
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-TKKPKGFAFVTFMFPEHAVK 65

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

 Score = 59.4 bits (144), Expect = 3e-13
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 3   SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 62
            +  +     S  +  T   + V  +  +     +   F  FG++  +++P     +  H
Sbjct: 46  VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKH 104

Query: 63  RGFGFVEFITKNEAK 77
           RGF FVEF    +A 
Sbjct: 105 RGFAFVEFELAEDAA 119

>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 = 57.6 bits (140), Expect = 5e-13
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
            SS         + V N+ ++     +  +F+ +G +  V +P++   +   RGF FV 
Sbjct: 3  SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH-TKAPRGFAFVR 61

Query: 70 FITKNEAKR 78
          F  + +A+ 
Sbjct: 62 FHDRRDAQD 70

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

 Score = 57.7 bits (140), Expect = 6e-13
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G  + V  +  +A + ++ + F  +GE+K + L      +G  +G+  VE+ T  EA+ 
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQA 80

>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 = 57.2 bits (139), Expect = 8e-13
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + I V N+    ++++++ELF+ FG +  + L K    +G  +GF F+ F  + +A R
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-TGQSKGFAFISFHRREDAAR 72

>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 = 56.8 bits (138), Expect = 9e-13
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          T   + V  +  +     +   F  FG++  +++P     +  HRGF FVEF    +A 
Sbjct: 6  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAA 63

>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 = 59.2 bits (144), Expect = 2e-12
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 9   KRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
           K K ++ A   G +I++RN+  +   ++ + E F+ FG ++ + +P        +    F
Sbjct: 199 KSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF 258

Query: 68  VEFITKNEAKR 78
           + F  K+ A+R
Sbjct: 259 MVFENKDSAER 269

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

 Score = 55.4 bits (134), Expect = 5e-11
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 15  VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITK 73
           V+  T   + + N P    Q  + +L +    +   +RLP     +   R F +++  +K
Sbjct: 112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNT--SRRFAYIDVTSK 169

Query: 74  NEAKR 78
            +A+ 
Sbjct: 170 EDARY 174

>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 = 49.6 bits (119), Expect = 6e-09
 Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 3/62 (4%)

Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
           +  + +LV+N+P    Q++V + FK  G +  V +         +  F  +EF   + A
Sbjct: 38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD---SLKKNFRFARIEFARYDGA 94

Query: 77 KR 78
            
Sbjct: 95 LA 96

>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 = 56.1 bits (136), Expect = 2e-12
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
           S        K+ V  +  Q  + +V  LF+ FG +    + +     G  +G  FV+F 
Sbjct: 7  GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKFS 64

Query: 72 TKNEAKR 78
          +  EA+ 
Sbjct: 65 SHTEAQA 71

>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 = 57.6 bits (140), Expect = 2e-12
 Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 8   VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
           ++R           K+ +  +P      +V+EL  +FG LK   L K    +GL +G+ F
Sbjct: 82  IRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAF 140

Query: 68  VEFITKNEAKRV 79
            E++  N   + 
Sbjct: 141 CEYVDINVTDQA 152

>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 = 43.8 bits (104), Expect = 4e-07
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 77
          ++ V NIPF   +  + + F A   L  +      P   V     + F F+EF + +E  
Sbjct: 6  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 78 RV 79
          + 
Sbjct: 66 QA 67

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

 Score = 57.1 bits (138), Expect = 2e-12
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 20  GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            + + V N+ ++     +  +F+ +G +  V +P+    +   RGF FV F  K +A+ 
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-TKESRGFAFVRFHDKRDAED 104

>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 = 56.4 bits (136), Expect = 6e-12
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 20  GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           G  + V +I  +A++ E++E F  +GE+K + L      +G  +G+  VE+ T  +A  
Sbjct: 72  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALA 129

>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 = 55.0 bits (133), Expect = 6e-12
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + + V  +  +  +  + ELF   G +    +PK  V +G H+G+GFVEF+++ +A  
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-TGQHQGYGFVEFLSEEDADY 72

>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 = 54.6 bits (132), Expect = 7e-12
 Identities = 13/74 (17%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 5  ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
          +  ++   ++   +    +L +N+ F   + E++E+F+   E++ V         G  +G
Sbjct: 1  SHMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKG 54

Query: 65 FGFVEFITKNEAKR 78
            ++EF ++ +A++
Sbjct: 55 IAYIEFKSEADAEK 68

>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 = 55.1 bits (133), Expect = 8e-12
 Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          G  + V  +  +A + ++ + F  +GE+K + L      +G  +G+  VE+ T  EA+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQ 78

>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 = 54.6 bits (132), Expect = 9e-12
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          G  + V +I  +A++ E++E F  +GE+K + L      +G  +G+  VE+ T  +A  
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALA 83

>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 = 54.6 bits (132), Expect = 9e-12
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 7/77 (9%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          GS  ++   +S +    T  ++ V NIPF+ +  ++ ++F  FG++  V +     GS  
Sbjct: 1  GSSGSSGNSESKS----TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-- 54

Query: 62 HRGFGFVEFITKNEAKR 78
           +GFGFV F    +A R
Sbjct: 55 -KGFGFVTFENSADADR 70

>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 = 54.1 bits (131), Expect = 1e-11
 Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          S + V ++ F   +  +  +F+ FG++  + L K    +G  +G+GF+ F     A+R
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD-TGRSKGYGFITFSDSECARR 62

>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 = 54.2 bits (131), Expect = 1e-11
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 4/76 (5%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          GS   +        A     +I V N+P   +  ++E++F  +G ++ + L  +  G   
Sbjct: 4  GSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--- 60

Query: 62 HRGFGFVEFITKNEAK 77
             F FVEF    +A+
Sbjct: 61 -PPFAFVEFEDPRDAE 75

>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 = 53.8 bits (130), Expect = 2e-11
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           S++ V N+P    + E+ +LF+ +G+   V + K        +GFGF+   T+  A+ 
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-------DKGFGFIRLETRTLAEI 66

>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 = 54.3 bits (131), Expect = 2e-11
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
                  +TG+K+LV N+ F    ++++ELF  FG LK   +      SG   G   V 
Sbjct: 25 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR--SGRSLGTADVH 82

Query: 70 FITKNEAKR 78
          F  + +A +
Sbjct: 83 FERRADALK 91

>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 = 53.9 bits (130), Expect = 2e-11
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
             S+    TG  + +R +P++A ++++   F     ++ V +       G   G   VE
Sbjct: 5  SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGP--DGRVTGEADVE 61

Query: 70 FITKNEAKR 78
          F T  +A  
Sbjct: 62 FATHEDAVA 70

>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 = 53.8 bits (130), Expect = 2e-11
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
            + V  +  +     +   F  FG++  +++P     +  HRGF FVEF    +A 
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-TEKHRGFAFVEFELAEDAA 68

>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 = 53.7 bits (129), Expect = 2e-11
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
          SS  + ++ + IL +N+P     +E++E F  FG L  V LP+             VEF+
Sbjct: 2  SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-------GITAIVEFL 54

Query: 72 TKNEAKR 78
             EA++
Sbjct: 55 EPLEARK 61

>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 = 54.5 bits (131), Expect = 3e-11
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 20  GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
            + + V N+ ++     +  +F+ +G +  V +P+    +   RGF FV F  K +A+
Sbjct: 70  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-TKESRGFAFVRFHDKRDAE 126

>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 = 53.5 bits (129), Expect = 3e-11
 Identities = 13/58 (22%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           ++ V ++ F   +  +  +F+ FG ++ ++L      +G  +G+GF+ F     AK+
Sbjct: 27 MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE-TGRSKGYGFITFSDSECAKK 83

>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 = 53.4 bits (129), Expect = 3e-11
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 1/69 (1%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
             S + K       + N+P+   +  ++E F+       VRLP++       +GFG+ E
Sbjct: 5  SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAE 63

Query: 70 FITKNEAKR 78
          F   +    
Sbjct: 64 FEDLDSLLS 72

>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 = 53.4 bits (129), Expect = 3e-11
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
                  +TG K+LV N+ F    ++++ELF  FG LK   +      SG   G   V 
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVH 76

Query: 70 FITKNEAKR 78
          F  K +A +
Sbjct: 77 FERKADALK 85

>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 = 55.4 bits (134), Expect = 4e-11
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 18  QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
            T + + V N+P    Q + EEL + FG L+   L      +G  +G+GF E++ K+ A 
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-TGQSKGYGFAEYMKKDSAA 151

Query: 78  R 78
           R
Sbjct: 152 R 152

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

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 12/70 (17%), Positives = 21/70 (30%), Gaps = 3/70 (4%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSE-VEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
                 A      + V  +P      + +     A     F +L       G  +GF  +
Sbjct: 174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ--DGQLKGFAVL 231

Query: 69  EFITKNEAKR 78
           E+ T   A+ 
Sbjct: 232 EYETAEMAEE 241

>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 = 40.0 bits (94), Expect = 1e-05
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 8/59 (13%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            KIL+R +P      EV +L   +          K      ++G  FV  +   +A+ 
Sbjct: 22 RRKILIRGLPGDVTNQEVHDLLSDYE--------LKYCFVDKYKGTAFVTLLNGEQAEA 72

>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 = 52.7 bits (127), Expect = 4e-11
 Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEF 70
           ++  K   + I V+N+PF     E+ + F  +  +   V L       G+  G   V F
Sbjct: 7  GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE--KGMPTGEAMVAF 64

Query: 71 ITKNEAKR 78
           +++EA  
Sbjct: 65 ESRDEATA 72

>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 = 52.6 bits (127), Expect = 4e-11
 Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 9/67 (13%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
          SS  + +  +K+ V NI       E+   F+ +G +    +          + + FV   
Sbjct: 2  SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV---------KDYAFVHME 52

Query: 72 TKNEAKR 78
             +A  
Sbjct: 53 RAEDAVE 59

>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 = 52.7 bits (127), Expect = 4e-11
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
          SS  +  T   + +R  PF   +  V E       +  +R+ +   G+    G+ FV+F 
Sbjct: 2  SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNAHGN--KTGYIFVDFS 58

Query: 72 TKNEAKR 78
           + E K+
Sbjct: 59 NEEEVKQ 65

>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 = 52.2 bits (126), Expect = 5e-11
 Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + S + V N+PF    +++  +F  +G++  V + K    +   +G  F+ F+ K+ A+ 
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKGVAFILFLDKDSAQN 73

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 53.3 bits (128), Expect = 5e-11
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGF 67
          KR  S    + G  + ++ +PF+A+   V + FK    ++  + +     G     G GF
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK--ATGEGF 71

Query: 68 VEFITKNEAKR 78
          VEF  + + K 
Sbjct: 72 VEFRNEADYKA 82

>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 = 53.2 bits (128), Expect = 6e-11
 Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 9   KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
           +   +         + V  +     + ++ E+F  +G +  V +      S   RGF FV
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRRSRGFAFV 93

Query: 69  EFITKNEAKR 78
            F   ++AK 
Sbjct: 94  YFENVDDAKE 103

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 54.1 bits (130), Expect = 6e-11
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 16  AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
             +TG+K+LV N+ F    ++++ELF  FG LK   +      SG   G   V F  + +
Sbjct: 84  GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD--RSGRSLGTADVHFERRAD 141

Query: 76  AKR 78
           A +
Sbjct: 142 ALK 144

>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 = 52.2 bits (126), Expect = 6e-11
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 5/77 (6%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          GS  ++  R + +        + V  +     + ++ E+F  +G +  V +      S  
Sbjct: 1  GSSGSSGNRANPD----PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRR 55

Query: 62 HRGFGFVEFITKNEAKR 78
           RGF FV F   ++AK 
Sbjct: 56 SRGFAFVYFENVDDAKE 72

>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 = 51.7 bits (125), Expect = 7e-11
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKR 78
           I V N+ + A   E+E  F   G +  V +   K   SG  +GF ++EF  K   + 
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF--SGHPKGFAYIEFSDKESVRT 63

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 52.9 bits (127), Expect = 7e-11
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 9   KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
                 V   TG  + +R +P++A ++++   F     ++ V +       G   G   V
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGP--DGRVTGEADV 91

Query: 69  EFITKNEAKR 78
           EF T  EA  
Sbjct: 92  EFATHEEAVA 101

>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 = 51.9 bits (125), Expect = 9e-11
 Identities = 9/57 (15%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
            + + +IP+   + ++ +L    G +  +++      +G  +G+ F+EF     + 
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-TGRSKGYAFIEFRDLESSA 58

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

 Score = 51.6 bits (124), Expect = 1e-10
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAK 77
             I++RNI        +      +  L    +RL K    +  +RGF FV+  +  +A 
Sbjct: 9  MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQ-TQQNRGFAFVQLSSAMDAS 67

Query: 78 RV 79
          ++
Sbjct: 68 QL 69

>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 = 51.5 bits (124), Expect = 1e-10
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEF 70
           S+  K   + I V+N+PF     E+ + F  +  +   V L       G+  G   V F
Sbjct: 7  GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EKGMPTGEAMVAF 64

Query: 71 ITKNEAKR 78
           +++EA  
Sbjct: 65 ESRDEATA 72

>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 = 51.3 bits (123), Expect = 2e-10
 Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
              ++ +  IP   K+ E+ E      E +  V +         +RGF FVE+ +   A
Sbjct: 6  SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 77 KR 78
            
Sbjct: 66 AM 67

>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 = 52.6 bits (127), Expect = 2e-10
 Identities = 13/69 (18%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           +   +   +    +L +N+ F   + E++E+F+   E++ V         G  +G  ++E
Sbjct: 89  KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKGIAYIE 142

Query: 70  FITKNEAKR 78
           F ++ +A++
Sbjct: 143 FKSEADAEK 151

>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 = 46.1 bits (110), Expect = 6e-08
 Identities = 9/62 (14%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
            T   + + N+      +E++           + +      +G +R FG+V+F +  + 
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR--TGTNRKFGYVDFESAEDL 67

Query: 77 KR 78
          ++
Sbjct: 68 EK 69

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

 Score = 51.2 bits (123), Expect = 2e-10
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
            A    +   + NIP  A ++++  LF+ FG +   +           +G  F+++ T 
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-------EKGCCFIKYDTH 73

Query: 74 NEAKR 78
           +A  
Sbjct: 74 EQAAV 78

>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 = 51.1 bits (123), Expect = 2e-10
 Identities = 15/62 (24%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
            ++   + V NIP++A + +++++F   G +   RL      +G  +G+GF E+  +  
Sbjct: 4  VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQET 62

Query: 76 AK 77
          A 
Sbjct: 63 AL 64

>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 = 52.1 bits (125), Expect = 3e-10
 Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           +      +    + V N+ F   + ++ ELF   G++K + +    +      GF FVE
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KKTACGFCFVE 87

Query: 70 FITKNEAKR 78
          + ++ +A+ 
Sbjct: 88 YYSRADAEN 96

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 50.8 bits (122), Expect = 3e-10
 Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 6/56 (10%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          K+ V N+   A + E+E  F  +G L+ V + +         GF FVEF    +A+
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP------PGFAFVEFEDPRDAE 51

>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 = 51.3 bits (123), Expect = 3e-10
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 1  MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGS 59
            +E       +    +     + V N+ + +   ++E  F + G +  + +   K   S
Sbjct: 17 AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF--S 74

Query: 60 GLHRGFGFVEFITKNEAKR 78
          G  +G+ ++EF  +N    
Sbjct: 75 GHPKGYAYIEFAERNSVDA 93

>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 = 50.7 bits (122), Expect = 3e-10
 Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR--GFGFVEFITKNEAK 77
           S + ++N+ F   +  ++ +F   G +K   + KK   +G+    GFGFVE+    +A+
Sbjct: 5  SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64

Query: 78 R 78
          +
Sbjct: 65 K 65

>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 = 50.3 bits (121), Expect = 4e-10
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
              S + K       + N+P+   +  ++E F+       VRLP++       +GFG+ 
Sbjct: 8  HHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYA 66

Query: 69 EFITKNEAKR 78
          EF   +    
Sbjct: 67 EFEDLDSLLS 76

>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 = 50.8 bits (122), Expect = 4e-10
 Identities = 12/61 (19%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          +    + +RN+P++    E+ ++F  +G ++ +R+      +   RG  +V +    +AK
Sbjct: 6  EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN----TPETRGTAYVVYEDIFDAK 61

Query: 78 R 78
           
Sbjct: 62 N 62

>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 = 50.4 bits (121), Expect = 4e-10
 Identities = 15/67 (22%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
          SS +      K+ +  IP    + +++ LF+ FG++  + + K    +G+H+G  F+ + 
Sbjct: 5  SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-TGMHKGCAFLTYC 63

Query: 72 TKNEAKR 78
           +  A +
Sbjct: 64 ERESALK 70

>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 = 50.5 bits (121), Expect = 4e-10
 Identities = 11/71 (15%), Positives = 25/71 (35%), Gaps = 3/71 (4%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGF 67
                          + NIPF   + +V +  +     +  V +      +G   G   
Sbjct: 4  GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQAL 61

Query: 68 VEFITKNEAKR 78
          V+F  +++A++
Sbjct: 62 VQFKNEDDARK 72

>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 = 50.4 bits (121), Expect = 5e-10
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 10/80 (12%)

Query: 2  GSEATTVKRKSSNVAKQTGSK---ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG 58
          GS   T + +  +V  Q+  K   +    I        + + F  FG++  +R+      
Sbjct: 4  GSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP---- 59

Query: 59 SGLHRGFGFVEFITKNEAKR 78
              +G+ FV F T   A  
Sbjct: 60 ---EKGYSFVRFSTHESAAH 76

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 51.0 bits (122), Expect = 5e-10
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
                 +     K+ V N+     ++E+E  F  +G L+ V + +         GF FVE
Sbjct: 63  HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN------PPGFAFVE 116

Query: 70  FITKNEAK 77
           F    +A 
Sbjct: 117 FEDPRDAA 124

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 50.2 bits (120), Expect = 5e-10
 Identities = 9/69 (13%), Positives = 30/69 (43%), Gaps = 8/69 (11%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
                ++++ ++++V  +P      ++++  +  G++ +  + +         G G VE
Sbjct: 5  SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 56

Query: 70 FITKNEAKR 78
          F+ K +   
Sbjct: 57 FVRKEDMTY 65

>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 = 50.4 bits (121), Expect = 5e-10
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          G E   +   SS    +    + ++N+  +  + ++  LF  F E K   +  +M  +G 
Sbjct: 7  GEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGR 65

Query: 62 HRGFGFVEFITKNEAKR 78
           RG  F+ F  K  A +
Sbjct: 66 MRGQAFITFPNKEIAWQ 82

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 50.0 bits (120), Expect = 5e-10
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
                + + +++ VR  P   ++SE+ E+F  FG +K V++           GF FVEF
Sbjct: 22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---------GFAFVEF 72

Query: 71 ITKNEAKR 78
               A +
Sbjct: 73 EEAESAAK 80

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.9 bits (120), Expect = 6e-10
 Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           K+ V  + F   +  +E++F  +G++  V + K    +   RGFGFV F   ++AK 
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSRGFGFVTFENIDDAKD 69

>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 = 49.6 bits (119), Expect = 7e-10
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 2/62 (3%)

Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          ++    + V N+  + ++  + ELF   G L  V + K     G  + FGFV F      
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD--REGKPKSFGFVCFKHPESV 70

Query: 77 KR 78
            
Sbjct: 71 SY 72

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 50.3 bits (120), Expect = 8e-10
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 3  SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGL 61
          +    + R S++        + +R +PF   + E+ + F     +   + LP    G   
Sbjct: 25 TGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-- 82

Query: 62 HRGFGFVEFITKNEAKR 78
            G  FV+F ++  A++
Sbjct: 83 ITGEAFVQFASQELAEK 99

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.9 bits (119), Expect = 9e-10
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMV 57
           S   T    +  ++K+    + +R +PF A   EV   F     +    + +       
Sbjct: 5  SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD 64

Query: 58 GSGLHRGFGFVEFITKNEAKR 78
          G     G  FV F  +  A+ 
Sbjct: 65 GR--PTGDAFVLFACEEYAQN 83

>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 = 49.7 bits (119), Expect = 1e-09
 Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 15/83 (18%)

Query: 2  GSEATTVKRKSSNVAKQT-----GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKK 55
          GS   ++K ++SNV  +       S++ + N+     K+S+VE +F  +G +    +   
Sbjct: 4  GSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--- 60

Query: 56 MVGSGLHRGFGFVEFITKNEAKR 78
                H+G+ FV++  +  A+ 
Sbjct: 61 ------HKGYAFVQYSNERHARA 77

>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 = 49.4 bits (118), Expect = 1e-09
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 3/56 (5%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + V  +PF A +++V + F     +  V L K     G + G G V+F++  +   
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH--VGRNNGNGLVKFLSPQDTFE 71

>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 = 48.7 bits (117), Expect = 1e-09
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 9/57 (15%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
           K+ + N+P +A + E+  LF+ +G++    + K          +GFV    K  A+
Sbjct: 9  VKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK---------NYGFVHIEDKTAAE 56

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 50.2 bits (121), Expect = 1e-09
 Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 8   VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
            KR      +    KI V  I    +  E EE F  +G +   +L      +G  RGFGF
Sbjct: 75  PKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGF 133

Query: 68  VEFITKNEAKRV 79
           V + + +   RV
Sbjct: 134 VTYDSADAVDRV 145

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 44.4 bits (106), Expect = 2e-07
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           K+ +  + +   +  + E F  +G +  +++ K    +G  RGFGF+ F   +    V
Sbjct: 4  CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPA-TGRSRGFGFLSFEKPSSVDEV 61

>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 = 49.7 bits (119), Expect = 1e-09
 Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 1  MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
             +   +     N        ++V  IP    + ++ +LF+ +G ++ V++      + 
Sbjct: 23 QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-TR 81

Query: 61 LHRGFGFVEFITKNEAKR 78
            RG+GFV+F + + A++
Sbjct: 82 QSRGYGFVKFQSGSSAQQ 99

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 48.9 bits (117), Expect = 2e-09
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
              +   K    ++ V NIPF+ +  ++ ++F  FG++  V +     GS   +GFGFV
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFV 74

Query: 69 EFITKNEAKR 78
           F    +A R
Sbjct: 75 TFENSADADR 84

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

 Score = 48.3 bits (116), Expect = 2e-09
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
                +I VRN+PF      +++ F   G + +  +    + +G  +G G V+F +   
Sbjct: 4  GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI---KMENGKSKGCGVVKFESPEV 60

Query: 76 AKR 78
          A+R
Sbjct: 61 AER 63

>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 = 47.9 bits (115), Expect = 2e-09
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
           I V N+ + A   +V+ELF  FG++  V+L      +   +GFGFVE   ++ ++
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEMQEESVSE 57

>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 = 48.7 bits (116), Expect = 2e-09
 Identities = 9/69 (13%), Positives = 31/69 (44%), Gaps = 8/69 (11%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           +    ++++ ++++V  +P      ++++  +  G++ +  + +         G G VE
Sbjct: 6  GRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVE 57

Query: 70 FITKNEAKR 78
          F+ K +   
Sbjct: 58 FVRKEDMTY 66

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

 Score = 48.5 bits (116), Expect = 2e-09
 Identities = 9/59 (15%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            ++    +    +++ ++++ + +GE++ V +      +  H G   V F +   AK 
Sbjct: 6  LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR-TRKHLGLARVLFTSTRGAKE 63

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 49.5 bits (119), Expect = 3e-09
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 9   KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
              S         K+ +  I  +  ++++  +F +FG+++  R+ +     GL RG  FV
Sbjct: 84  PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP--DGLSRGCAFV 141

Query: 69  EFITKNEAKR 78
            F T+  A+ 
Sbjct: 142 TFTTRAMAQT 151

>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 = 48.4 bits (116), Expect = 8e-09
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-KMVGSGLHRGFGFVEFITKNEAKRV 79
          K+ V  +P    + ++ ELF+ +G +  + + + +       +G  FV F T+  A   
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

>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 = 48.5 bits (116), Expect = 3e-09
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
          A + GS + V N+ ++    +++E+F   G +    + +     G  RG G V F    E
Sbjct: 11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED--KDGKSRGIGTVTFEQSIE 68

Query: 76 AKR 78
          A +
Sbjct: 69 AVQ 71

>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 = 47.6 bits (114), Expect = 3e-09
 Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 9/66 (13%)

Query: 13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 72
          S+ +     KI V N+       E+  LF+  G +             + + + FV    
Sbjct: 2  SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECD---------VVKDYAFVHMEK 52

Query: 73 KNEAKR 78
          + +AK 
Sbjct: 53 EADAKA 58

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

 Score = 49.6 bits (119), Expect = 3e-09
 Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 20  GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            ++I V ++       +++ +F+AFG++K   L +    +G H+G+GF+E+     ++ 
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQSSQD 182

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

 Score = 47.3 bits (113), Expect = 3e-08
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
          A    S++ V +I ++  +  + + F  FG +K + +    V +  H+GF FVE+     
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSV-TMKHKGFAFVEYEVPEA 82

Query: 76 AKRV 79
          A+  
Sbjct: 83 AQLA 86

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 48.1 bits (114), Expect = 6e-09
 Identities = 12/81 (14%), Positives = 23/81 (28%), Gaps = 5/81 (6%)

Query: 2   GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVG 58
           G +               G  + +R +P+     +V+              V       G
Sbjct: 26  GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG 85

Query: 59  SGLHRGFGFVEFITKNEAKRV 79
                G  FVE  ++++ K  
Sbjct: 86  R--QSGEAFVELGSEDDVKMA 104

>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 = 48.7 bits (117), Expect = 6e-09
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + ++V  +P    Q E   LF + GE++  +L +  + +G   G+GFV +I   +A++ 
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYIDPKDAEKA 60

>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 = 43.3 bits (103), Expect = 5e-07
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 8   VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
           V     + A    + + V  +P    Q E+E+LF  +G +   R+      +G+ RG GF
Sbjct: 76  VSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGF 134

Query: 68  VEFITKNEAKRV 79
           + F  + EA+  
Sbjct: 135 IRFDKRIEAEEA 146

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

 Score = 47.2 bits (113), Expect = 6e-09
 Identities = 9/60 (15%), Positives = 25/60 (41%), Gaps = 10/60 (16%)

Query: 20 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           S++ + N+P +   + ++  +F  +G +  + +            FGF++F      + 
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 60

>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 = 48.3 bits (116), Expect = 6e-09
 Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + ++V  +P      E+  LF+A G +   R+ +    +G   G+ FV+F ++ +++R
Sbjct: 3  NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-TGYSYGYAFVDFTSEMDSQR 60

>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 = 44.1 bits (105), Expect = 2e-07
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 1/71 (1%)

Query: 8   VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
           V            + + V N+P      +++ +F  +G +    + +  + +G  RG  F
Sbjct: 77  VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAF 135

Query: 68  VEFITKNEAKR 78
           V +  + EA+ 
Sbjct: 136 VRYNKREEAQE 146

>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 = 47.0 bits (112), Expect = 6e-09
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 8/58 (13%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          S ILV+N+P  +   EV +L K +          K      ++   FV  +   +A+ 
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYD--------LKYCYVDRNKRTAFVTLLNGEQAQN 55

>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 = 47.7 bits (114), Expect = 7e-09
 Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 74
          V      K+ +  +  +  +  ++ +F   G +  V L K    +   RGF F+ F    
Sbjct: 2  VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR--TSKSRGFAFITFENPA 59

Query: 75 EAKRV 79
          +AK  
Sbjct: 60 DAKNA 64

>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 = 46.8 bits (112), Expect = 7e-09
 Identities = 10/59 (16%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           S + +R +       ++ +L + +G++   +       +   +G+GFV+F + + A++
Sbjct: 5  SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-TNKCKGYGFVDFDSPSAAQK 62

>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 = 47.2 bits (113), Expect = 7e-09
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 3/60 (5%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
              + V N+     +  + +LF   G  K  ++  +      +  + FVEF    +A  
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS---NDPYCFVEFYEHRDAAA 70

>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 = 46.9 bits (112), Expect = 8e-09
 Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 9/77 (11%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          GS  ++     S  +K     +++ N+ + A +  ++E+F+       +++P+    +G 
Sbjct: 1  GSSGSSGNSTWSGESK----TLVLSNLSYSATEETLQEVFEKATF---IKVPQNQ--NGK 51

Query: 62 HRGFGFVEFITKNEAKR 78
           +G+ F+EF +  +AK 
Sbjct: 52 SKGYAFIEFASFEDAKE 68

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 47.0 bits (112), Expect = 8e-09
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 9  KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFG 66
             S N         + +R +PF   + E+ + F     +   + LP    G     G  
Sbjct: 3  SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR--STGEA 60

Query: 67 FVEFITKNEAKR 78
          FV+F ++  A++
Sbjct: 61 FVQFASQEIAEK 72

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 47.2 bits (112), Expect = 8e-09
 Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 5/64 (7%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
           G  + +R +P+     +V+           +  V       G     G  FVE  ++++
Sbjct: 16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR--QSGEAFVELESEDD 73

Query: 76 AKRV 79
           K  
Sbjct: 74 VKLA 77

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 46.9 bits (112), Expect = 9e-09
 Identities = 9/60 (15%), Positives = 25/60 (41%), Gaps = 10/60 (16%)

Query: 20 GSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           S++ + N+P +   + ++  +F  +G +  + +            FGF++F      + 
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---------KNAFGFIQFDNPQSVRD 72

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 48.3 bits (114), Expect = 1e-08
 Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 23  ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + ++  P  A   +++E  +  G++  +++ +        +G  FV F +   AK+
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKK 165

>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 = 48.4 bits (116), Expect = 1e-08
 Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          V ++     ++ + E F   G +  +R+ + M+ +    G+ +V F    +A+R 
Sbjct: 20 VGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-TRRSLGYAYVNFQQPADAERA 73

>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 = 44.2 bits (105), Expect = 4e-07
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 3/69 (4%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           ++  ++ K     I ++N+        + + F AFG +   ++   +      +G+GFV 
Sbjct: 93  QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV---VCDENGSKGYGFVH 149

Query: 70  FITKNEAKR 78
           F T+  A+R
Sbjct: 150 FETQEAAER 158

>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 = 46.9 bits (112), Expect = 1e-08
 Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          G         + +  ++    +    +  + +  ++E+ F A G+++ VR+      S  
Sbjct: 7  GKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-SRR 65

Query: 62 HRGFGFVEFITKNEAKRV 79
           +G  +VEF         
Sbjct: 66 SKGIAYVEFCEIQSVPLA 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 = 46.5 bits (111), Expect = 1e-08
 Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 7/58 (12%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          +K+ + N+       ++ +LF         ++        L  G+ FV++  +N A R
Sbjct: 9  NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-------LLKSGYAFVDYPDQNWAIR 59

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 48.1 bits (115), Expect = 1e-08
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 5   ATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRG 64
           A + +      A  T  KI V  I    ++  + + F+ +G+++ + +     GSG  RG
Sbjct: 89  AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRG 147

Query: 65  FGFVEFITKNEAKRV 79
           F FV F   +   ++
Sbjct: 148 FAFVTFDDHDSVDKI 162

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 43.1 bits (102), Expect = 9e-07
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
          K +S    +Q   K+ +  + F+     +   F+ +G L    + +    +   RGFGFV
Sbjct: 3  KSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSRGFGFV 60

Query: 69 EFITKNEAKRV 79
           + T  E    
Sbjct: 61 TYATVEEVDAA 71

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 46.4 bits (110), Expect = 1e-08
 Identities = 8/63 (12%), Positives = 19/63 (30%), Gaps = 5/63 (7%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAF---GELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
              I  + +P+     +V   F           +       G    RG   +E  ++ +
Sbjct: 10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK--RRGDALIEMESEQD 67

Query: 76 AKR 78
           ++
Sbjct: 68 VQK 70

>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 = 46.5 bits (111), Expect = 2e-08
 Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 10/84 (11%)

Query: 2  GSEATT-VKRKSSNV-----AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK 55
          GS  ++ +K            +Q  + + + N+P    + E+E + K FG++   R+   
Sbjct: 1  GSSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRI--- 57

Query: 56 MV-GSGLHRGFGFVEFITKNEAKR 78
          +   SG  RG GF    +  + + 
Sbjct: 58 LRDSSGTSRGVGFARMESTEKCEA 81

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.1 bits (107), Expect = 5e-08
 Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 8/80 (10%)

Query: 1  MGSEATTVKRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS 59
          MG           +  K   S ++ +R +     ++++ E  + FG + +V +       
Sbjct: 1  MGHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP----- 55

Query: 60 GLHRGFGFVEFITKNEAKRV 79
             +    VEF     A   
Sbjct: 56 --KKRQALVEFEDVLGACNA 73

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 45.1 bits (107), Expect = 5e-08
 Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 7  TVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFG 66
          +     S   +Q   K+ +RNIP   +   ++ L   +G ++        V +       
Sbjct: 2  SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ----VNTDSETAVV 57

Query: 67 FVEFITKNEAKR 78
           V + +K++A++
Sbjct: 58 NVTYSSKDQARQ 69

>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 = 45.4 bits (108), Expect = 5e-08
 Identities = 13/77 (16%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          G    ++    S      G+ + + ++P +    ++ ++F  FG +   ++      + L
Sbjct: 7  GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ-TNL 65

Query: 62 HRGFGFVEFITKNEAKR 78
           + FGFV +     A+ 
Sbjct: 66 SKCFGFVSYDNPVSAQA 82

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 44.9 bits (107), Expect = 5e-08
 Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
           K   + + V  I  +  ++E+   F  +G +K V++      +G+ +G+GFV F    +
Sbjct: 5  GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVD 62

Query: 76 AKRV 79
           +++
Sbjct: 63 VQKI 66

>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 = 44.9 bits (107), Expect = 5e-08
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          GS  ++     S    Q    + V+ +     +   E L ++F      R+      +G 
Sbjct: 1  GSSGSSGPNARS----QPSKTLFVKGLSEDTTE---ETLKESFDGSVRARIVTDRE-TGS 52

Query: 62 HRGFGFVEFITKNEAK 77
           +GFGFV+F ++ +AK
Sbjct: 53 SKGFGFVDFNSEEDAK 68

>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 = 45.0 bits (107), Expect = 5e-08
 Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 8/59 (13%)

Query: 21 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           KIL VRN+     +  +E+ F         R+ K        R + FV F  + +A  
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVE 66

>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 = 44.9 bits (107), Expect = 5e-08
 Identities = 8/57 (14%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + + N+      +E++           + +     G+   R FG+V+F +  + ++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN--RKFGYVDFESAEDLEK 73

>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 = 44.3 bits (105), Expect = 7e-08
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRL----PKKMVGSGLHRGFGFVEFITKNEAK 77
          ++ V NIPF   +  + + F A   L  +      P   V     + F F+EF + +E  
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 78 R 78
          +
Sbjct: 68 Q 68

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 44.7 bits (106), Expect = 8e-08
 Identities = 12/70 (17%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFV 68
              +    G  + + ++P +   +++   F  FG +   ++    +   + L + FGFV
Sbjct: 31 AGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV---FIDKQTSLSKCFGFV 87

Query: 69 EFITKNEAKR 78
           F   + A+ 
Sbjct: 88 SFDNPDSAQV 97

>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 = 9e-08
 Identities = 8/55 (14%), Positives = 24/55 (43%), Gaps = 2/55 (3%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          V N+     +  +++ F+  G +  +++      +  +  + FVE+   ++A   
Sbjct: 5  VGNLDKAITEDILKQYFQVGGPIANIKIMIDK--NNKNVNYAFVEYHQSHDANIA 57

>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 = 1e-07
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 1/69 (1%)

Query: 10  RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
            +S   +      + V ++        +   FK F       +   M  +G  RG+GFV 
Sbjct: 77  FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ-TGSSRGYGFVS 135

Query: 70  FITKNEAKR 78
           F ++++A+ 
Sbjct: 136 FTSQDDAQN 144

>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 = 44.1 bits (105), Expect = 9e-08
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 3/70 (4%)

Query: 9  KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFV 68
                + +     + V+N+        + + F  FG +   ++   M+  G  +GFGFV
Sbjct: 4  GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV---MMEGGRSKGFGFV 60

Query: 69 EFITKNEAKR 78
           F +  EA +
Sbjct: 61 CFSSPEEATK 70

>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 = 44.2 bits (105), Expect = 1e-07
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 9/67 (13%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
          S +        + VRN+     +  +E+ F  FG+L+ V+  K          + F+ F 
Sbjct: 3  SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK---------DYAFIHFD 53

Query: 72 TKNEAKR 78
           ++ A +
Sbjct: 54 ERDGAVK 60

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.3 bits (105), Expect = 1e-07
 Identities = 10/58 (17%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           + ++  P  A   +++E  +  G++  +++ +        +G  FV F +   AK+ 
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKF 68

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 43.8 bits (104), Expect = 1e-07
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
             V N+PF   Q +++ +FK    ++ VRL +    +   +GF +VEF   +  K 
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKE 71

>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 = 44.3 bits (105), Expect = 1e-07
 Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + V ++  +    +++  F  FG +   R+ K M  +G  +G+GFV F  K +A+ 
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAEN 72

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 43.4 bits (103), Expect = 2e-07
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          + S+     GSK+ V          E+++ F  +GE+  V +PK        R F FV F
Sbjct: 2  RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTF 55

Query: 71 ITKNEAKRV 79
               A+ +
Sbjct: 56 ADDKVAQSL 64

>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 = 43.3 bits (103), Expect = 2e-07
 Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + V ++        +   FK F       +   M  +G  RG+GFV F ++++A+ 
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQN 58

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 43.2 bits (102), Expect = 2e-07
 Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 8/68 (11%)

Query: 12 SSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 70
          S +  K + S ++ VR +     ++++ E  + FG + +V +          +    VEF
Sbjct: 6  SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-------FKRQALVEF 58

Query: 71 ITKNEAKR 78
             + AK 
Sbjct: 59 ENIDSAKE 66

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 43.4 bits (102), Expect = 3e-07
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 8/72 (11%)

Query: 9  KRKSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
               + +    S+++ +R +P    + EV  L   FG++  + + K        +   F
Sbjct: 19 SHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAF 71

Query: 68 VEFITKNEAKRV 79
          +E  T+  A  +
Sbjct: 72 IEMNTEEAANTM 83

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

 Score = 42.8 bits (101), Expect = 5e-07
 Identities = 14/65 (21%), Positives = 22/65 (33%), Gaps = 9/65 (13%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFIT 72
          + I V+ +        V + FK  G +K         + L      +G  +G   V F  
Sbjct: 8  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-TGKLKGEATVSFDD 66

Query: 73 KNEAK 77
             AK
Sbjct: 67 PPSAK 71

>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 = 43.9 bits (103), Expect = 5e-07
 Identities = 8/59 (13%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 22  KILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            + + N+ +     ++ E   + G  ++  ++  +    +G  +GF  V   ++  +K+
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKK 127

>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 = 43.9 bits (104), Expect = 6e-07
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 18  QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEA 76
             G+ + V+N+        +E+ F  FG ++   +   +V   G   G GFVEF  K  A
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV---VVDDRGRATGKGFVEFAAKPPA 150

Query: 77  KRV 79
           ++ 
Sbjct: 151 RKA 153

>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 = 41.2 bits (97), Expect = 5e-06
 Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 7/58 (12%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          ++ V N+P    + + + LF+ +GE   V + +        RGFGF+   ++  A+  
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-------RGFGFIRLESRTLAEIA 74

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 41.8 bits (99), Expect = 6e-07
 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 6/64 (9%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
               S + V        + E+ E F  +G++  V +PK        R F FV F     
Sbjct: 1  GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQI 54

Query: 76 AKRV 79
          A+ +
Sbjct: 55 AQSL 58

>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 = 41.9 bits (99), Expect = 7e-07
 Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 7/75 (9%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV---GSGLH 62
              + +    + I V+ +        V + FK  G +K       P   +     +G  
Sbjct: 3  HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 63 RGFGFVEFITKNEAK 77
          +G   V F     AK
Sbjct: 63 KGEATVSFDDPPSAK 77

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 43.5 bits (102), Expect = 7e-07
 Identities = 12/73 (16%), Positives = 29/73 (39%), Gaps = 1/73 (1%)

Query: 6   TTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF 65
           +T ++ + N  +   + +   N P +  +    E+    G  +   + K   G       
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSV-KVFSGKSERSSS 167

Query: 66  GFVEFITKNEAKR 78
           G +E+ +K++A  
Sbjct: 168 GLLEWDSKSDALE 180

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.8 bits (98), Expect = 8e-07
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 8/59 (13%)

Query: 21 SKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          S+++ +R +P    + EV  L   FG++  + + K        +   F+E  T+  A  
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK-------GKNQAFIEMNTEEAANT 67

>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 = 42.0 bits (99), Expect = 9e-07
 Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 11/83 (13%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPK-KMV 57
          GS  ++             S I V+ +       ++ + FK  G +K       P   + 
Sbjct: 1  GSSGSSGDPDED----SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY 56

Query: 58 ---GSGLHRGFGFVEFITKNEAK 77
              +G  +G   V +     AK
Sbjct: 57 LDKETGKPKGDATVSYEDPPTAK 79

>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 = 9e-07
 Identities = 10/80 (12%), Positives = 31/80 (38%), Gaps = 5/80 (6%)

Query: 3   SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV---GS 59
           +  T     + +  +   + + V +  +     ++ ++ ++ G    V L  K      +
Sbjct: 38  NNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL--KFAENRAN 95

Query: 60  GLHRGFGFVEFITKNEAKRV 79
           G  +G+  V   ++N   ++
Sbjct: 96  GQSKGYAEVVVASENSVHKL 115

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 41.4 bits (98), Expect = 1e-06
 Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
          SS  +    +KI V  IP    ++E+ E FK FG +  V +          RGFGF+ F 
Sbjct: 2  SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA-EKQRPRGFGFITFE 60

Query: 72 TKNEAKRV 79
           +    + 
Sbjct: 61 DEQSVDQA 68

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

 Score = 41.4 bits (97), Expect = 1e-06
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL 61
          GS  ++             + + V N+P  A+ S+++   +  G      +P ++   G 
Sbjct: 1  GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGS-----VPLRLTWQG- 54

Query: 62 HRGFGFVEFITKNEAKRV 79
           R   F+ +     A++ 
Sbjct: 55 PRRRAFLHYPDSAAAQQA 72

>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 = 41.0 bits (97), Expect = 1e-06
 Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          +   + V ++  +   + +   F  FG +   R+ K M  +G  +G+GFV F  K +A+ 
Sbjct: 5  SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAEN 63

>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 = 1e-06
 Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 6/70 (8%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFV 68
              +       +I ++N+P      ++++L +    E  F       V +    G G +
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSS-----VNTRDFDGTGAL 72

Query: 69 EFITKNEAKR 78
          EF ++     
Sbjct: 73 EFPSEEILVE 82

>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 = 41.1 bits (97), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 8/58 (13%)

Query: 25 VRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + N+  + K+ E+++    +F  FG++  + + +    S   RG  FV F   + A  
Sbjct: 13 INNLNEKIKKDELKKSLHAIFSRFGQILDILVSR----SLKMRGQAFVIFKEVSSATN 66

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.8 bits (96), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 6/58 (10%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           + V   P     +++ E F AFG +  V + K          F  VE       + V
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD------KGVFAIVEMGDVGAREAV 61

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 41.0 bits (96), Expect = 2e-06
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 11 KSSNVAKQTGSKIL-VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
           S +      S++L +R +P +  ++EV  L   FG++  + + K        +   F+E
Sbjct: 5  SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK-------GKNQAFLE 57

Query: 70 FITKNEAKRV 79
            T+  A  +
Sbjct: 58 LATEEAAITM 67

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 42.5 bits (99), Expect = 2e-06
 Identities = 11/56 (19%), Positives = 27/56 (48%), Gaps = 1/56 (1%)

Query: 23  ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + V  + +   +S++   F+ +G +K + +      SG  RG+ F+E+  + +   
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVY-SKRSGKPRGYAFIEYEHERDMHS 159

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 40.3 bits (95), Expect = 2e-06
 Identities = 9/54 (16%), Positives = 25/54 (46%), Gaps = 7/54 (12%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          V  +     ++++   F  FGE++ + + ++       +   F++F T+  A+ 
Sbjct: 17 VGGLGDTITETDLRNHFYQFGEIRTITVVQR-------QQCAFIQFATRQAAEV 63

>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 = 40.3 bits (95), Expect = 2e-06
 Identities = 8/59 (13%), Positives = 26/59 (44%), Gaps = 3/59 (5%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + + N+ +     ++ E   + G  ++  ++  +    +G  +GF  V   ++  +K+
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-NGQSKGFALVGVGSEASSKK 60

>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 = 39.9 bits (94), Expect = 4e-06
 Identities = 7/54 (12%), Positives = 20/54 (37%), Gaps = 7/54 (12%)

Query: 25 VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          V  +      + +   F  FG ++ +   K          F ++++ + + A+ 
Sbjct: 22 VGGLGPNTSLAALAREFDRFGSIRTIDHVK-------GDSFAYIQYESLDAAQA 68

>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 = 39.9 bits (94), Expect = 5e-06
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
            I ++N+        + + F AFG    +   K +      +G+GFV F T+  A+R
Sbjct: 6  GNIFIKNLDKSIDNKALYDTFSAFGN---ILSCKVVCDENGSKGYGFVHFETQEAAER 60

>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 = 39.6 bits (93), Expect = 6e-06
 Identities = 12/68 (17%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFI 71
          S+ +    + + + ++     ++ +   F   GE +  V++ +  + +G+  G+ FVEF 
Sbjct: 2  SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL-TGIPAGYCFVEFA 60

Query: 72 TKNEAKRV 79
              A++ 
Sbjct: 61 DLATAEKC 68

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

 Score = 39.3 bits (92), Expect = 9e-06
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 7/65 (10%)

Query: 20 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
             I+V   P          +  +  LF   G++  +  P     +G  +GF FVE  + 
Sbjct: 6  DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA-TGKTKGFLFVECGSM 64

Query: 74 NEAKR 78
          N+AK+
Sbjct: 65 NDAKK 69

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.6 bits (90), Expect = 2e-05
 Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 9/65 (13%)

Query: 20 GSKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
           S I+V N+P       +  ++ + ++F  FG++     P++    G  +G+ F+E+ + 
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASP 71

Query: 74 NEAKR 78
            A  
Sbjct: 72 AHAVD 76

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

 Score = 38.7 bits (90), Expect = 2e-05
 Identities = 11/79 (13%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 4  EATTVKRKSSNVAKQTGSKILVRNIPFQAKQSE----VEELFKAFGELKFVRLPKKMVGS 59
             +    S+    +    +L+ NI  +  + +    +  L  + G++  + +      S
Sbjct: 13 HMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL----S 68

Query: 60 GLHRGFGFVEFITKNEAKR 78
            + G  ++ F T+  A+ 
Sbjct: 69 DDNSGKAYIVFATQESAQA 87

>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 = 38.4 bits (89), Expect = 2e-05
 Identities = 7/56 (12%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          +    +     ++++  + +  G +  + +P        ++ + F  + T  E+KR
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-------NKPYSFARYRTTEESKR 78

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 37.8 bits (88), Expect = 2e-05
 Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 9/64 (14%)

Query: 21 SKILVRNIP------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 74
          S I+V N+P       +  ++ + ++F  FG++     P++    G  +G+ F+E+ +  
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE---DGKTKGYIFLEYASPA 58

Query: 75 EAKR 78
           A  
Sbjct: 59 HAVD 62

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 37.1 bits (87), Expect = 3e-05
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          KI V  +     + ++ E F  FGE++ + LP     +   RGF F+ F  +   K++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMD-NKTNKRRGFCFITFKEEEPVKKI 57

>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 = 38.7 bits (89), Expect = 5e-05
 Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 8/60 (13%)

Query: 23 ILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          I + N+  + K+ E+++    +F  FG++  + + +    S   RG  FV F   + A  
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR----SLKMRGQAFVIFKEVSSATN 67

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

 Score = 37.5 bits (86), Expect = 1e-04
 Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 6/54 (11%)

Query: 25  VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + N+P +  +  +  LF  F   K VRL              FVEF  + +A  
Sbjct: 212 LTNLPEETNELMLSMLFNQFPGFKEVRLVPG------RHDIAFVEFDNEVQAGA 259

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 37.3 bits (87), Expect = 5e-05
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 1  MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
          M     TV  +     K+   K+ +  + F+  +  +   ++ +G+L    +  +   S 
Sbjct: 8  MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV-MRDPASK 66

Query: 61 LHRGFGFVEFITKNEAKRV 79
            RGFGFV F +  E    
Sbjct: 67 RSRGFGFVTFSSMAEVDAA 85

>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 = 36.8 bits (86), Expect = 6e-05
 Identities = 14/60 (23%), Positives = 30/60 (50%), Gaps = 4/60 (6%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 78
          S I + N+  +  +  + + F AFG +  ++ PK M    +G  +G+ F+ F + + +  
Sbjct: 6  SGIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

>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 = 37.1 bits (86), Expect = 7e-05
 Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 5/59 (8%)

Query: 25 VRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 78
          V  +  +    EV    E F  FG++  V +       GS       +V +I   +A R
Sbjct: 20 VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALR 78

>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 = 37.1 bits (86), Expect = 1e-04
 Identities = 8/63 (12%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 20  GSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMVGSGLHRGFGFVEFITKNE 75
             +I V+N+    ++ +++ +F  + +     + +    +++  G  +G  F+    +  
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 76  AKR 78
           A +
Sbjct: 105 AAK 107

>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 = 36.1 bits (84), Expect = 1e-04
 Identities = 7/43 (16%), Positives = 13/43 (30%), Gaps = 7/43 (16%)

Query: 36 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           +   F  FG +  + +          R   FV +     A +
Sbjct: 29 LLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMESADQ 64

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 36.0 bits (84), Expect = 1e-04
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 10 RKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVE 69
                A Q  S ++V  +P++  + +++E F  FGE+  V++ KK + +G  +GFGFV 
Sbjct: 5  SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHSKGFGFVR 63

Query: 70 FITKNEAKRV 79
          F       +V
Sbjct: 64 FTEYETQVKV 73

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 36.6 bits (84), Expect = 2e-04
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 10/72 (13%)

Query: 11 KSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFG 66
            + +A    S +L   V N+ +      + ++F  FG  LK +   K        +   
Sbjct: 34 VDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN------QFQA 87

Query: 67 FVEFITKNEAKR 78
           +++     A+ 
Sbjct: 88 LLQYADPVSAQH 99

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 35.2 bits (82), Expect = 2e-04
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           K+ V  + +   + ++++ F  FGE+    + K    +G  RGFGF+ F      ++V
Sbjct: 12 GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI-KMDPNTGRSRGFGFILFKDAASVEKV 69

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
             +G K+ +  + +Q  Q  + E F  FGE+K   +  +   +   RGFGFV F+ +  
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAG 79

Query: 76 AKRV 79
            +V
Sbjct: 80 VDKV 83

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 34.8 bits (81), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          KI V  +       +V+  F+ FG++    L      +  HRGFGFV F +++  ++V
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-TTNRHRGFGFVTFESEDIVEKV 57

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 35.4 bits (81), Expect = 3e-04
 Identities = 13/80 (16%), Positives = 32/80 (40%), Gaps = 9/80 (11%)

Query: 2  GSEATTVKRKSSNVAKQTGSKIL---VRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG 58
          GS    + R  +      G+K+L   ++N  +      +  +    G+++ + + K+   
Sbjct: 4  GSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR--- 60

Query: 59 SGLHRGFGFVEFITKNEAKR 78
             +     VEF +   A++
Sbjct: 61 ---NGIQAMVEFESVLCAQK 77

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 35.0 bits (81), Expect = 4e-04
 Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFGFVEFITKNEAKR 78
          +KI V  +P+    + + + F+ FG+++   +   +    +G  RG+GFV    +  A+R
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV---ITDRQTGKSRGYGFVTMADRAAAER 74

Query: 79 V 79
           
Sbjct: 75 A 75

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 35.3 bits (81), Expect = 4e-04
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRV 79
          K+ V  +P    + E+   F+ FG L      K         +G+ F+ F  ++  + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 34.4 bits (80), Expect = 4e-04
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          K+ +  + +Q  Q  + E F  FGE+K   +  +   +   RGFGFV F+ +    +V
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLV-MRDPLTKRSRGFGFVTFMDQAGVDKV 58

>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 Length = 112

 Score = 34.9 bits (80), Expect = 4e-04
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 8/79 (10%)

Query: 2  GSEATTVKRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSG 60
          G +      +  +  ++ G  I + N+P      S V +L + +G++K   L +      
Sbjct: 7  GKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------ 60

Query: 61 LHRGFGFVEFITKNEAKRV 79
            +   F+E  T+ +A  +
Sbjct: 61 -MKSQAFIEMETREDAMAM 78

>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 = 35.0 bits (80), Expect = 8e-04
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 23  ILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + + NIP    + +++ LF + G  +K  +  +K       R    ++  +  EA +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMGSVEEAVQ 204

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	79
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.89
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.84
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.83
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.83
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.83
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.83
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.82
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.82
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.82
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.82
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.82
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.82
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.82
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.82
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.82
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.82
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.82
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.82
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.81
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.81
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.81
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.81
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.81
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.8
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.8
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.8
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.8
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.8
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.8
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.8
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.8
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.8
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.79
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.79
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.79
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.79
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.79
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.79
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.79
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.78
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.78
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.78
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.78
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.78
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.78
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.78
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.78
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.78
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.77
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.77
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.77
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.76
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.76
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.76
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.76
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.74
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.74
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.74
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.74
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.74
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.73
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.72
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.72
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.72
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.72
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.72
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.55
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.71
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.71
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.7
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.7
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.7
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.69
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.69
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.69
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.69
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.69
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.68
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.68
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.68
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.68
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.67
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.65
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.65
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.65
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.65
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.64
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.63
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.63
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.63
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.63
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.62
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.61
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.61
1x5p_A	97	Negative elongation factor E; structure genomics,	99.61
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.61
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.6
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.6
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.58
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.57
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.57
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.57
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.56
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.55
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.55
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.54
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.52
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.51
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.51
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.49
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.45
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.45
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.44
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.37
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.37
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.36
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.3
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.27
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.24
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.91
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.53
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.48
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.23
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.19
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.96
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.92
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.77
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.74
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.54
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.3
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.02
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.29
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.27
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	94.56
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	92.99
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	92.64

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.89  E-value=1e-22  Score=106.53  Aligned_cols=62  Identities=29%  Similarity=0.596  Sum_probs=57.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++++|||+|||+++++++|+++|++||.|..++++.++ .+|.++|||||+|.+.++|++|
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~kG~afV~f~~~~~A~~A   77 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDK-VAGHSLGYGFVNYVTAKDAERA   77 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECS-SSCCEEEEEEEEESSHHHHHHH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecC-CCCcccccEEEEECCHHHHHHH
Confidence            3568899999999999999999999999999999999987 7899999999999999999865

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.85  E-value=7.8e-21  Score=96.84  Aligned_cols=64  Identities=22%  Similarity=0.516  Sum_probs=58.2

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   69 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDP-NTGRSRGFGFILFKDAASVEKV   69 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEESSTHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecC-CCCccccEEEEEECCHHHHHHH
Confidence            445678999999999999999999999999999999999886 7899999999999999998764

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

Probab=99.84  E-value=7.9e-21  Score=101.01  Aligned_cols=61  Identities=15%  Similarity=0.236  Sum_probs=57.2

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++ .+++++|||||+|.+.++|++|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~-~tg~~rG~aFV~f~~~~~A~~A   64 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHP-RTRKHLGLARVLFTSTRGAKET   64 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCceeeEEEEEECCHHHHHHH
Confidence            457899999999999999999999999999999999997 7899999999999999999865

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=2.1e-21  Score=100.11  Aligned_cols=58  Identities=31%  Similarity=0.566  Sum_probs=54.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+|||+|||+++++++|+++|++|| .|..++++.++ .+|.++|||||+|.+.++|++|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~-~t~~~rg~aFV~F~~~~~A~~A   60 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNK-SSGQSRGFAFVEFSHLQDATRW   60 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCS-SSCCCSSEEEEECSSHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecC-CCCCcCceEEEEecCHHHHHHH
Confidence            5899999999999999999999999 79999999987 8899999999999999999865

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.1e-20  Score=99.53  Aligned_cols=61  Identities=16%  Similarity=0.344  Sum_probs=56.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++ . +.++|||||+|.+.++|++|
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~-~-g~~rG~aFV~F~~~e~a~~A   68 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-H-KAFKGSIFVVFDSIESAKKF   68 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCC-T-TSCCCEEEEEESSHHHHHHH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECC-C-CCCccEEEEEECCHHHHHHH
Confidence            4457899999999999999999999999999999999995 4 99999999999999999764

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=2.2e-20  Score=98.80  Aligned_cols=67  Identities=24%  Similarity=0.563  Sum_probs=60.1

Q ss_pred             cCcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        12 ~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+......++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   73 (111)
T 1x4h_A            7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP-DTEHSKGCAFAQFMTQEAAQKC   73 (111)
T ss_dssp             CCCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCCBCSEEEEEESSHHHHHHH
T ss_pred             CCCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCCCccEEEEEECCHHHHHHH
Confidence            334456678999999999999999999999999999999999987 7889999999999999998764

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

Probab=99.83  E-value=5.4e-21  Score=99.42  Aligned_cols=62  Identities=21%  Similarity=0.389  Sum_probs=56.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCC--eeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGE--LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~--i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...-.+|||+|||+.+++++|+++|++||.  +..|+++.++ .+|+++|||||+|.+.++|++|
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~-~tg~srG~aFV~f~~~~~A~~A   69 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDK-QTQQNRGFAFVQLSSAMDASQL   69 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCS-SSSSCSSEEEEECSSSHHHHHH
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecC-CCCCCceEeEEEECCHHHHHHH
Confidence            445679999999999999999999999995  6789999997 8899999999999999998864

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=3.7e-20  Score=96.94  Aligned_cols=64  Identities=31%  Similarity=0.648  Sum_probs=58.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   73 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL-KTGHSKGFGFVRFTEYETQVKV   73 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHH
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecC-CCCCccceEEEEECCHHHHHHH
Confidence            345567899999999999999999999999999999999986 7899999999999999999864

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.83  E-value=3.2e-20  Score=98.89  Aligned_cols=64  Identities=17%  Similarity=0.386  Sum_probs=58.2

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   83 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK-QTNLSKCFGFVSYDNPVSAQAA   83 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS-SSCSEEEEEEEECSSHHHHHHH
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCCcCccEEEEECCHHHHHHH
Confidence            444567899999999999999999999999999999999886 6899999999999999998764

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=4.6e-20  Score=98.39  Aligned_cols=66  Identities=24%  Similarity=0.530  Sum_probs=59.6

Q ss_pred             CcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        13 ~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ........++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   75 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR-QTGKSRGYGFVTMADRAAAERA   75 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS-SSCCCCSEEEEEESSHHHHHHH
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcC-CCCccceEEEEEECCHHHHHHH
Confidence            34455678999999999999999999999999999999999987 7899999999999999999864

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=2.7e-20  Score=97.75  Aligned_cols=65  Identities=26%  Similarity=0.429  Sum_probs=59.2

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....+.++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~a   74 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDK-TTNQSRGFGFVKFKDPNCVGTV   74 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECS-SSCCEEEEEEEEESSTTHHHHH
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC-CCCCcceEEEEEECCHHHHHHH
Confidence            3446678999999999999999999999999999999999987 7899999999999999998764

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

Probab=99.83  E-value=3.2e-20  Score=97.53  Aligned_cols=64  Identities=20%  Similarity=0.495  Sum_probs=58.5

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   71 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR-FTGMHKGCAFLTYCERESALKA   71 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCS-SSCSCCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC-CCCCcceEEEEEECCHHHHHHH
Confidence            445668899999999999999999999999999999999987 7899999999999999998764

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=5.6e-20  Score=95.65  Aligned_cols=64  Identities=28%  Similarity=0.491  Sum_probs=58.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   68 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA-EKQRPRGFGFITFEDEQSVDQA   68 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCT-TTCSCCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCCCCceEEEEECCHHHHHHH
Confidence            345567999999999999999999999999999999999887 7889999999999999999864

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

Probab=99.82  E-value=5.7e-20  Score=96.43  Aligned_cols=64  Identities=25%  Similarity=0.484  Sum_probs=58.6

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   73 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-VTGQHQGYGFVEFLSEEDADYA   73 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCSBCSCEEEEESSHHHHHHH
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCcCCcEEEEEECCHHHHHHH
Confidence            445678999999999999999999999999999999999986 6899999999999999999864

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

Probab=99.82  E-value=6e-20  Score=96.50  Aligned_cols=65  Identities=23%  Similarity=0.424  Sum_probs=58.6

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        17 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   81 (106)
T 1p27_B           17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA   81 (106)
T ss_dssp             BCCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTSSEEEEEEEEESCHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecC-CCCceeeEEEEEECCHHHHHHH
Confidence            3445567899999999999999999999999999999999887 7899999999999999998764

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

Probab=99.82  E-value=4.2e-20  Score=96.71  Aligned_cols=65  Identities=20%  Similarity=0.432  Sum_probs=58.9

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   71 (103)
T 2dnm_A            7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP-HTKAPRGFAFVRFHDRRDAQDA   71 (103)
T ss_dssp             SSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCS-SSCSBCSCEEEEESSSSHHHHH
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCCCCeEEEEEECCHHHHHHH
Confidence            3445668999999999999999999999999999999999887 7789999999999999998764

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

Probab=99.82  E-value=7.9e-20  Score=96.11  Aligned_cols=65  Identities=71%  Similarity=1.082  Sum_probs=58.8

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecc-cCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKK-MVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .......++|||+|||+.+++++|+++|++||.|..+.++.+ + .++.++|||||+|.+.++|++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-~~~~~~g~afV~f~~~~~a~~A   74 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT-GTGAHRGFGFVDFITKQDAKKA   74 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS-SSCSSCSEEEEEESSHHHHHHH
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCC-CCCCcCceEEEEECCHHHHHHH
Confidence            344567899999999999999999999999999999999887 5 6899999999999999999864

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

Probab=99.82  E-value=5e-20  Score=94.93  Aligned_cols=64  Identities=22%  Similarity=0.460  Sum_probs=58.2

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   74 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKGVAFILFLDKDSAQNC   74 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCS-SSCCCTTCEEEEESCHHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCCcccEEEEEECCHHHHHHH
Confidence            445668899999999999999999999999999999999886 7788999999999999998764

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

Probab=99.82  E-value=8.1e-20  Score=95.18  Aligned_cols=65  Identities=26%  Similarity=0.520  Sum_probs=58.5

Q ss_pred             CcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        13 ~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......+.++|||+|||+.+++++|+++|++||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~a~~A   74 (100)
T 2do4_A           10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN--RAGKPKGLAYVEYENESQASQA   74 (100)
T ss_dssp             CCSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC--TTSCEEEEEEEEESSHHHHHHH
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEEC--CCCCEEeEEEEEECCHHHHHHH
Confidence            3444567899999999999999999999999999999999998  5889999999999999998764

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.82  E-value=9.2e-20  Score=97.03  Aligned_cols=65  Identities=23%  Similarity=0.498  Sum_probs=58.9

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....+.++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   73 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDM-ATGKSKGYGFVSFFNKWDAENA   73 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCCcceEEEEEECCHHHHHHH
Confidence            3445678999999999999999999999999999999999886 6899999999999999999864

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.9e-20  Score=96.29  Aligned_cols=63  Identities=21%  Similarity=0.396  Sum_probs=56.8

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|.+||.|.. +.++.+  .+++++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~--~~g~~~G~afV~F~~~~~a~~A   73 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD--FQGRSTGEAFVQFASQEIAEKA   73 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC--SSSCBCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC--CCCCcceEEEEEECCHHHHHHH
Confidence            34566799999999999999999999999999987 888887  6899999999999999999865

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

Probab=99.82  E-value=6.2e-20  Score=94.66  Aligned_cols=64  Identities=22%  Similarity=0.359  Sum_probs=57.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   73 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-QSRRSRGFAFVYFENVDDAKEA   73 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECS-SSSSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcC-CCCCcccEEEEEECCHHHHHHH
Confidence            334567899999999999999999999999999999999886 7789999999999999999864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.7e-20  Score=100.10  Aligned_cols=62  Identities=23%  Similarity=0.464  Sum_probs=56.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   85 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP-ASKRSRGFGFVTFSSMAEVDAA   85 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT-TTSSCCSEEEEECSSHHHHHHH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCcCceEEEEeCCHHHHHHH
Confidence            3446899999999999999999999999999999999987 7899999999999999998764

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

Probab=99.82  E-value=4.7e-20  Score=93.55  Aligned_cols=61  Identities=16%  Similarity=0.385  Sum_probs=56.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~A   63 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK-TTNKCKGYGFVDFDSPSAAQKA   63 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCS-SSCSCCSEEEEEESCHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCCcCcEEEEEECCHHHHHHH
Confidence            467899999999999999999999999999999999887 7899999999999999999864

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

Probab=99.82  E-value=1.2e-19  Score=95.25  Aligned_cols=61  Identities=25%  Similarity=0.416  Sum_probs=56.4

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~A~~A   72 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG--PDGSSKGCAFVKFSSHTEAQAA   72 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC--SSSCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcCcEEEEEeCCHHHHHHH
Confidence            456899999999999999999999999999999999998  5789999999999999999764

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.82  E-value=7.8e-20  Score=92.61  Aligned_cols=62  Identities=24%  Similarity=0.451  Sum_probs=57.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   65 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAA   65 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECC-CCCccccEEEEEECCHHHHHHH
Confidence            4567999999999999999999999999999999998887 7889999999999999999764

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

Probab=99.82  E-value=6.2e-20  Score=94.73  Aligned_cols=63  Identities=24%  Similarity=0.374  Sum_probs=56.6

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++  ++.++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~--~g~~~g~afV~f~~~~~a~~A   73 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR--EGKPKSFGFVCFKHPESVSYA   73 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT--TSCEEEEEEEEESSTHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC--CCCCceEEEEEECCHHHHHHH
Confidence            345567899999999999999999999999999999999984  589999999999999999764

>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=99.82  E-value=8.2e-20  Score=92.89  Aligned_cols=61  Identities=25%  Similarity=0.519  Sum_probs=55.6

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   64 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDM-ATGKSKGYGFVSFFNKWDAENA   64 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            457899999999999999999999999999999999886 7899999999999999999864

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.82  E-value=7.3e-20  Score=97.81  Aligned_cols=63  Identities=19%  Similarity=0.414  Sum_probs=57.5

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~A   98 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK-QTSLSKCFGFVSFDNPDSAQVA   98 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCS-SSSCCCCEEEEEEESSHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCCcCcEEEEEECCHHHHHHH
Confidence            34567899999999999999999999999999999999887 7899999999999999998764

>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=99.82  E-value=9.4e-20  Score=96.35  Aligned_cols=65  Identities=26%  Similarity=0.455  Sum_probs=58.7

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   84 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAA   84 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCT-TTSSBCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcceEEEEEECCHHHHHHH
Confidence            3445667899999999999999999999999999999999886 7899999999999999998764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=9e-20  Score=94.80  Aligned_cols=62  Identities=18%  Similarity=0.339  Sum_probs=57.4

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCee-EEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELK-FVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~-~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|. .+.++.++ .++.++|||||+|.+.++|++|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   68 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNR-LTGIPAGYCFVEFADLATAEKC   68 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECS-SSCCEEEEEEEECSCHHHHHHH
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecC-CCCCcCCEEEEEeCCHHHHHHH
Confidence            45679999999999999999999999999999 99999987 7899999999999999999864

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=4.8e-20  Score=97.68  Aligned_cols=64  Identities=28%  Similarity=0.523  Sum_probs=55.0

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~tg~~kg~afV~f~~~~~A~~A   83 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-LTKRSRGFGFVTFMDQAGVDKV   83 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCT-TTCCCTTCEEEEESSHHHHHHH
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECC-CCCCcCcEEEEEECCHHHHHHH
Confidence            334567999999999999999999999999999999999986 7899999999999999998764

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

Probab=99.81  E-value=1.1e-19  Score=94.54  Aligned_cols=62  Identities=26%  Similarity=0.557  Sum_probs=57.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   66 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS-LTKKPKGFAFVTFMFPEHAVKA   66 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT-TTCCCCSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecC-CCCCcCeEEEEEECCHHHHHHH
Confidence            4567899999999999999999999999999999999886 6899999999999999998764

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

Probab=99.81  E-value=5.5e-20  Score=96.26  Aligned_cols=64  Identities=27%  Similarity=0.575  Sum_probs=58.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   73 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-TTGQSKGFAFISFHRREDAARA   73 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecC-CCCceeeEEEEEECCHHHHHHH
Confidence            345568999999999999999999999999999999999886 7899999999999999999864

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.81  E-value=1.4e-19  Score=94.16  Aligned_cols=65  Identities=22%  Similarity=0.289  Sum_probs=58.8

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE--------EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .......++|||+|||+.+++++|+++|++||.|..        +.++.++ .+|.++|||||+|.+.++|++|
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-~~g~~~G~afV~f~~~~~a~~A   79 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR-ETGKLKGEATVSFDDPPSAKAA   79 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECT-TTCSEEEEEEEEBSSHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecC-CCCCeeeEEEEEECCHHHHHHH
Confidence            344566899999999999999999999999999999        9999887 7899999999999999998764

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

Probab=99.81  E-value=2.2e-20  Score=97.65  Aligned_cols=61  Identities=26%  Similarity=0.453  Sum_probs=56.4

Q ss_pred             CCCCeEEEeCCCC------CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPF------QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~------~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+      .+++++|+++|++||.|..+.++.++ .+|+++|||||+|.+.++|++|
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~-~tg~~kG~afV~f~~~~~A~~A   70 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDE-ATGKTKGFLFVECGSMNDAKKI   70 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHH
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcC-CCCccceEEEEEECCHHHHHHH
Confidence            3468999999999      99999999999999999999999997 7799999999999999999865

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.3e-19  Score=95.07  Aligned_cols=63  Identities=22%  Similarity=0.531  Sum_probs=56.5

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCC-CCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS-GLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~-~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|.+|| |..+.++.++ .+ +.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~-~~~g~~~g~afV~f~~~~~a~~A   73 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP-SNPERLKGFGYAEFEDLDSLLSA   73 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCS-SCTTSBCSCEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCC-CCCCCcCeEEEEEECCHHHHHHH
Confidence            3345679999999999999999999999999 9999999886 55 89999999999999999864

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

Probab=99.81  E-value=1.4e-19  Score=95.83  Aligned_cols=65  Identities=20%  Similarity=0.474  Sum_probs=58.8

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +......++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~F~~~~~A~~A   84 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS-ETGRSKGYGFITFSDSECAKKA   84 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEET-TTTEEEEEEEEEESCHHHHHHH
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCccceEEEEEECCHHHHHHH
Confidence            3445667899999999999999999999999999999999887 7889999999999999999864

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

Probab=99.81  E-value=2.1e-19  Score=92.73  Aligned_cols=61  Identities=25%  Similarity=0.537  Sum_probs=56.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   63 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS-DTGRSKGYGFITFSDSECARRA   63 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCS-SSCCCCSEEEEEESCHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecC-CCCceeeEEEEEECCHHHHHHH
Confidence            467899999999999999999999999999999999987 7899999999999999999764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2e-19  Score=93.95  Aligned_cols=63  Identities=27%  Similarity=0.535  Sum_probs=57.6

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   70 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENIDDAKDA   70 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS-SSCSCCSEEEEECSSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCCcccEEEEEECCHHHHHHH
Confidence            34567999999999999999999999999999999999886 7888999999999999998764

>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=99.81  E-value=2.1e-19  Score=93.05  Aligned_cols=59  Identities=15%  Similarity=0.399  Sum_probs=55.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   60 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP-QTGRSKGYAFIEFRDLESSASA   60 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT-TTCCBCSEEEEEESSHHHHHHH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCC-CCCccceEEEEEECCHHHHHHH
Confidence            5799999999999999999999999999999999886 7899999999999999999764

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=6.2e-20  Score=97.64  Aligned_cols=60  Identities=18%  Similarity=0.389  Sum_probs=55.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   83 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR-NSRRSKGIAYVEFCEIQSVPLA   83 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC-CSSSCCCCEEEEESCGGGHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecC-CCCccCcEEEEEeCcHHHHHHH
Confidence            35799999999999999999999999999999999887 7789999999999999998864

>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=99.80  E-value=1.6e-19  Score=91.05  Aligned_cols=58  Identities=22%  Similarity=0.456  Sum_probs=54.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~a~~a   59 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQNA   59 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcC-CCCCccceEEEEECCHHHHHHH
Confidence            689999999999999999999999999999999887 7899999999999999998764

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.80  E-value=1.4e-19  Score=96.66  Aligned_cols=58  Identities=24%  Similarity=0.470  Sum_probs=52.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||.|..++++.++   +.++|||||+|.+.++|++|
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~---~~~kg~afV~f~~~~~A~~A   61 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE---NGSKGYGFVHFETQEAAERA   61 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET---TEEEEEEEEEESCHHHHHHH
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC---CCCCceEEEEECCHHHHHHH
Confidence            35689999999999999999999999999999999873   45789999999999999865

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

Probab=99.80  E-value=1.3e-19  Score=98.65  Aligned_cols=64  Identities=22%  Similarity=0.359  Sum_probs=58.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~~G~afV~F~~~~~A~~A  104 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-QSRRSRGFAFVYFENVDDAKEA  104 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCS-SSSCCCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            445567899999999999999999999999999999999887 7889999999999999999864

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.80  E-value=2.3e-19  Score=93.94  Aligned_cols=62  Identities=26%  Similarity=0.511  Sum_probs=56.5

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++|| |..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   72 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK-DTDKFKGFCYVEFDEVDSLKEA   72 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECS-SSCSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecC-CCCccceEEEEEECCHHHHHHH
Confidence            345678999999999999999999999997 9999999987 7899999999999999999864

>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=99.80  E-value=4e-20  Score=94.90  Aligned_cols=58  Identities=14%  Similarity=0.390  Sum_probs=52.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcC--CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+|||+|||+++++++|+++|++||  .|..++++.++ .+|+++|||||+|.+.++|++|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~-~~g~~kG~afV~f~~~~~a~~A   61 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR-ANGQSKGFALVGVGSEASSKKL   61 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECT-TTCCEEEEEEECC-CHHHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecC-CCCccCcEEEEEECCHHHHHHH
Confidence            5799999999999999999999999  99999999987 7899999999999999998865

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.80  E-value=2.4e-19  Score=91.48  Aligned_cols=60  Identities=27%  Similarity=0.448  Sum_probs=55.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~a   64 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDK-FSGHPKGFAYIEFSDKESVRTS   64 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESC-SSSSCCEEEEEEESSTHHHHHH
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecC-CCCCcceEEEEEECCHHHHHHH
Confidence            45899999999999999999999999999999999886 6899999999999999998764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.80  E-value=1.9e-19  Score=100.76  Aligned_cols=60  Identities=10%  Similarity=0.349  Sum_probs=55.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcC--CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||  .|..++++.++ .+|+++|||||+|.+.++|++|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~-~tg~skGfaFV~f~~~~~A~~A  115 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENR-ANGQSKGYAEVVVASENSVHKL  115 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            458999999999999999999999999  99999999987 8899999999999999999865

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.80  E-value=1e-19  Score=90.37  Aligned_cols=57  Identities=30%  Similarity=0.546  Sum_probs=53.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~a   57 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-TTNRHRGFGFVTFESEDIVEKV   57 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCS-SSTTSCBEEEEECSCHHHHHHH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcCcEEEEEECCHHHHHHH
Confidence            58999999999999999999999999999999886 6899999999999999998764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=3.7e-20  Score=92.28  Aligned_cols=58  Identities=29%  Similarity=0.551  Sum_probs=54.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~a   58 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-LTKRSRGFGFVTFMDQAGVDKV   58 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCC-CSSSCSSEEEECCCCTTHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCC-CCCCcCceEEEEEcCHHHHHHH
Confidence            579999999999999999999999999999999886 7899999999999999998764

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=4e-19  Score=93.06  Aligned_cols=62  Identities=19%  Similarity=0.385  Sum_probs=56.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHh-cCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKA-FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|.+ ||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~--~~g~~~g~afV~f~~~~~a~~A   67 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD--QTGVSKGYGFVKFTDELEQKRA   67 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEEC--TTCCEEEEEEEEESCHHHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEEC--CCCCccceEEEEECCHHHHHHH
Confidence            3456789999999999999999999999 999999999998  5888999999999999998764

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

Probab=99.80  E-value=2.7e-19  Score=96.56  Aligned_cols=65  Identities=23%  Similarity=0.424  Sum_probs=58.8

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +....+.++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   80 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA   80 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCT-TTSSBCSCEEEEESSHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            3445567899999999999999999999999999999999886 6899999999999999999865

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=3.7e-19  Score=94.55  Aligned_cols=63  Identities=25%  Similarity=0.560  Sum_probs=57.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|.+||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~--~~g~~~g~afV~f~~~~~a~~A   82 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD--SSGTSRGVGFARMESTEKCEAV   82 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSCEEEEEEEEESCHHHHHHH
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEEC--CCCCcceEEEEEECCHHHHHHH
Confidence            44556799999999999999999999999999999999998  5889999999999999998764

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

Probab=99.80  E-value=4.8e-19  Score=96.76  Aligned_cols=64  Identities=23%  Similarity=0.426  Sum_probs=58.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A  121 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAA  121 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCT-TTCCCCSEEEEEESCHHHHHHH
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecC-CCCCcCcEEEEEECCHHHHHHH
Confidence            334567899999999999999999999999999999999887 7889999999999999999864

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.80  E-value=6.9e-20  Score=90.95  Aligned_cols=57  Identities=28%  Similarity=0.582  Sum_probs=53.4

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   57 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN-KTNKRRGFCFITFKEEEPVKKI   57 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSC-CCSSSCCCEEEECSSSHHHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCCcCCEEEEEECCHHHHHHH
Confidence            58999999999999999999999999999999887 7899999999999999998764

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

Probab=99.80  E-value=1.4e-19  Score=94.53  Aligned_cols=62  Identities=24%  Similarity=0.451  Sum_probs=57.4

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   70 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAA   70 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS-SSCCCSSEEEECCSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecC-CCCCcceEEEEEECCHHHHHHH
Confidence            4568999999999999999999999999999999999887 7889999999999999999864

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.8e-19  Score=94.37  Aligned_cols=56  Identities=23%  Similarity=0.366  Sum_probs=51.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|.++.++.+       +|||||+|.+.++|++|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-------kGfaFVeF~~~~~A~~A   68 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-------KNQAFIEMNTEEAANTM   68 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-------CCEEEEEECCHHHHHHH
Confidence            456799999999999999999999999999999998775       49999999999998764

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.5e-19  Score=93.43  Aligned_cols=61  Identities=18%  Similarity=0.403  Sum_probs=56.5

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEE-EeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+ .++.++ .++.++|||||+|.+.++|++|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~A   64 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP-DTGNSKGYAFINFASFDASDAA   64 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT-TTCSCCSEEEEEBSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcC-CCCCcCeEEEEEECCHHHHHHH
Confidence            357899999999999999999999999999999 998886 7899999999999999999864

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

Probab=99.79  E-value=4.4e-19  Score=97.07  Aligned_cols=62  Identities=23%  Similarity=0.498  Sum_probs=57.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A  100 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR-ETRQSRGYGFVKFQSGSSAQQA  100 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET-TTTEEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcC-CCCCcceEEEEEECCHHHHHHH
Confidence            4556899999999999999999999999999999999887 7889999999999999999864

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.6e-19  Score=96.23  Aligned_cols=62  Identities=18%  Similarity=0.306  Sum_probs=56.6

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCe-eEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+++++++|+++|++||.| ..++++.+  .+++++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d--~~g~~~G~afV~F~~~~~a~~A   73 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQALVQFKNEDDARKS   73 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC--TTSSCSSCEEEECSSHHHHHHH
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEEC--CCCCcceEEEEEECCHHHHHHH
Confidence            34567899999999999999999999999999 88999998  5899999999999999999865

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

Probab=99.79  E-value=3e-19  Score=92.64  Aligned_cols=61  Identities=26%  Similarity=0.538  Sum_probs=55.1

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCC---CCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVG---SGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++ .   ++.++|||||+|.+.++|++|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~gt~~~~g~afV~f~~~~~a~~A   66 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK-NKAGVLLSMGFGFVEYKKPEQAQKA   66 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEE-CTTCCEEEEEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCCCcCcccEEEEEECCHHHHHHH
Confidence            457899999999999999999999999999999998875 3   458999999999999999864

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.79  E-value=1.2e-19  Score=98.70  Aligned_cols=63  Identities=24%  Similarity=0.427  Sum_probs=56.1

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE--EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKF--VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..  |+++.++ .+|+++|||||+|.+. +|.+|
T Consensus        18 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~-~tg~~rG~aFV~f~~~-~a~~A   82 (131)
T 2m2b_A           18 SSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDK-QTQLNRGFAFIQLSTI-EAAQL   82 (131)
T ss_dssp             CCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCS-SSSSBCSCEEEECCHH-HHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcC-CCCCcceEEEEEECCH-HHHHH
Confidence            33456789999999999999999999999999976  9999997 7999999999999999 87654

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=7.9e-19  Score=92.70  Aligned_cols=64  Identities=23%  Similarity=0.443  Sum_probs=55.2

Q ss_pred             cCcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        12 ~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .......+.++|||+|||+.+++++|+++|++||.|..+.+..+    +.++|||||+|.+.++|++|
T Consensus        14 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~----~~~~g~afV~f~~~~~A~~A   77 (109)
T 1x4a_A           14 IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR----RGGPPFAFVEFEDPRDAEDA   77 (109)
T ss_dssp             SSCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS----SSSSCCEEEEESCHHHHHHH
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC----CCCCcEEEEEECCHHHHHHH
Confidence            33445567799999999999999999999999999999998554    45789999999999999864

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.79  E-value=3.6e-19  Score=103.25  Aligned_cols=61  Identities=18%  Similarity=0.304  Sum_probs=55.9

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+++++++|+++|++||.|.+|+++.++ .+++++|||||+|.+.++|++|
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~~G~afV~F~~~~~A~~A   73 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM-ITRRSLGYAYVNFQQPADAERA   73 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeccc-CCCCccccccceeCCHHHHHHH
Confidence            346899999999999999999999999999999999987 7899999999999999999865

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.79  E-value=5.6e-19  Score=92.88  Aligned_cols=63  Identities=33%  Similarity=0.505  Sum_probs=57.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|.+||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus        24 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~a~~A   86 (107)
T 3ulh_A           24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD--RSGRSLGTADVHFERKADALKA   86 (107)
T ss_dssp             CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEC--TTSCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcceEEEEEECCHHHHHHH
Confidence            34456789999999999999999999999999999999998  5889999999999999999864

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.79  E-value=2.6e-19  Score=96.05  Aligned_cols=63  Identities=17%  Similarity=0.291  Sum_probs=56.7

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCC---eeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGE---LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|++||.   |..++++.++  .|+++|||||+|.+.++|++|
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~--~g~~~G~afV~F~~~~~a~~A   77 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR--EGRQSGEAFVELESEDDVKLA   77 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS--SSCEEEEEEEEBSSHHHHHHH
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC--CCCCCeEEEEEECCHHHHHHH
Confidence            33556789999999999999999999999998   8999999985  599999999999999999865

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.9e-19  Score=94.34  Aligned_cols=64  Identities=19%  Similarity=0.277  Sum_probs=57.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCee--------EEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--------FVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|.        .+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   81 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK-ETGKPKGDATVSYEDPPTAKAA   81 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT-TTCSBCSEEEEEBSSHHHHHHH
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeC-CCCCeeeEEEEEECCHHHHHHH
Confidence            3456789999999999999999999999999998        69998887 7899999999999999999865

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4e-19  Score=95.61  Aligned_cols=58  Identities=24%  Similarity=0.362  Sum_probs=52.0

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        26 ~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-------kG~AFVeF~~~e~A~~A   83 (119)
T 2ad9_A           26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-------KNQAFIEMNTEEAANTM   83 (119)
T ss_dssp             SCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-------GTEEEEECSCHHHHHHH
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-------CCEEEEEECCHHHHHHH
Confidence            34456789999999999999999999999999999998876       59999999999999865

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.79  E-value=4.7e-19  Score=94.77  Aligned_cols=61  Identities=21%  Similarity=0.398  Sum_probs=56.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~F~~~~~A~~A   64 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD--RTSKSRGFAFITFENPADAKNA   64 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECS--TTTTCCCEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEEC--CCCCcccEEEEEECCHHHHHHH
Confidence            456789999999999999999999999999999999998  5889999999999999999865

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

Probab=99.79  E-value=1.1e-18  Score=91.22  Aligned_cols=63  Identities=30%  Similarity=0.561  Sum_probs=55.8

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .......++|||+|||+.+++++|+++|++||.|..+.++.++  . .++|||||+|.+.++|++|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~--~-~~~g~afV~f~~~~~a~~A   71 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--R-GSKGFGFVTFENSADADRA   71 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--T-TTCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC--C-CCcEEEEEEECCHHHHHHH
Confidence            3445678999999999999999999999999999999999873  3 3889999999999999864

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=9.4e-20  Score=98.32  Aligned_cols=63  Identities=24%  Similarity=0.385  Sum_probs=54.4

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+.+++++|+++|.+||.|..+.++.+. .+|.++|||||+|.+.++|++|
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~-~~g~~~G~afV~F~~~~~a~~A   83 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-PNGKATGEGFVEFRNEADYKAA   83 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-TTSSEEEEEEEEBSSSHHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEEC-CCCCCCeEEEEEECCHHHHHHH
Confidence            34567899999999999999999999999998875454444 7899999999999999998865

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

Probab=99.79  E-value=9.9e-20  Score=95.32  Aligned_cols=62  Identities=24%  Similarity=0.533  Sum_probs=56.7

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A   66 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQETALSA   66 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET-TTTEEEEEEEEECSCHHHHHHH
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCC-CCCccceEEEEEECCHHHHHHH
Confidence            3456899999999999999999999999999999999886 7899999999999999999864

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.79  E-value=1.6e-19  Score=94.38  Aligned_cols=61  Identities=23%  Similarity=0.583  Sum_probs=55.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~a~~A   66 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD--RTGVSKGYGFVSFYNDVDVQKI   66 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEEC--TTSCEEEEEEEEESSCCCHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEEC--CCCCccceEEEEECCHHHHHHH
Confidence            445689999999999999999999999999999999998  5889999999999999998764

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.79  E-value=4.8e-19  Score=96.16  Aligned_cols=62  Identities=23%  Similarity=0.451  Sum_probs=54.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCee--EEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|++| .|.  .|.++.++  .|+++|||||+|.+.++|++|
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~--~GrsrGfaFV~F~~~e~A~~A  100 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP--EGKITGEAFVQFASQELAEKA  100 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS--SSSSCSEEEEEESSTTHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC--CCCCceEEEEEECCHHHHHHH
Confidence            334567899999999999999999999999 577  89999985  499999999999999999865

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

Probab=99.79  E-value=8.7e-19  Score=93.06  Aligned_cols=62  Identities=26%  Similarity=0.408  Sum_probs=56.5

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|.+||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~--~~g~~~g~afV~f~~~~~a~~A   72 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED--KDGKSRGIGTVTFEQSIEAVQA   72 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEEC--TTCSEEEEEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCeeeEEEEEECCHHHHHHH
Confidence            3456789999999999999999999999999999999998  4689999999999999998764

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.79  E-value=2.7e-19  Score=98.24  Aligned_cols=63  Identities=17%  Similarity=0.266  Sum_probs=56.8

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCC---eeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGE---LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|++||.   |..++++.++  .|+++|||||+|.+.++|++|
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~--~g~srG~aFV~F~~~e~a~~A  104 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR--EGRQSGEAFVELGSEDDVKMA  104 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECS--SSCEEEEEEEECSSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECC--CCCCCeEEEEEECCHHHHHHH
Confidence            34456789999999999999999999999998   8899999985  499999999999999999865

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

Probab=99.79  E-value=9e-19  Score=97.53  Aligned_cols=62  Identities=23%  Similarity=0.412  Sum_probs=57.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..|.++.++ .++.++|||||+|.+.++|++|
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   97 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKKTACGFCFVEYYSRADAENA   97 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            3467899999999999999999999999999999999987 7889999999999999999865

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.7e-19  Score=93.91  Aligned_cols=61  Identities=23%  Similarity=0.382  Sum_probs=54.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+++++++|+++|++||. ..++++.+  .+++++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d--~~g~~~G~afV~F~~~~~a~~A   71 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIG--PDGRVTGEADVEFATHEDAVAA   71 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEES--SSSCEEEEEEEECSSSHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEEC--CCCCEeeEEEEEECCHHHHHHH
Confidence            3456789999999999999999999999995 49999998  5899999999999999999865

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.78  E-value=4.9e-19  Score=89.21  Aligned_cols=57  Identities=25%  Similarity=0.482  Sum_probs=51.7

Q ss_pred             CCeEEEeCCCCCC------CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQA------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+      ++++|+++|++||.|..+.++.   .+|.++|||||+|.+.++|++|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~---~~g~~~g~afV~f~~~~~A~~A   63 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE---EDGKTKGYIFLEYASPAHAVDA   63 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC---BTTBCCCEEEEEESSHHHHHHH
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC---CCCcEeEEEEEEECCHHHHHHH
Confidence            3789999999999      7799999999999999999883   5789999999999999999865

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.4e-19  Score=96.07  Aligned_cols=60  Identities=23%  Similarity=0.479  Sum_probs=54.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+++++++|+++|++| .|..++++.++  .|+++|||||+|.+.++|++|
T Consensus        13 ~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~--~g~~~G~afV~F~~~~~a~~A   72 (109)
T 2dnn_A           13 NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH--VGRNNGNGLVKFLSPQDTFEA   72 (109)
T ss_dssp             CHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT--TCCCCSEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC--CCCCCeEEEEEECCHHHHHHH
Confidence            4446899999999999999999999999 79999999984  599999999999999999865

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=3e-19  Score=95.15  Aligned_cols=61  Identities=25%  Similarity=0.470  Sum_probs=53.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCC---CCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS---GLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|. +.++.++ .+   |+++|||||+|.+.++|++|
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~-~~~~~g~~~G~aFV~f~~~~~a~~A   68 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKA-ESKSYFPPKGYAFLLFQEESSVQAL   68 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSS-SSCCCSCTTSEEEECCSSHHHHHHH
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecC-CCCCCCCcccEEEEEECCHHHHHHH
Confidence            34578999999999999999999999999999 7777765 44   78999999999999998764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.1e-19  Score=98.27  Aligned_cols=61  Identities=23%  Similarity=0.321  Sum_probs=55.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCe----eEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGEL----KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i----~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+++++++|+++|++||.|    ..|.++.+  .+|+++|||||+|.+.++|++|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d--~~gr~~G~aFV~F~~~~~A~~A   84 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY--PDGRPTGDAFVLFACEEYAQNA   84 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC--TTSCEEEEEEECCSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC--CCCCEeeEEEEEECCHHHHHHH
Confidence            4567899999999999999999999999875    68999888  6899999999999999999865

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.78  E-value=5.6e-19  Score=92.91  Aligned_cols=62  Identities=24%  Similarity=0.440  Sum_probs=54.6

Q ss_pred             ccCCCCCeEEEeCCCCCC------CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQA------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+      ++++|+++|++||.|..+.++ .  .+|.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~--~~g~~~G~afV~f~~~~~A~~A   77 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-E--EDGKTKGYIFLEYASPAHAVDA   77 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-C--BTTBSCCEEEEEECSSSHHHHH
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-C--CCCCeeeEEEEEECCHHHHHHH
Confidence            344557899999999999      789999999999999999988 3  5789999999999999998764

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=7.6e-19  Score=91.90  Aligned_cols=62  Identities=23%  Similarity=0.472  Sum_probs=56.1

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.+   ++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~---~g~~~g~afV~f~~~~~A~~A   71 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME---GGRSKGFGFVCFSSPEEATKA   71 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC---SSSEEEEEEEEESSHHHHHHH
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC---CCCcCEEEEEEECCHHHHHHH
Confidence            44567899999999999999999999999999999999876   688899999999999999864

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.78  E-value=5.8e-19  Score=100.48  Aligned_cols=64  Identities=20%  Similarity=0.412  Sum_probs=58.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         8 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   71 (196)
T 1l3k_A            8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP-NTKRSRGFGFVTYATVEEVDAA   71 (196)
T ss_dssp             CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcC-CCCCccceEEEEeCCHHHHHHH
Confidence            345567899999999999999999999999999999999886 7889999999999999999864

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

Probab=99.78  E-value=1.7e-18  Score=90.56  Aligned_cols=62  Identities=18%  Similarity=0.270  Sum_probs=54.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++   +.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~~~g~afV~f~~~~~a~~A   71 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH---TSNDPYCFVEFYEHRDAAAA   71 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC---CSSCCEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC---CCCCCEEEEEECCHHHHHHH
Confidence            445678999999999999999999999999999999999874   23689999999999999764

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

Probab=99.78  E-value=5e-19  Score=90.04  Aligned_cols=60  Identities=20%  Similarity=0.515  Sum_probs=54.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCC-cceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL-HRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~-~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++ .++. ++|||||+|.+.++|++|
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~~~~~~~g~afV~f~~~~~a~~A   63 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVER-MHPHLSKGYAYVEFENPDEAEKA   63 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET-TEEEEECSEEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCC-CCCCCCCcEEEEEEecHHHHHHH
Confidence            56899999999999999999999999999999998885 4444 899999999999999864

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

Probab=99.78  E-value=1.4e-18  Score=89.13  Aligned_cols=60  Identities=25%  Similarity=0.515  Sum_probs=54.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+   ++.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~---~g~~~g~afV~f~~~~~a~~a   64 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVAERA   64 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES---SSCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc---CCCcceEEEEEECCHHHHHHH
Confidence            456899999999999999999999999999999998864   688999999999999998764

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=9e-19  Score=92.35  Aligned_cols=61  Identities=23%  Similarity=0.311  Sum_probs=55.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCC-eeEEEee-cccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLP-KKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~~~~~-~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|.+||. |..+.++ .++ .++.++|||||+|.+.++|++|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~-~~g~~~g~afV~f~~~~~A~~A   68 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA-DKMKNRGFAFVEYESHRAAAMA   68 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC-TTTTTCCEEEEEESSHHHHHHH
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCC-CCCCcCcEEEEEecCHHHHHHH
Confidence            45789999999999999999999999998 9999998 665 6789999999999999998764

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

Probab=99.78  E-value=9.9e-19  Score=98.26  Aligned_cols=64  Identities=27%  Similarity=0.467  Sum_probs=57.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+.+|.+||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A  130 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAA  130 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTSSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecC-CCCcEeeEEEEEECCHHHHHHH
Confidence            344557889999999999999999999999999999999887 7899999999999999998764

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.78  E-value=1.1e-18  Score=89.51  Aligned_cols=58  Identities=29%  Similarity=0.489  Sum_probs=49.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ......++|||+|||+++++++|+++|++||.|.++.++.+      ++|||||+|.+.++|++
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~------srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP------FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS------CCSEEEEEESCHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC------CCCEEEEEECCHHHHHH
Confidence            34567899999999999999999999999999999998764      57999999999999863

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.78  E-value=1.2e-18  Score=96.97  Aligned_cols=62  Identities=23%  Similarity=0.465  Sum_probs=57.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A  128 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR-YTKESRGFAFVRFHDKRDAEDA  128 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCS-SCTTSCCEEEEEESBHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC-CCCccceEEEEEECCHHHHHHH
Confidence            3457899999999999999999999999999999999986 7899999999999999998764

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.78  E-value=3.2e-19  Score=94.16  Aligned_cols=63  Identities=13%  Similarity=0.211  Sum_probs=56.6

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCC---eeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGE---LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+++++++|+++|++||.   |..++++.++  .|+++|||||+|.+.++|++|
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~--~g~~~G~afV~F~~~~~a~~A   71 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR--DGKRRGDALIEMESEQDVQKA   71 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCT--TSTTCSEEEEEBSSHHHHHHH
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECC--CCCEeeEEEEEECCHHHHHHH
Confidence            34567899999999999999999999999988   8999999985  499999999999999998864

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

Probab=99.77  E-value=2.8e-19  Score=92.79  Aligned_cols=62  Identities=24%  Similarity=0.342  Sum_probs=55.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~-~~g~~~g~afV~f~~~~~a~~A   73 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAA   73 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEEC-CCCCeeeEEEEEECCHHHHHHH
Confidence            4456899999999999999999999999999887777766 7889999999999999999864

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.77  E-value=9e-19  Score=94.25  Aligned_cols=60  Identities=18%  Similarity=0.426  Sum_probs=55.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~a~~A   94 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDK-FSGHPKGYAYIEFAERNSVDAA   94 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEEC-TTSSCEEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCCcccEEEEEECCHHHHHHH
Confidence            46899999999999999999999999999999999886 7899999999999999998764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=1.8e-18  Score=93.17  Aligned_cols=62  Identities=32%  Similarity=0.516  Sum_probs=56.6

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++||.|..+.++.+  .+|.++|||||+|.+.++|++|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~g~~~g~afV~f~~~~~A~~A   92 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD--RSGRSLGTADVHFERRADALKA   92 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECC--SSSSCCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEC--CCCCEeeEEEEEECCHHHHHHH
Confidence            3456789999999999999999999999999999999998  5888999999999999998764

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

Probab=99.77  E-value=4.1e-19  Score=97.23  Aligned_cols=65  Identities=22%  Similarity=0.429  Sum_probs=58.5

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +....+.++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        41 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~-~~g~~~G~afV~F~~~~~A~~A  105 (135)
T 2lea_A           41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR-YTKESRGFAFVRFHDKRDAEDA  105 (135)
T ss_dssp             CSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCS-SSSSCCSCCEEECSCHHHHHHH
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            3445567899999999999999999999999999999999886 6899999999999999998864

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=88.49  Aligned_cols=61  Identities=23%  Similarity=0.464  Sum_probs=56.0

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++| .|..+.++.+  .+|+++|||||+|.+.++|++|
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~--~~g~~~g~afV~f~~~~~a~~A   66 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN--AHGNKTGYIFVDFSNEEEVKQA   66 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC--TTSCEEEEEEEECSSHHHHHHH
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC--CCCCCceEEEEEECCHHHHHHH
Confidence            34567999999999999999999999999 8999999988  6899999999999999999865

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.8e-18  Score=90.76  Aligned_cols=56  Identities=21%  Similarity=0.337  Sum_probs=50.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-------kg~aFVef~~~~~A~~A   67 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-------KNQAFLELATEEAAITM   67 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-------CCEEEEEECCHHHHHHH
Confidence            456789999999999999999999999999999988765       59999999999998764

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

Probab=99.77  E-value=3.2e-19  Score=92.01  Aligned_cols=61  Identities=23%  Similarity=0.333  Sum_probs=54.3

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~-~~g~~~g~afV~f~~~~~a~~A   73 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAA   73 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEEC-TTSCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeC-CCCCEeeEEEEEECCHHHHHHH
Confidence            346899999999999999999999999999888887776 7889999999999999998864

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=2.9e-18  Score=90.34  Aligned_cols=56  Identities=20%  Similarity=0.292  Sum_probs=50.4

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-------kg~aFVef~~~~~A~~A   67 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-------KRQALVEFENIDSAKEC   67 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-------CCEEEEEECCHHHHHHH
Confidence            455789999999999999999999999999999988664       59999999999998764

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.77  E-value=4.2e-19  Score=92.67  Aligned_cols=64  Identities=22%  Similarity=0.515  Sum_probs=53.2

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+++++++|+++|++|| |..+.++.++..+|+++|||||+|.+.++|++|
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A   77 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA   77 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHH
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHH
Confidence            3455679999999999999999999999999 999999887423788999999999999999864

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

Probab=99.77  E-value=1.3e-18  Score=102.31  Aligned_cols=60  Identities=13%  Similarity=0.372  Sum_probs=55.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcC--CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFG--ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++||  .|..|+|+.++ .+++++|||||+|.+.++|++|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~-~tg~skGfaFV~f~~~~~a~~A  128 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR-ANGQSKGFALVGVGSEASSKKL  128 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECT-TTCCEEEEEEEEESCTTHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecC-CCCccceEEEEEECCHHHHHHH
Confidence            567899999999999999999999999  99999999997 7999999999999999998765

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=1e-18  Score=91.85  Aligned_cols=56  Identities=16%  Similarity=0.235  Sum_probs=50.5

Q ss_pred             CCCCCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+ .+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-------kg~aFVef~~~~~A~~A   68 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-------INEAFIEMATTEDAQAA   68 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-------SSCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-------CCEEEEEECCHHHHHHH
Confidence            34678999999999 9999999999999999999998776       38999999999999764

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.76  E-value=3.8e-18  Score=89.31  Aligned_cols=56  Identities=18%  Similarity=0.271  Sum_probs=50.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|.++.++..       +|+|||+|.+.++|.+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-------kg~AFVef~~~~~A~~A   73 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-------KRQALVEFEDVLGACNA   73 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-------CCEEEEEECCHHHHHHH
Confidence            446789999999999999999999999999999988764       48999999999999765

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.76  E-value=1.3e-18  Score=96.99  Aligned_cols=60  Identities=22%  Similarity=0.538  Sum_probs=56.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~a~~A   61 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDP-ATGRSRGFGFLSFEKPSSVDEV   61 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCT-TTSSCCSCEEEEESSTHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECC-CCCCccceEEEEEccHHHHHHH
Confidence            46899999999999999999999999999999999986 7899999999999999998764

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2e-18  Score=91.40  Aligned_cols=63  Identities=29%  Similarity=0.534  Sum_probs=55.6

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .......++|||+|||+.+++++|+++|++||.|..+.++.++   +.++|||||+|.+.++|++|
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~~kg~afV~f~~~~~A~~A   85 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE---RGSKGFGFVTFENSADADRA   85 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT---TBCTTEEEEECCCSHHHHHH
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC---CCCceEEEEEECCHHHHHHH
Confidence            3445668999999999999999999999999999999998873   34889999999999998864

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.76  E-value=4.5e-19  Score=97.67  Aligned_cols=61  Identities=25%  Similarity=0.371  Sum_probs=53.6

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+++++++|+++|++|| +..+.++.++  .++++|||||+|.+.++|++|
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~--~g~srGfaFV~F~~~e~A~~A  102 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP--DGRVTGEADVEFATHEEAVAA  102 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS--SSCSSCCCEEECSHHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC--CCCCceEEEEEeCCHHHHHHH
Confidence            345678999999999999999999999999 7799999985  599999999999999999865

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.76  E-value=5e-19  Score=90.55  Aligned_cols=57  Identities=32%  Similarity=0.532  Sum_probs=52.8

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.+ |++|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~-a~~a   58 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEMQEES-VSEA   58 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCS-SSCCCCEEEEEEECTTH-HHHH
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcC-CCCCcceEEEEEECCHH-HHHH
Confidence            589999999999999999999999999999999887 77999999999999999 7654

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.2e-18  Score=88.24  Aligned_cols=59  Identities=22%  Similarity=0.317  Sum_probs=52.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHH----HHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..+.++.++  .+  +|||||+|.+.++|++|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~--~~--rg~afV~f~~~~~A~~A   68 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT--DY--QLKAVVQMENLQDAIGA   68 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCC--ST--TCCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCC--CC--CeEEEEEECCHHHHHHH
Confidence            4467899999999999999999    999999999999999884  33  79999999999999865

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=2e-18  Score=92.07  Aligned_cols=56  Identities=25%  Similarity=0.419  Sum_probs=50.4

Q ss_pred             CCCCCeEEEeCCCCC-CCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||++ +++++|+++|++||.|..+.++..       +|||||+|.+.++|++|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-------kg~aFVef~~~~~A~~A   78 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-------KSQAFIEMETREDAMAM   78 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-------TTEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-------CCEEEEEECCHHHHHHH
Confidence            456789999999998 999999999999999999998654       59999999999998764

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.75  E-value=4.9e-18  Score=95.00  Aligned_cols=60  Identities=22%  Similarity=0.428  Sum_probs=54.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCC--CcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG--LHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++ .++  .++|||||+|.+.++|++|
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~~~~~~~g~afV~f~~~~~A~~A   63 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR-SQNPPQSKGCCFVTFYTRKAALEA   63 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEC-SSSSCEEEEEEEEEESSHHHHHHH
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecC-CCCCCCcceEEEEEECCHHHHHHH
Confidence            56899999999999999999999999999999999885 454  8999999999999998764

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

Probab=99.74  E-value=6.6e-18  Score=87.56  Aligned_cols=63  Identities=17%  Similarity=0.340  Sum_probs=51.8

Q ss_pred             ccCcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          11 KSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        11 ~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+........++|||+|||+.+++++|+++|++||.|. +.++.+     .++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~-----~~~g~afV~f~~~~~a~~A   72 (97)
T 2e5j_A           10 SPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ-----GPRRRAFLHYPDSAAAQQA   72 (97)
T ss_dssp             CCCCSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE-----TTTTEEEEECSSHHHHHHH
T ss_pred             CCCCCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC-----CCCcEEEEEECCHHHHHHH
Confidence            33344456678999999999999999999999999986 555443     5679999999999998764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.74  E-value=1.1e-17  Score=92.86  Aligned_cols=59  Identities=27%  Similarity=0.576  Sum_probs=55.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~-~~~~~~g~afV~f~~~~~A~~a   60 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-ITGQSLGYGFVNYIDPKDAEKA   60 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-CCCcceeEEEEEECCHHHHHHH
Confidence            5799999999999999999999999999999999886 6899999999999999999864

>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=99.74  E-value=3.9e-18  Score=90.45  Aligned_cols=64  Identities=22%  Similarity=0.304  Sum_probs=55.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHH---HHhHhcCCeeEEEeecccCC---CCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVE---ELFKAFGELKFVRLPKKMVG---SGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~---~~f~~~g~i~~~~~~~~~~~---~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+   ++|.+||.|..+.++.++ .   ++.++|||||+|.+.++|++|
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~-~~~~~~~~~G~afV~f~~~~~A~~A   79 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST-SYAGSQGPSASAYVTYIRSEDALRA   79 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS-SCCSSSCCCEEEEEEESSHHHHHHH
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCC-CcCccCCCCeEEEEEECcHHHHHHH
Confidence            344567899999999999999999   999999999999998875 3   335679999999999999865

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.2e-18  Score=86.51  Aligned_cols=56  Identities=27%  Similarity=0.475  Sum_probs=50.5

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.+      ++|||||+|.+.++|+++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS------CCSCCEEECSCHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC------CCCEEEEEECCHHHHHHH
Confidence            35789999999999999999999999999999998654      579999999999998754

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

Probab=99.74  E-value=8.6e-18  Score=93.56  Aligned_cols=60  Identities=23%  Similarity=0.576  Sum_probs=55.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~a   61 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-KTGYSYGYAFVDFTSEMDSQRA   61 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeC-CCCccceEEEEEECCHHHHHHH
Confidence            46899999999999999999999999999999999886 7899999999999999999764

>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=99.73  E-value=1.3e-17  Score=88.59  Aligned_cols=59  Identities=20%  Similarity=0.474  Sum_probs=52.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+    +.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~----~~~~g~afV~f~~~~~A~~A   63 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT----PETRGTAYVVYEDIFDAKNA   63 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS----TTTTTCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCCcEEEEEECCHHHHHHH
Confidence            345789999999999999999999999999999999876    34589999999999998764

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-17  Score=83.80  Aligned_cols=58  Identities=17%  Similarity=0.375  Sum_probs=51.8

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-------kg~afV~f~~~~~A~~a   64 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-------QQCAFIQFATRQAAEVA   64 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-------GTEEEEEESSHHHHHHH
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-------CCEEEEEECCHHHHHHH
Confidence            34556789999999999999999999999999999998765       59999999999998764

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

Probab=99.73  E-value=2e-17  Score=89.88  Aligned_cols=59  Identities=17%  Similarity=0.292  Sum_probs=50.7

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHH----HHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+    ++|++||.|..|.+..    +++++|||||+|.+.++|+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~----~~~~rG~aFV~F~~~~~A~~A   88 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL----SDDNSGKAYIVFATQESAQAF   88 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC----CCSSCCCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc----CCCcCCEEEEEECCHHHHHHH
Confidence            4557899999999999999876    6999999999887743    467899999999999998765

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

Probab=99.73  E-value=1e-17  Score=87.26  Aligned_cols=59  Identities=20%  Similarity=0.522  Sum_probs=51.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+.+++++|+++|.+||.|   .++.+  .++.++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~--~~g~~~g~afV~f~~~~~A~~A   69 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN--QNGKSKGYAFIEFASFEDAKEA   69 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC--SSSCBCSEEEEECSSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC--CCCCEeeEEEEEECCHHHHHHH
Confidence            45568999999999999999999999999976   56665  5788999999999999999864

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3.2e-17  Score=86.49  Aligned_cols=56  Identities=16%  Similarity=0.472  Sum_probs=50.7

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+++++++|+++|.+||.|..+.++.+        |||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--------g~afV~f~~~~~a~~A   66 (108)
T 1x4c_A           11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVEFVRKEDMTYA   66 (108)
T ss_dssp             CCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--------TEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--------CEEEEEECCHHHHHHH
Confidence            3456899999999999999999999999999999998764        8999999999998865

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

Probab=99.72  E-value=2.7e-18  Score=91.28  Aligned_cols=62  Identities=23%  Similarity=0.336  Sum_probs=51.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|.+||.|..+.+..+. .++.++|||||+|.+.++|++|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~g~~~g~afV~f~~~~~a~~A   83 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGRMRGQAFITFPNKEIAWQA   83 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE-ECSSSCSEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEc-CCCccceEEEEEECCHHHHHHH
Confidence            4457899999999999999999999999998544333332 4678899999999999998764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.72  E-value=9.7e-19  Score=91.20  Aligned_cols=61  Identities=15%  Similarity=0.252  Sum_probs=53.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|.. .++.++ .++.++|||||+|.+.++|++|
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~-~~g~~~g~afV~f~~~~~a~~A   74 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV-RTGTNRKFGYVDFESAEDLEKA   74 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE-EEETTTTEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecC-CCCCcCcEEEEEECCHHHHHHH
Confidence            345789999999999999999999999998877 555554 6788999999999999999865

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.72  E-value=1.9e-17  Score=94.17  Aligned_cols=60  Identities=33%  Similarity=0.540  Sum_probs=55.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..|.++.+  .++.++|||||+|.+.++|++|
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d--~~g~~kG~afV~F~~~~~A~~A  145 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD--RSGRSLGTADVHFERRADALKA  145 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCC--TTSSCSCCEEEEESCHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCEeeEEEEEeCCHHHHHHH
Confidence            34689999999999999999999999999999999998  5888999999999999999864

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.72  E-value=1.3e-17  Score=88.77  Aligned_cols=59  Identities=17%  Similarity=0.267  Sum_probs=51.1

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+++++++|+++|++|| .|..+.+..+     .++|||||+|.+.++|++|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~-----~~rGfaFV~F~~~e~A~~A   83 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR-----DFDGTGALEFPSEEILVEA   83 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC-----SSSCCEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC-----CCCCEEEEEECCHHHHHHH
Confidence            345678999999999999999999999999 8999887543     3689999999999999865

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.9e-17  Score=85.07  Aligned_cols=58  Identities=12%  Similarity=0.303  Sum_probs=51.1

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.+..+       +|||||+|.+.++|++|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-------~g~afV~f~~~~~A~~A   69 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-------DSFAYIQYESLDAAQAA   69 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-------SCCEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-------CCEEEEEECCHHHHHHH
Confidence            34456789999999999999999999999999999988654       58999999999999864

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.72  E-value=2e-17  Score=95.17  Aligned_cols=58  Identities=17%  Similarity=0.332  Sum_probs=54.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|++||.|..++++.+  .++.++|||||+|.+.++|++|
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~--~~~~~kG~aFVeF~~~e~A~~A  166 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKF  166 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC--TTCCEEEEEEEEESSHHHHHHH
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEEC--CCCCcccEEEEEECCHHHHHHH
Confidence            489999999999999999999999999999999998  5688999999999999999865

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

Probab=99.72  E-value=1e-17  Score=86.65  Aligned_cols=60  Identities=23%  Similarity=0.383  Sum_probs=52.0

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHH----HHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+.+++++|+    ++|++||.|..+.++.    ++.++|||||+|.+.++|++|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~----~~~~~g~afV~f~~~~~A~~A   67 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR----SLKMRGQAFVIFKEVSSATNA   67 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH----HHHHTTCEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc----CCCcCcEEEEEeCCHHHHHHH
Confidence            34567899999999999999999    9999999999998864    366789999999999998764

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.72  E-value=3.2e-17  Score=93.25  Aligned_cols=61  Identities=26%  Similarity=0.559  Sum_probs=55.9

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|.+|
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~g~~~g~afV~F~~~~~A~~A  162 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVDKI  162 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecC-CCCCccceEEEEECCHHHHHHH
Confidence            345899999999999999999999999999999999886 6899999999999999999864

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

Probab=99.55  E-value=5.4e-19  Score=94.29  Aligned_cols=62  Identities=23%  Similarity=0.303  Sum_probs=56.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE--------EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKF--------VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|++||.|..        +.++.++ .++.++|||||+|.+.++|++|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   73 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR-ETGKLKGEATVSFDDPPSAKAA   73 (116)
Confidence            456789999999999999999999999999988        8888886 6789999999999999999875

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

Probab=99.71  E-value=4.5e-18  Score=98.00  Aligned_cols=61  Identities=23%  Similarity=0.423  Sum_probs=54.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A   86 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS-VTMKHKGFAFVEYEVPEAAQLA   86 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC--CC-CCCSEEEEEESSHHHHHHH
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecC-CCCccCceEEEEeCCHHHHHHH
Confidence            446899999999999999999999999999999999886 6889999999999999999864

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

Probab=99.71  E-value=2.5e-17  Score=85.56  Aligned_cols=58  Identities=28%  Similarity=0.501  Sum_probs=51.5

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-------kg~afV~f~~~~~a~~a   67 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-------KGFGFIRLETRTLAEIA   67 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-------TTEEEEECSSSHHHHHH
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-------CCEEEEEECCHHHHHHH
Confidence            33456789999999999999999999999999999998765       59999999999998764

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.71  E-value=4.8e-17  Score=90.93  Aligned_cols=61  Identities=25%  Similarity=0.508  Sum_probs=55.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.+  .+|.++|||||+|.+.++|.+|
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~--~~g~~~g~afV~f~~~~~A~~A  152 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTA  152 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC--TTSCEEEEEEEEESSHHHHHHH
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEEC--CCCCEEEEEEEEECCHHHHHHH
Confidence            345789999999999999999999999999999999988  5789999999999999999865

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

Probab=99.71  E-value=2.4e-17  Score=91.42  Aligned_cols=57  Identities=14%  Similarity=0.280  Sum_probs=52.3

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+++++++|+++|++||.|..+.++.+  ..+.++|||||+|.+.++|++|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~--~~~~~~g~afV~f~~~~~a~~A   57 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID--KNNKNVNYAFVEYHQSHDANIA   57 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECC--CC-CCEEEEEEEESSHHHHHHH
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEEC--CCCCCCCEEEEEeCCHHHHHHH
Confidence            58999999999999999999999999999999988  5688999999999999998764

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.70  E-value=2e-17  Score=89.78  Aligned_cols=52  Identities=15%  Similarity=0.284  Sum_probs=49.3

Q ss_pred             CCeEEEeCC----CCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecC
Q psy3346          20 GSKILVRNI----PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT   72 (79)
Q Consensus        20 ~~~l~v~nl----~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~   72 (79)
                      ++.|||+||    |+.+++.+|+++|+.||+|.++.++.|+ .+|.++|||||+|.+
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp-~Tg~slGfgfVef~d   57 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDP-NSALPLHVYLIKYAS   57 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECT-TTCCEEEEEEEECC-
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecC-CCCceeeEEEEEECC
Confidence            378999999    9999999999999999999999999999 999999999999996

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.70  E-value=4.1e-17  Score=103.28  Aligned_cols=61  Identities=18%  Similarity=0.455  Sum_probs=56.3

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|.++|.+||.|..|.|+.++ .++.++|||||+|.+.++|++|
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~-~tg~~kG~aFV~F~~~e~A~~A  160 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK-RSGKPRGYAFIEYEHERDMHSA  160 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccC-CCCCccceEEEeeccHHHHHHH
Confidence            345799999999999999999999999999999999886 7899999999999999998865

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

Probab=99.70  E-value=8.1e-17  Score=89.27  Aligned_cols=63  Identities=21%  Similarity=0.425  Sum_probs=57.6

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|.+|
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~A~~A  145 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDM-QTGSSRGYGFVSFTSQDDAQNA  145 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHH
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecC-CCCCcceEEEEEeCCHHHHHHH
Confidence            34567899999999999999999999999999999999886 7899999999999999999865

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

Probab=99.70  E-value=5e-17  Score=84.72  Aligned_cols=61  Identities=23%  Similarity=0.446  Sum_probs=52.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|+.|+   .+.++.++ .++.++|||||+|.+.++|++|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~-~~~~~~g~afV~f~~~~~A~~A   70 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDR-ETGSSKGFGFVDFNSEEDAKAA   70 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECS-SSCSEEEEEEEECSSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecC-CCCCcCcEEEEEECCHHHHHHH
Confidence            4456689999999999999999999999774   56677765 6889999999999999999864

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.69  E-value=4.4e-17  Score=83.34  Aligned_cols=53  Identities=21%  Similarity=0.333  Sum_probs=48.4

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..-|||+||++.+++++|+++|.+||+|.++++...       +|||||+|.+.++|++|
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~-------kGfaFVey~~~~eA~~A   59 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-------QGIALCKYTTREEANKA   59 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC-------CcEEEEEECCHHHHHHH
Confidence            567999999999999999999999999999998653       69999999999999865

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

Probab=99.69  E-value=1.1e-16  Score=84.47  Aligned_cols=57  Identities=19%  Similarity=0.402  Sum_probs=51.4

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-------~g~afV~f~~~~~a~~A   77 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-------KGYSFVRFSTHESAAHA   77 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-------CCEEEEEECCHHHHHHH
Confidence            3456789999999999999999999999999999998775       59999999999998764

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

Probab=99.69  E-value=1.3e-16  Score=89.07  Aligned_cols=61  Identities=28%  Similarity=0.573  Sum_probs=56.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~g~~~g~afV~f~~~~~A~~A  152 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQA  152 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TTCSEEEEEEEEESSTTHHHHH
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecC-CCCCcceEEEEEeCCHHHHHHH
Confidence            446899999999999999999999999999999999886 6899999999999999998864

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.69  E-value=6e-17  Score=84.34  Aligned_cols=53  Identities=32%  Similarity=0.540  Sum_probs=48.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+.+++++|+++|++||.|..+.++.+      ++|||||+|.+.++|++|
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~------~~g~afV~f~~~~~a~~A   53 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN------PPGFAFVEFEDPRDAEDA   53 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS------SSSEEEEECSSHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC------CCCEEEEEECCHHHHHHH
Confidence            58999999999999999999999999999998764      579999999999999865

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-16  Score=81.53  Aligned_cols=54  Identities=24%  Similarity=0.500  Sum_probs=49.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++         +|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---------~g~afV~f~~~~~A~~A   58 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---------KNYGFVHIEDKTAAEDA   58 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---------TTEEEEEESSHHHHHHH
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---------CCEEEEEECCHHHHHHH
Confidence            4567899999999999999999999999999999885         38999999999998764

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

Probab=99.69  E-value=4.4e-17  Score=86.46  Aligned_cols=55  Identities=33%  Similarity=0.515  Sum_probs=49.2

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++..       +|||||+|.+.++|++|
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-------~g~afV~f~~~~~A~~A   62 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-------GITAIVEFLEPLEARKA   62 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-------SSCEEEEESCHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-------CCEEEEEeCCHHHHHHH
Confidence            34689999999999999999999999999999988654       58999999999999864

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=5.6e-17  Score=86.61  Aligned_cols=57  Identities=14%  Similarity=0.331  Sum_probs=49.5

Q ss_pred             cCCCCCeEEE--eCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILV--RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v--~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||  +||++.+++++|+++|++||.|..+.++.+       +|||||+|.+.++|++|
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-------rgfaFV~f~~~~~A~~A   79 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-------KPYSFARYRTTEESKRA   79 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-------CSCEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-------CCEEEEEECCHHHHHHH
Confidence            3445688999  779999999999999999999999887543       59999999999999865

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

Probab=99.69  E-value=1.1e-16  Score=83.28  Aligned_cols=56  Identities=21%  Similarity=0.354  Sum_probs=49.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||..+++++|+++|++||.|..+.+...       +|||||+|.+.++|++|
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~-------~g~afV~f~~~~~A~~A   79 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-------KGCCFIKYDTHEQAAVC   79 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETT-------TTEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecC-------CCEEEEEECCHHHHHHH
Confidence            345789999999999999999999999999999988643       59999999999998764

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.69  E-value=9.8e-17  Score=88.74  Aligned_cols=59  Identities=27%  Similarity=0.446  Sum_probs=52.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..++++.+      ++|||||+|.+.++|++|
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~~g~afV~f~~~~~a~~A  126 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN------PPGFAFVEFEDPRDAADA  126 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS------SCSEEEEEESSHHHHHHH
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC------CCcEEEEEECCHHHHHHH
Confidence            33456789999999999999999999999999999998775      479999999999998764

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.69  E-value=5.5e-17  Score=90.28  Aligned_cols=60  Identities=32%  Similarity=0.527  Sum_probs=55.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A  145 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTYDSADAVDRV  145 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSS-SSSTTSEEEEEEESSHHHHHHH
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcC-CCCccceEEEEEECCHHHHHHH
Confidence            45789999999999999999999999999999999886 6899999999999999999864

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.68  E-value=7.7e-17  Score=85.20  Aligned_cols=57  Identities=32%  Similarity=0.660  Sum_probs=49.6

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .......++|||+|||+.+++++|+++|++||.|..+.++         +|||||+|.+.++|++|
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---------kg~afV~f~~~~~A~~A   81 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---------NGFAFVEFEEAESAAKA   81 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---------TTEEEEECSSHHHHHHH
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---------CCEEEEEECCHHHHHHH
Confidence            3445668999999999999999999999999999999886         49999999999999864

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.68  E-value=2.4e-16  Score=87.45  Aligned_cols=62  Identities=27%  Similarity=0.515  Sum_probs=56.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|.+|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~A  146 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRIEAEEA  146 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecC-CCCCccceEEEEeCCHHHHHHH
Confidence            3457899999999999999999999999999999998886 6888999999999999999865

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.68  E-value=5.1e-17  Score=86.66  Aligned_cols=55  Identities=16%  Similarity=0.474  Sum_probs=47.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|.+||.|..+.++.+        |||||+|.+.++|++|
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--------g~afV~f~~~~~a~~A   67 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVEFVRKEDMTYA   67 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--------SEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--------CEEEEEECCHHHHHHH
Confidence            356789999999999999999999999999999988654        9999999999999865

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

Probab=99.68  E-value=2.7e-16  Score=87.44  Aligned_cols=62  Identities=19%  Similarity=0.438  Sum_probs=56.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||..+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|.+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~~~~~g~afV~f~~~~~A~~A  147 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK-LTGRPRGVAFVRYNKREEAQEA  147 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcC-CCCCcceEEEEEECCHHHHHHH
Confidence            3457899999999999999999999999999999998885 6899999999999999999865

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

Probab=99.68  E-value=2e-16  Score=91.03  Aligned_cols=61  Identities=23%  Similarity=0.560  Sum_probs=56.6

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|.+|
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~-~~g~~~g~afV~F~~~~~A~~A  183 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDP-TTGKHKGYGFIEYEKAQSSQDA  183 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecC-CCCCcCceEEEEecCHHHHHHH
Confidence            456899999999999999999999999999999999886 7899999999999999999765

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

Probab=99.67  E-value=3.3e-17  Score=84.58  Aligned_cols=57  Identities=23%  Similarity=0.556  Sum_probs=50.0

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+    .  .++.++|||||+|.+.++|++|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~--~~~~~~g~afV~f~~~~~a~~A   69 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----S--QDGKSKGIAYIEFKSEADAEKN   69 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----E--ETTEEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----C--CCCCcceEEEEEECCHHHHHHH
Confidence            4457899999999999999999999999977655    3  5788999999999999999864

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

Probab=99.67  E-value=2.7e-16  Score=89.51  Aligned_cols=61  Identities=28%  Similarity=0.593  Sum_probs=56.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~-~~~~~~g~afV~f~~~~~a~~A  172 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQA  172 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECT-TTCSEEEEEEEEESSSSHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecC-CCCCcceEEEEEECCHHHHHHH
Confidence            567899999999999999999999999999999999886 6899999999999999998764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=4.6e-16  Score=80.14  Aligned_cols=56  Identities=23%  Similarity=0.350  Sum_probs=47.5

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..|  +.++ .++.   ||||+|.+.++|++|
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~-~~g~---~afV~f~~~~~a~~a   61 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDK-DKGV---FAIVEMGDVGAREAV   61 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECS-SSCC---EEEEEESSHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcC-CCCc---EEEEEECCHHHHHHH
Confidence            356799999999999999999999999999987  4443 3444   999999999998764

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.66  E-value=4.3e-16  Score=80.85  Aligned_cols=56  Identities=16%  Similarity=0.532  Sum_probs=49.0

Q ss_pred             ccCCCCCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+ .+++++|+++|++||.|..+.+.         +|||||+|.+.++|++|
T Consensus        17 ~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---------~g~afV~f~~~~~A~~A   73 (97)
T 2xnq_A           17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---------NAFGFIQFDNPQSVRDA   73 (97)
T ss_dssp             --CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---------SSEEEEEESSHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---------CCEEEEEECCHHHHHHH
Confidence            4456689999999998 99999999999999999999872         58999999999999764

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.66  E-value=3.3e-16  Score=79.40  Aligned_cols=55  Identities=25%  Similarity=0.552  Sum_probs=49.1

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhc----C-------CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAF----G-------ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++|    |       .|..+.+..+       +|||||+|.+.++|++|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-------kg~afV~f~~~~~a~~A   69 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-------KNFAFLEFRSVDETTQA   69 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-------SSEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-------CcEEEEEcCCHHHHHHH
Confidence            357899999999999999999999999    8       8998887654       59999999999999865

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

Probab=99.65  E-value=3e-16  Score=81.14  Aligned_cols=54  Identities=17%  Similarity=0.543  Sum_probs=47.8

Q ss_pred             CCCCCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+ .+++++|+++|++||.|..+.+.         +|||||+|.+.++|++|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~---------~g~afV~f~~~~~A~~A   61 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---------NAFGFIQFDNPQSVRDA   61 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---------TTEEEEEESCHHHHHHH
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---------CCEEEEEECCHHHHHHH
Confidence            45688999999999 99999999999999999999873         48999999999998764

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.9e-16  Score=80.51  Aligned_cols=59  Identities=19%  Similarity=0.330  Sum_probs=49.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEE-EeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|.+||.|..+ .++.++ .+    |.|||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~-~~----~~afV~f~~~~~a~~A   70 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-ET----AVVNVTYSSKDQARQA   70 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS-SS----EEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-CC----CEEEEEECCHHHHHHH
Confidence            34457899999999999999999999999999999 477764 23    3399999999998764

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

Probab=99.65  E-value=6e-16  Score=81.70  Aligned_cols=53  Identities=25%  Similarity=0.596  Sum_probs=47.8

Q ss_pred             CCCCeEEEeCCCCC-CCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+. +++++|+++|++||.|..+.+         ++|||||+|.+.++|++|
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---------~~g~afV~f~~~~~A~~A   78 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---------HKGYAFVQYSNERHARAA   78 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---------ETTEEEEECSSSHHHHHH
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---------eCCEEEEEECCHHHHHHH
Confidence            34589999999999 999999999999999999987         359999999999998764

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.7e-16  Score=79.19  Aligned_cols=56  Identities=20%  Similarity=0.345  Sum_probs=49.4

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.         +||||+|.+.++|++|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~---------~~afV~f~~~~~a~~A   60 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK---------DYAFVHMERAEDAVEA   60 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS---------SEEEEEESCHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC---------CEEEEEECCHHHHHHH
Confidence            3455678999999999999999999999999999998752         4999999999998764

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.65  E-value=3e-16  Score=86.21  Aligned_cols=62  Identities=15%  Similarity=0.336  Sum_probs=50.7

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEE--eecc---cCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVR--LPKK---MVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~--~~~~---~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.  ++.+   . .++.++|||||+|.+.++|++|
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~-~~g~~~g~afV~f~~~~~A~~A  108 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM-KEGRMKGQAFIGLPNEKAAAKA  108 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE-EETTTEEEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec-cCCCcccEEEEEeCCHHHHHHH
Confidence            45678999999999999999999999999987641  1111   1 3678899999999999998865

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.9e-16  Score=78.63  Aligned_cols=54  Identities=24%  Similarity=0.353  Sum_probs=48.6

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+.++.         +||||+|.+.++|++|
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~---------~~afV~f~~~~~a~~A   59 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK---------DYAFVHMEKEADAKAA   59 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS---------SCEEEEESCHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC---------CEEEEEECCHHHHHHH
Confidence            45678999999999999999999999999999998752         4999999999998764

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.64  E-value=8.6e-16  Score=80.27  Aligned_cols=54  Identities=22%  Similarity=0.434  Sum_probs=48.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+.+++++|+++|.+||.|..+.++         ++||||+|.+.++|++|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---------~~~afV~f~~~~~a~~A   61 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---------KDYAFIHFDERDGAVKA   61 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---------SSCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---------CCEEEEEeCCHHHHHHH
Confidence            3457899999999999999999999999999999874         36999999999999864

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

Probab=99.64  E-value=4.7e-16  Score=93.29  Aligned_cols=64  Identities=22%  Similarity=0.327  Sum_probs=51.3

Q ss_pred             CcccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        13 ~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ........++|||+|||+.+++++|+++|++||.|..+.++.++  .+ ++|||||+|.+.++|++|
T Consensus        34 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~-~~g~afV~f~~~~~A~~A   97 (292)
T 2ghp_A           34 ALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KK-NFRFARIEFARYDGALAA   97 (292)
T ss_dssp             --------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT--TS-SSEEEEEEESSHHHHHHH
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC--CC-CcEEEEEEECCHHHHHHH
Confidence            34445668999999999999999999999999999999998873  33 479999999999999865

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.63  E-value=7.8e-16  Score=86.61  Aligned_cols=57  Identities=14%  Similarity=0.233  Sum_probs=49.6

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+|||+||++.+++++|+++|++||.|.++.+..+     .++|||||+|.+.++|++|
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k-----~~rgfAFVeF~d~~~A~~A  100 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHA  100 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES-----SSCEEEEEEESCHHHHHHH
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCCEEEEEECCHHHHHHH
Confidence            34567999999999999999999999999999998643     2468999999999998764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.1e-15  Score=78.22  Aligned_cols=55  Identities=22%  Similarity=0.421  Sum_probs=48.0

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhc--CCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAF--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++|  |.|..+.++         +|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---------~g~afV~f~~~~~A~~A   67 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---------RDYAFVHFSNREDAVEA   67 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---------SSEEEEEESSHHHHHHH
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---------CCeEEEEeCCHHHHHHH
Confidence            34567899999999999999999999999  888887653         47999999999998764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.63  E-value=1e-15  Score=88.69  Aligned_cols=58  Identities=24%  Similarity=0.449  Sum_probs=52.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+|||+|||+.+++++|+++|++||.|..++++.++   +.++|||||+|.+.++|++|
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~---~~~~g~~fV~f~~~~~a~~A  159 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE---NGSKGYGFVHFETQEAAERA  159 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET---TEEEEEEEEEESSHHHHHHH
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC---CCCceEEEEEeCCHHHHHHH
Confidence            45789999999999999999999999999999998873   45789999999999999875

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.63  E-value=1.2e-15  Score=90.75  Aligned_cols=60  Identities=27%  Similarity=0.450  Sum_probs=55.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+  .+|.++|||||+|.+.++|.+|
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~A~~A  153 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD--DRGRATGKGFVEFAAKPPARKA  153 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE--TTSCEEEEEEEEESSHHHHHHH
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC--CCCCcCcEEEEEeCCHHHHHHH
Confidence            35689999999999999999999999999999999998  6899999999999999999765

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

Probab=99.62  E-value=4.6e-16  Score=79.88  Aligned_cols=55  Identities=22%  Similarity=0.294  Sum_probs=46.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCC-eeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||. |..+.+.        ++|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~--------~~g~afV~f~~~~~A~~A   60 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--------KSGYAFVDYPDQNWAIRA   60 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--------ETTEEEECCSCHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc--------CCCEEEEEECCHHHHHHH
Confidence            446789999999999999999999999998 5555542        359999999999998764

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.62  E-value=1.2e-15  Score=88.30  Aligned_cols=56  Identities=18%  Similarity=0.294  Sum_probs=50.6

Q ss_pred             CCCCeEEEeCCC-CCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIP-FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+||| +.+++++|+++|++||.|.+++++.+      .+|||||+|.+.++|++|
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~------~~g~afV~f~~~~~A~~A   58 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS------KPGAAMVEMADGYAVDRA   58 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT------STTCEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC------CCCEEEEEECCHHHHHHH
Confidence            357899999999 89999999999999999999998765      269999999999999865

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

Probab=99.61  E-value=2.2e-15  Score=90.03  Aligned_cols=60  Identities=23%  Similarity=0.385  Sum_probs=53.0

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHH----HHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVE----ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+    ++|++||.|..|.+..    +++++|||||+|.+.++|++|
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~----~~~~~g~afV~f~~~~~a~~A   68 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR----SLKMRGQAFVIFKEVSSATNA   68 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC----CCCcceEEEEEECCHHHHHHH
Confidence            45668999999999999999976    8999999999998765    467889999999999999865

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.61  E-value=3.6e-15  Score=89.15  Aligned_cols=61  Identities=33%  Similarity=0.557  Sum_probs=56.2

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|.+|
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A  153 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSE-RTGQSKGYGFAEYMKKDSAARA  153 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeC-CCCccceEEEEEECCHHHHHHH
Confidence            456899999999999999999999999999999998886 7899999999999999998764

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

Probab=99.61  E-value=4.5e-15  Score=76.77  Aligned_cols=55  Identities=18%  Similarity=0.329  Sum_probs=47.9

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+||  .+++++|+++|++||.|..+.+..       ++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~-------~~g~afV~f~~~~~a~~A   65 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP-------PRNCAFVTYEKMESADQA   65 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET-------TTTEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC-------CCCEEEEEECCHHHHHHH
Confidence            3456789999995  899999999999999999998843       469999999999998865

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.61  E-value=2.7e-15  Score=87.70  Aligned_cols=59  Identities=20%  Similarity=0.297  Sum_probs=52.6

Q ss_pred             ccCCCCCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+ .+++++|+++|++||.|..+.++.++      +|||||+|.+.++|++|
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~------~g~afV~F~~~~~A~~A   88 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK------KENALVQMADGNQAQLA   88 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT------SCCEEEEESCHHHHHHH
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC------CCEEEEEECCHHHHHHH
Confidence            3445678999999999 99999999999999999999998872      68999999999999864

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.60  E-value=3.2e-15  Score=81.39  Aligned_cols=56  Identities=16%  Similarity=0.329  Sum_probs=48.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceE-EEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF-GFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a   79 (79)
                      ..-..|||+||++.+++++|+++|++||.|.++.+...      .+|+ |||+|.+.++|++|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~------~~gfqAFVef~~~~~A~~A   82 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK------NNQFQALLQYADPVSAQHA   82 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE------TTEEEEEEEESCHHHHHHH
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC------CCCcEEEEEECCHHHHHHH
Confidence            44567899999999999999999999999999988654      2577 99999999999865

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.60  E-value=2.3e-15  Score=87.19  Aligned_cols=58  Identities=16%  Similarity=0.228  Sum_probs=51.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCe--eEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGEL--KFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i--~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++||.|  ..+++..+  . +..+|+|||+|.+.++|.+|
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~--~-~~~~g~gfV~f~~~~~A~~A  181 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSG--K-SERSSSGLLEWDSKSDALET  181 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSC--C-SSSSEEEEEECSSHHHHHHH
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcC--C-CCCceEEEEEeCCHHHHHHH
Confidence            45789999999999999999999999998  88888776  3 55679999999999999765

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.58  E-value=5.4e-15  Score=88.38  Aligned_cols=62  Identities=19%  Similarity=0.237  Sum_probs=56.1

Q ss_pred             cCCCCCeEEEeCCCCCC-CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+ ++++|+++|++||.|..+.++.+  .+|.++|+|||+|.+.++|.+|
T Consensus       180 ~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~--~~g~~~g~afV~f~~~~~A~~A  242 (284)
T 3smz_A          180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG--QDGQLKGFAVLEYETAEMAEEA  242 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEEC--SSCCEEEEEEEECSSHHHHHHH
T ss_pred             ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEEC--CCCCcccEEEEEeCCHHHHHHH
Confidence            34567899999999995 99999999999999999999988  6889999999999999999865

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.57  E-value=7.6e-15  Score=79.40  Aligned_cols=52  Identities=15%  Similarity=0.247  Sum_probs=45.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceE-EEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGF-GFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~-~fv~f~~~~~a~~a   79 (79)
                      ..|||+||++.+++++|+++|++||.|..+.+...       .|| |||+|.+.++|+.|
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-------~Gf~aFVef~~~~~A~~A   78 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-------NGIQAMVEFESVLCAQKA   78 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-------SSEEEEEEESSHHHHHHH
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-------CCCEEEEEECCHHHHHHH
Confidence            35789999999999999999999999999988542       276 99999999998765

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.57  E-value=2.3e-15  Score=76.68  Aligned_cols=53  Identities=28%  Similarity=0.538  Sum_probs=47.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++| .|..+.+.       +++|||||+|.+.++|++|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-------~~~g~afV~f~~~~~a~~A   56 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-------RNKRTAFVTLLNGEQAQNA   56 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-------GGGTEEEECCSCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-------CCCcEEEEEECCHHHHHHH
Confidence            56899999999999999999999999 89998874       3579999999999998764

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.57  E-value=4.1e-16  Score=87.46  Aligned_cols=63  Identities=14%  Similarity=0.260  Sum_probs=52.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|.+||.+..+ ++.+. .++.++|||||+|.+.++|++|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~-~~~~~~g~afV~f~~~~~a~~A   70 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDV-RTGTNRKFGYVDFESAEDLEKA   70 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEE-EEETTTTEEEEEESSHHHHHHH
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEEC-CCCccccEEEEEECCHHHHHHH
Confidence            345678999999999999999999999999876653 33333 5788899999999999999865

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

Probab=99.57  E-value=6.8e-15  Score=88.23  Aligned_cols=62  Identities=23%  Similarity=0.486  Sum_probs=54.7

Q ss_pred             CCCCCeEEEeCCCCC-CCHHHHHHHhHhcCCeeEEEeecccCC-CCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVG-SGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+. +++++|+++|++||.|..+.++.+. . +|.++|||||+|.+.++|.+|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~-~~tg~~~g~afV~F~~~~~A~~A  270 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQ-KEHSFNNCCAFMVFENKDSAERA  270 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCC-C---CCCEEEEEEESSHHHHHHH
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecC-CcCCCCceEEEEEeCCHHHHHHH
Confidence            445789999999999 9999999999999999999999884 3 489999999999999999865

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.56  E-value=6.3e-15  Score=87.61  Aligned_cols=58  Identities=24%  Similarity=0.508  Sum_probs=50.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+++++++|+++|++||.|..+.+..+       +|||||+|.+.++|.+|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-------kg~afV~f~~~~~A~~A   74 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-------RGFGFIRLESRTLAEIA   74 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-------TTEEEEECSSHHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-------CcEEEEEECCHHHHHHH
Confidence            33455689999999999999999999999999999988654       59999999999998764

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.55  E-value=7.5e-15  Score=86.93  Aligned_cols=56  Identities=20%  Similarity=0.371  Sum_probs=50.3

Q ss_pred             CCCCCeEEEeCCCCCC---------CHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQA---------KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||..+         ++++|+++|++||.|..|+++..       +|||||+|.+.++|+.|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-------kG~AFV~F~~~~~Ae~A  195 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-------KNCGFVKFKYQANAEFA  195 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-------GTEEEEEESSHHHHHHH
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-------CCEEEEEeCCHHHHHHH
Confidence            4567899999999998         79999999999999999998765       59999999999999865

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.55  E-value=9.7e-15  Score=81.82  Aligned_cols=57  Identities=23%  Similarity=0.556  Sum_probs=50.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+.+++++|+++|++||.|..+    .  .++.++|||||+|.+.++|.+|
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~--~~~~~~g~afV~f~~~~~A~~A  152 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----S--QDGKSKGIAYIEFKSEADAEKN  152 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----C--SSSSCCSEEEEECSSHHHHHHH
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----c--CCCCCceEEEEEECCHHHHHHH
Confidence            3456899999999999999999999999987665    3  6788999999999999999865

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.54  E-value=8.7e-15  Score=83.54  Aligned_cols=55  Identities=20%  Similarity=0.301  Sum_probs=50.0

Q ss_pred             CCCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+ .+++++|+++|++||.|..+.++.++      +|||||+|.+.++|++|
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~------~g~afV~f~~~~~a~~A   57 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK------KENALVQMADGNQAQLA   57 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC------SSCCEEECTTTHHHHHH
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC------CCEEEEEECCHHHHHHH
Confidence            368999999999 99999999999999999999998772      68999999999998764

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=8.3e-14  Score=73.30  Aligned_cols=62  Identities=16%  Similarity=0.104  Sum_probs=51.2

Q ss_pred             CCCCeEEEeCCCC-----CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPF-----QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~-----~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|+|.||..     +-++++|++.|++||.|.++.++.++..++.++|+|||+|.+.++|++|
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~A   72 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKA   72 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHH
Confidence            4578999999963     2368999999999999999999887413467899999999999999865

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

Probab=99.52  E-value=5.2e-14  Score=84.04  Aligned_cols=57  Identities=25%  Similarity=0.364  Sum_probs=50.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||..+++++|+++|++||.|..++++.++      +|||||+|.+.++|.+|
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~------~g~afV~f~~~~~A~~A  260 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR------HDIAFVEFDNEVQAGAA  260 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC------CcEEEEEeCCHHHHHHH
Confidence            3456899999999999999999999999999999998662      58999999999999865

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

Probab=99.51  E-value=4.7e-14  Score=78.67  Aligned_cols=54  Identities=26%  Similarity=0.568  Sum_probs=46.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhc----C-------CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAF----G-------ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++|    |       .|..+.+..       ++|||||+|.+.++|++|
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-------~~g~afV~f~~~~~A~~A   67 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-------DKNFAFLEFRSVDETTQA   67 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-------TTTEEEEEESSHHHHHHH
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-------CCCEEEEEeCCHHHHHHH
Confidence            46899999999999999999999999    6       566665433       469999999999999865

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.49  E-value=6.8e-14  Score=86.45  Aligned_cols=56  Identities=16%  Similarity=0.361  Sum_probs=48.7

Q ss_pred             CCCCCeEEEeC--CCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRN--IPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~n--l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+..+|||+|  |++.+++++|+++|++||.|..+.++.       ++|||||+|.+.++|++|
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-------~kgfaFV~f~~~~~A~~A   72 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-------NKPYSFARYRTTEESKRA   72 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-------TCSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-------CCCEEEEEECCHHHHHHH
Confidence            45568999999  588999999999999999999987743       359999999999999875

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

Probab=99.47  E-value=1.4e-13  Score=78.17  Aligned_cols=54  Identities=24%  Similarity=0.482  Sum_probs=44.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcC-----------CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFG-----------ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g-----------~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||           .|..+.+       +.++|||||+|.+.++|++|
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-------~~~~g~afV~F~~~~~A~~A   67 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-------NQDKNFAFLEFRSVDETTQA   67 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-------ETTTTEEEEEESCSHHHHHH
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-------cCCCCEEEEEeCCHHHHHHH
Confidence            468999999999999999999999994           4444443       44579999999999999865

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.45  E-value=3.1e-13  Score=69.77  Aligned_cols=50  Identities=20%  Similarity=0.373  Sum_probs=42.1

Q ss_pred             CCCeEEEeCCCCCCCHHH----HHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSE----VEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~----l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.|||+|||+.+++++    |+++|++|| .|..|        ++   |+|||.|.+.++|++|
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--------tg---G~AfV~F~~~esA~~A   62 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--------TG---CSAILRFINQDSAERA   62 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--------CT---TCEEEEESSHHHHHHH
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--------ec---CEEEEEECCHHHHHHH
Confidence            344599999999999987    558999995 98886        23   9999999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.45  E-value=1.8e-13  Score=78.04  Aligned_cols=56  Identities=20%  Similarity=0.344  Sum_probs=49.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||..+++++|+++|++|| .|..+.+..+      .+|+|||+|.+.++|.+|
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~------~~g~afV~f~~~~~A~~A  174 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMGSVEEAVQA  174 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST------TSSCEEEECSSHHHHHHH
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC------CCcEEEEEeCCHHHHHHH
Confidence            3478999999999999999999999999 9999988654      268999999999999865

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.44  E-value=2.9e-13  Score=79.07  Aligned_cols=55  Identities=20%  Similarity=0.352  Sum_probs=49.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcC-CeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++|| .|..+.+..+      .+|||||+|.+.++|.+|
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~------~~g~afV~f~~~~~A~~A  205 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK------DRKMALIQMGSVEEAVQA  205 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS------STTCEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC------CCcEEEEEECCHHHHHHH
Confidence            468999999999999999999999999 9999988553      258999999999999864

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.37  E-value=1.2e-13  Score=72.59  Aligned_cols=53  Identities=15%  Similarity=0.290  Sum_probs=43.9

Q ss_pred             EeCCCCCCCHHHHHHHh------------HhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          25 VRNIPFQAKQSEVEELF------------KAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        25 v~nl~~~~~~~~l~~~f------------~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.|||+.+++++|++.|            ++||.|.++.++.+  ..++++|||||+|.+.++|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~--~~~~~~G~~fV~f~~~~~A~~A   84 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN--LGDHLVGNVYVKFRREEDAEKA   84 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS--SSSSSEEEEEEEESCHHHHHHH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeC--CCCCccEEEEEEECCHHHHHHH
Confidence            45677777777776666            99999999999988  4688999999999999999865

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=2.4e-12  Score=68.13  Aligned_cols=59  Identities=15%  Similarity=0.238  Sum_probs=47.2

Q ss_pred             cCCCCCeEEEeCCCCCCC-----------HHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAK-----------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~-----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|+|.||.....           +++|+++|++||.|..+.+ .++    .++|||||+|.+.++|++|
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~----~~~G~afV~f~~~~~A~~A   80 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR----HPDGVASVSFRDPEEADYC   80 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT----CTTCEEEEECSCHHHHHHH
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC----CCCEEEEEEECCHHHHHHH
Confidence            345678999999944432           5799999999999999965 442    2789999999999999865

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.36  E-value=7.4e-12  Score=65.36  Aligned_cols=54  Identities=20%  Similarity=0.201  Sum_probs=43.7

Q ss_pred             CCeEEEeCCC-------CCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIP-------FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~-------~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+|.|.-..       ..+++++|+++|++||.|..+.++.      .++|||||+|.+.++|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~------~~rGfaFVeF~~~~~A~~A   70 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS------KKPGTAVVEFATVKAAELA   70 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES------SSSSEEEEEESCHHHHHHH
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc------CCCCEEEEEECCHHHHHHH
Confidence            4456665433       4589999999999999999998863      4679999999999998764

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.30  E-value=7.5e-12  Score=65.75  Aligned_cols=60  Identities=18%  Similarity=0.305  Sum_probs=48.4

Q ss_pred             CCCeEEEeCC--CCCCC--------HHHHHHHhHhcCCeeEEEeecccCCC--CCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNI--PFQAK--------QSEVEELFKAFGELKFVRLPKKMVGS--GLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl--~~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+.|.+.|+  |....        +++|++.|++||.|.++.++.++ .+  +.++|++||+|.+.++|.+|
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~-~~~~~~~~G~~fV~f~~~~~A~~A   75 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPV-DGVEVPGCGKIFVEFTSVFDCQKA   75 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCB-TTBCCTTTTEEEEEESSHHHHHHH
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccC-CCCCcCCcEEEEEEECCHHHHHHH
Confidence            4678889997  33333        36899999999999999998875 33  36789999999999999875

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.27  E-value=1.6e-11  Score=66.01  Aligned_cols=57  Identities=18%  Similarity=0.276  Sum_probs=49.3

Q ss_pred             ccCCCCCeEEEeCCCCC-CCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecC-HHHHhc
Q psy3346          15 VAKQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT-KNEAKR   78 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~-~~~a~~   78 (79)
                      -.-..++.|||+||++. ++.++|+++|++||.|.+|.+..+.       ..|||.|.+ .++|..
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-------~tgfVrf~~~~~~A~~   71 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-------KEGIILFKEKAKEALG   71 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-------SEEEEEESSCHHHHHH
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-------CEEEEEECCChHHHHH
Confidence            44567899999999999 9999999999999999999998874       249999999 666654

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.24  E-value=1.9e-11  Score=65.49  Aligned_cols=61  Identities=21%  Similarity=0.211  Sum_probs=49.4

Q ss_pred             CCCeEEEeCCCC--CC---CHHHHHHHhHhcCCeeEEEeecccC---CCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPF--QA---KQSEVEELFKAFGELKFVRLPKKMV---GSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~--~~---~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|++.|+-.  ++   -+++|++.|++||.|.++.++.++.   .++.++|++||+|.+.++|.+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~A   87 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKA   87 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHH
Confidence            578999999832  22   3588999999999999999988741   1456789999999999999875

>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=98.91  E-value=5.6e-09  Score=55.52  Aligned_cols=57  Identities=14%  Similarity=0.105  Sum_probs=44.0

Q ss_pred             CCCCeEEEeCCCCCCC----------HHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAK----------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.+.|.+.|+=..-.          +++|++.|++||.|.++.+..+.     .+|++||+|.+.++|++|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~-----~~G~~fV~f~~~e~A~~A   71 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS-----AQGNVYVKCPSIAAAIAA   71 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC-----TTCCEEEECSSHHHHHHH
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC-----CcEEEEEEECCHHHHHHH
Confidence            3466788888733211          25789999999999999886652     489999999999999865

>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=98.53  E-value=1.7e-07  Score=54.28  Aligned_cols=47  Identities=23%  Similarity=0.193  Sum_probs=39.2

Q ss_pred             CHHHHHHHhHhcCCeeEEEeeccc---CCCCCcceEEEEEecCHHHHhcC
Q psy3346          33 KQSEVEELFKAFGELKFVRLPKKM---VGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        33 ~~~~l~~~f~~~g~i~~~~~~~~~---~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+++|.+.|++||.|.++.++.+.   ..++.++|++||+|.+.++|++|
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a  191 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKA  191 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHH
Confidence            457899999999999999987543   14558899999999999998865

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.48  E-value=6.5e-07  Score=45.75  Aligned_cols=54  Identities=24%  Similarity=0.383  Sum_probs=42.3

Q ss_pred             CCCCCeEEEeCCCC----CCCH----HHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPF----QAKQ----SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~----~~~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+++-||+|...+.    +.-.    .+|.+.|.+||.|..++++.++         +||+|.+.++|.+|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~---------~fVtF~d~~sAlaA   65 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK---------MWVTFLEGSSALNV   65 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS---------EEEEESSHHHHHHG
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC---------EEEEECChHHHHHH
Confidence            34567888887662    2333    5789999999999999998872         89999999998765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.23  E-value=7.4e-06  Score=43.21  Aligned_cols=56  Identities=11%  Similarity=0.118  Sum_probs=49.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhc-----CCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAF-----GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~-----g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|-+-|||-.+++..++.+.+++     |.+..+.+..+.       +-|+|+|.+...|-+|
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH-------~GAivef~d~~~AgKa   78 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF-------NGAIIIFRDSKFAAKM   78 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT-------TEEEEECSCHHHHHHH
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC-------CceEEEEccchhhHHH
Confidence            4458899999999999999999999999     999999998873       6699999999888654

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.19  E-value=3.1e-06  Score=43.49  Aligned_cols=54  Identities=17%  Similarity=0.276  Sum_probs=43.2

Q ss_pred             CCCCCeEEEeCCCCC-----C-CH---HHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQ-----A-KQ---SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~-----~-~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+++-||+|..++..     . .+   .+|.+.|.+||.|..+++..++         +||+|.+.++|.+|
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~---------~fVtF~d~~sAl~A   74 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---------MLVTFADSHSALSV   74 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---------EEEECSCSHHHHHH
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc---------EEEEEcChHHHHHH
Confidence            456789999888743     2 21   4688999999999999998872         99999999998764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.96  E-value=2.3e-05  Score=40.46  Aligned_cols=50  Identities=22%  Similarity=0.319  Sum_probs=40.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ....+++ ++|.+....+|.++|++||. -.|+++.|        --|||.|.+++.|..
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidD--------TsAlvvf~~~~~a~~   64 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDD--------TSAFVSLSQPEQVQI   64 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEET--------TEEEEECSCHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcC--------CeEEEEecCHHHHHH
Confidence            3455666 99999999999999999994 46677776        469999999998764

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.92  E-value=8.2e-05  Score=37.97  Aligned_cols=56  Identities=14%  Similarity=0.289  Sum_probs=43.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCC--cceEEEEEecCHHHHh
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL--HRGFGFVEFITKNEAK   77 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~   77 (79)
                      ++|-|++||+..+++++.+.+.....+....+...+ .+.+  .-+-|||.|.+.+++.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~-~s~~~~~~SRaYi~f~~~e~v~   59 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND-TSLYPHMYARAYINFKNQEDII   59 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESC-CSSTTCCCEEEEEEESSSHHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCc-cCCCCCcceEEEEEeCCHHHHH
Confidence            578999999999999999999988877776665543 2222  2356999999988754

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.77  E-value=3.3e-05  Score=39.98  Aligned_cols=47  Identities=26%  Similarity=0.326  Sum_probs=39.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      .+++ ++|.+....+|.++|++|| .-.|.++.|        --|||.|.+++.|..
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD--------TsAlvvf~~~~~a~~   54 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD--------TSAFVSLSQPEQVKI   54 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET--------TEEEEEEEEECHHHH
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC--------CeEEEEecCHHHHHH
Confidence            4555 9999999999999999999 557778777        469999999888754

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.74  E-value=0.00032  Score=36.50  Aligned_cols=52  Identities=19%  Similarity=0.216  Sum_probs=41.2

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHh---c--CCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKA---F--GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~---~--g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ....+|.|.|||+.+.++.|.-+|+.   -  |.|..+....         +-|+|+|.+.+.|++
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---------~~AvItF~d~~va~r   62 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---------CGGVLTFREPADAER   62 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---------TEEEEEESSHHHHHH
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---------CcEEEEEcChHHHHH
Confidence            35789999999999999999999976   2  4677765422         458999999998865

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.54  E-value=5.2e-05  Score=48.71  Aligned_cols=53  Identities=15%  Similarity=0.275  Sum_probs=39.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..+.|+|. .|..+++.+|.++|++||.|.++.+-.++      .-|+.|+|.+.+++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~------g~~~~vef~~~~~~~~  104 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF------GLYAVVEFCQKESIGS  104 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS------SEEEEEECC---CCHH
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC------CeEEEEEeCCHHHHHH
Confidence            35899997 79999999999999999999998876552      2699999999887653

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.30  E-value=0.00028  Score=36.34  Aligned_cols=58  Identities=9%  Similarity=0.200  Sum_probs=39.1

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCC-cceEEEEEecCHHHHh
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL-HRGFGFVEFITKNEAK   77 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~-~~g~~fv~f~~~~~a~   77 (79)
                      .-+|-|+.||+..|++++.+.+.+.-.+....+...+...+. .-.-|||.|.+.++..
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~   67 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDIL   67 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHH
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHH
Confidence            457899999999999998888876655544433333211111 2256899999998754

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.02  E-value=0.0023  Score=34.10  Aligned_cols=55  Identities=13%  Similarity=0.215  Sum_probs=43.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+-|.|-+.|+.. ...+...|++||.|.+.....       ...+-+|.|.++.+|++|
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~-------~~NWihI~Y~s~~~A~rA   75 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN-------TGNWMHIRYQSKLQARKA   75 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS-------SSSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC-------CCCeEEEEeCCHHHHHHH
Confidence            3456788888999985 566788899999998876522       236899999999999875

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.29  E-value=0.0071  Score=31.47  Aligned_cols=54  Identities=13%  Similarity=0.089  Sum_probs=39.6

Q ss_pred             CCCeEEEeCCCCCC-C----HHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQA-K----QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~-~----~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      -+++|+|.||+.++ .    .+.++.+|..|+.+....+...       -.-..|.|.++++|.+|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-------FRRirv~F~~~~~A~~A   62 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-------FKRVRINFSNPLSAADA   62 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-------TTEEEEECSSTTHHHHH
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-------ceEEEEEeCChHHHHHH
Confidence            36789999998876 2    2567899999998777655443       12357899999988754

>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=96.27  E-value=0.0033  Score=34.25  Aligned_cols=27  Identities=19%  Similarity=0.117  Sum_probs=20.4

Q ss_pred             EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          50 VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        50 ~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+..+.   ..++|||||+|.+.++|++|
T Consensus         3 ~kl~ln~---~~~~G~~fV~f~~~~~A~~a   29 (158)
T 2kn4_A            3 YKLILNG---KTLKGETTTEAVDAATAEKV   29 (158)
T ss_dssp             EEEEEEC---SSCEEEEEEECSSHHHHHHH
T ss_pred             EEEEecC---ccccchhHHHHHHHHhHHHH
Confidence            3455542   36889999999999999764

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=94.56  E-value=0.12  Score=33.57  Aligned_cols=49  Identities=22%  Similarity=0.322  Sum_probs=38.2

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ...++++ +|..+...+|.+.|+.||. ..|+++.+        ..|||.|.+.+.|..
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd--------t~a~V~~~~~~~a~~  488 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD--------TSAFVSLSQPEQVQI  488 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS--------SEEEEECSCHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC--------CeEEEEECCHHHHHH
Confidence            3455555 8999999999999999995 46666655        459999999998753

>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=92.99  E-value=0.021  Score=29.60  Aligned_cols=19  Identities=5%  Similarity=0.170  Sum_probs=0.0

Q ss_pred             CCCCeEEEeCCCCCCCHHH
Q psy3346          18 QTGSKILVRNIPFQAKQSE   36 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~   36 (79)
                      ...++|||+|||+++|++.
T Consensus        95 ~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           95 KEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             -------------------
T ss_pred             CCCCceEeCCCCCCccccc
Confidence            3456799999999998763

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=92.64  E-value=0.14  Score=27.74  Aligned_cols=60  Identities=17%  Similarity=0.150  Sum_probs=37.4

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecc-----------cCCCC-CcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKK-----------MVGSG-LHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~-----------~~~~~-~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....|.|-+.|++.+. .+...|++||.|.. .....+           +.... ....|-.|+|.++.+|++|
T Consensus         6 ~e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rA   78 (132)
T 3p3d_A            6 GELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDA   78 (132)
T ss_dssp             --CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHH
T ss_pred             CceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHH
Confidence            4456777788777554 56677999998865 222110           00011 1346889999999999875

---

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	79
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-08
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-08
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	6e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	8e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-06
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	5e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	9e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	9e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-04
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-04
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	0.001
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	0.001
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	0.002
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.002
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	0.003
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.003
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	0.004

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 1e-13
 Identities = 47/62 (75%), Positives = 52/62 (83%)

Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          KQT SKILVRNIPFQA Q E+ ELF  FGELK VRLPKKM G+G HRGFGFV+FITK +A
Sbjct: 5  KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 77 KR 78
          K+
Sbjct: 65 KK 66

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.0 bits (106), Expect = 1e-08
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          K+ +  + +Q  Q  + E F  FGE+K      +   +   RGFGFV F+ +    +V
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECL-VMRDPLTKRSRGFGFVTFMDQAGVDKV 58

>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 = 43.0 bits (101), Expect = 8e-08
 Identities = 11/57 (19%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + V ++     ++ + E F   G +  +R+ + M+ +    G+ +V F    +A+R
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-TRRSLGYAYVNFQQPADAER 57

>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 = 42.6 bits (100), Expect = 1e-07
 Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + + V N+P      +++ +F  +G +       +   +G  RG  FV +  + EA+ 
Sbjct: 6  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN-ILRDKLTGRPRGVAFVRYNKREEAQE 63

>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 = 41.5 bits (97), Expect = 3e-07
 Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          K+LV N+ F    ++++ELF  FG LK   +      SG   G   V F  K +A +
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR--SGRSLGTADVHFERKADALK 56

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.1 bits (96), Expect = 4e-07
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          KI V  +     + ++ E F  FGE++ +        +   RGF F+ F  +   K++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIE-LPMDNKTNKRRGFCFITFKEEEPVKKI 57

>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 = 41.2 bits (96), Expect = 4e-07
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLP--KKMVGSGLHRGFGFVEFITKNEAKRV 79
          + ++N+ F   +  ++ +F   G +K   +   K   G  L  GFGFVE+    +A++ 
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 59

>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 = 41.6 bits (97), Expect = 5e-07
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 1  MGSEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG 60
          M     TV  +     K+   K+ +  + F+  +  +   ++ +G+L       +   S 
Sbjct: 1  MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV-VMRDPASK 59

Query: 61 LHRGFGFVEFITKNEAKRV 79
            RGFGFV F +  E    
Sbjct: 60 RSRGFGFVTFSSMAEVDAA 78

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 6e-07
 Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 8  VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
          VKR     A Q  S ++V  +P++  + +++E F  FGE+  V++ K +  +G  +GFGF
Sbjct: 1  VKR-----AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK-TGHSKGFGF 54

Query: 68 VEFITKNEAKRV 79
          V F       +V
Sbjct: 55 VRFTEYETQVKV 66

>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 = 40.8 bits (95), Expect = 8e-07
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           ++ +  IP   K+ E+ E      E    V +         +RGF FVE+ +   A  
Sbjct: 2  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 60

>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 = 40.6 bits (95), Expect = 9e-07
 Identities = 14/63 (22%), Positives = 32/63 (50%), Gaps = 10/63 (15%)

Query: 17 KQTGSKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
          +   S++ + N+     K+S+VE +F  +G++             +H+GF FV+++ +  
Sbjct: 12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS---------VHKGFAFVQYVNERN 62

Query: 76 AKR 78
          A+ 
Sbjct: 63 ARA 65

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.3 bits (94), Expect = 1e-06
 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 7/65 (10%)

Query: 14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK 73
          N +      +    I        + + F  FG++  +R+          +G+ FV F T 
Sbjct: 12 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP-------EKGYSFVRFSTH 64

Query: 74 NEAKR 78
            A  
Sbjct: 65 ESAAH 69

>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 = 39.7 bits (92), Expect = 2e-06
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 4/61 (6%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPK----KMVGSGLHRGFGFVEFITKNEAK 77
          ++ V NIPF   +  + + F A   L  +          V     + F F+EF + +E  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 78 R 78
          +
Sbjct: 63 Q 63

>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 = 39.3 bits (91), Expect = 2e-06
 Identities = 10/57 (17%), Positives = 25/57 (43%)

Query: 23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          I + N+  +  +  + + F AFG +       +   +G  +G+ F+ F + + +   
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 57

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (93), Expect = 4e-06
 Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          K+ +  + F+     +   F+ +G L    + +    +   RGFGFV + T  E    
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-TKRSRGFGFVTYATVEEVDAA 64

>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 = 38.9 bits (90), Expect = 4e-06
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           + + V  +P    Q E+E+LF  +G +   R+    V     RG GF+ F  + EA+  
Sbjct: 6  DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGV-SRGVGFIRFDKRIEAEEA 64

>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 = 38.1 bits (88), Expect = 5e-06
 Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          + + ++V  +P      E+  LF+A G +   R+ +    +G   G+ FV+F ++ +++R
Sbjct: 1  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-TGYSYGYAFVDFTSEMDSQR 59

Query: 79 V 79
           
Sbjct: 60 A 60

>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 = 38.5 bits (89), Expect = 7e-06
 Identities = 11/64 (17%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKN 74
          +  +    + +RN+P++    E+ ++F  +G ++      ++  +   RG  +V +    
Sbjct: 2  LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ----IRVGNTPETRGTAYVVYEDIF 57

Query: 75 EAKR 78
          +AK 
Sbjct: 58 DAKN 61

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 8e-06
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          K+ +  + +   + ++++ F  FGE+    L    + +G  RGFGFV F       +V
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI-TGRSRGFGFVLFKESESVDKV 57

>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 = 37.6 bits (87), Expect = 1e-05
 Identities = 14/62 (22%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 77
          +    + V N+ F   + ++ ELF   G++K + +    +      GF FVE+ ++ +A+
Sbjct: 5  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-KKTACGFCFVEYYSRADAE 63

Query: 78 RV 79
            
Sbjct: 64 NA 65

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 1e-05
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          K+ +  + F+     +   F+ +G L       +   +   RGFGFV + T  E    
Sbjct: 8  KLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDPNTKRSRGFGFVTYATVEEVDAA 64

>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 = 3e-05
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          K+ +  +P      +V+EL  +FG LK      K   +GL +G+ F E++  N   +
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFN-LVKDSATGLSKGYAFCEYVDINVTDQ 58

>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 = 35.9 bits (82), Expect = 5e-05
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + ++V  +P    Q E   LF + GE++  +L +  + +G   G+GFV +I   +A++ 
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-TGQSLGYGFVNYIDPKDAEKA 60

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.5 bits (81), Expect = 5e-05
 Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          KI V  +       +V+  F+ FG++           +  HRGFGFV F +++  ++V
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAM-LMFDKTTNRHRGFGFVTFESEDIVEKV 57

>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 = 35.0 bits (80), Expect = 9e-05
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 13 SNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFIT 72
          ++  K   + I V+N+PF     E+ + F  +  +      K     G+  G   V F +
Sbjct: 2  ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFES 60

Query: 73 KNEAKR 78
          ++EA  
Sbjct: 61 RDEATA 66

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.8 bits (79), Expect = 9e-05
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + +LV+N+P    Q++V + FK  G +  V +   +     +  F  +EF   + A   
Sbjct: 1  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK---NFRFARIEFARYDGALAA 56

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 6/59 (10%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          S + V        + E+ E F  +G++  V +PK        R F FV F     A+ +
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP------FRAFAFVTFADDQIAQSL 58

>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 = 34.9 bits (80), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 7/59 (11%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          S++ V N+P    + E+ +LF+ +G           V     +GFGF+   T+  A+  
Sbjct: 9  SRLFVGNLPPDITEEEMRKLFEKYG-------KAGEVFIHKDKGFGFIRLETRTLAEIA 60

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 2e-04
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
          K     I ++N+        + + F AFG +   ++     GS  +    FV F T+  A
Sbjct: 5  KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYG---FVHFETQEAA 61

Query: 77 KRV 79
          +R 
Sbjct: 62 ERA 64

>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 = 34.6 bits (79), Expect = 2e-04
 Identities = 8/57 (14%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
          +I+V N+ +      + ++F  FG +  +    K      ++    +++     A+ 
Sbjct: 9  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQH 60

>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 = 34.6 bits (79), Expect = 2e-04
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
           + V  +  +  +  + ELF   G +       K   +G H+G+GFVEF+++ +A   
Sbjct: 11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTH-MPKDRVTGQHQGYGFVEFLSEEDADYA 67

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 3e-04
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           +    +  + +  ++E+ F A G+++ VR+      S   +G  +VEF        
Sbjct: 20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-SRRSKGIAYVEFCEIQSVPL 75

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.5 bits (76), Expect = 4e-04
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
             + V  +     + ++ E+F  +G +  V +      S   RGF FV F   ++AK 
Sbjct: 9  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-SRRSRGFAFVYFENVDDAKE 66

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.6 bits (76), Expect = 6e-04
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 3/67 (4%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
           S+    TG  + +R +P++A ++++   F     ++           G   G   VEF 
Sbjct: 7  GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD---GRVTGEADVEFA 63

Query: 72 TKNEAKR 78
          T  +A  
Sbjct: 64 THEDAVA 70

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.8 bits (74), Expect = 6e-04
 Identities = 8/57 (14%), Positives = 21/57 (36%), Gaps = 1/57 (1%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + + N P    Q  + +L +    +         +     R F +++  +K +A+ 
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSI-RLPSLRFNTSRRFAYIDVTSKEDARY 58

>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 = 33.1 bits (75), Expect = 6e-04
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 4/64 (6%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
          A     +I V N+P   +  ++E++F  +G ++ + L  +         F FVEF    +
Sbjct: 10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG----GPPFAFVEFEDPRD 65

Query: 76 AKRV 79
          A+  
Sbjct: 66 AEDA 69

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.7 bits (74), Expect = 0.001
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
          +K T  ++ V NIPF+ +  ++ ++F  F     +   + +      +GFGFV F    +
Sbjct: 7  SKSTPKRLHVSNIPFRFRDPDLRQMFGQF---GKILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 76 AKRV 79
          A R 
Sbjct: 64 ADRA 67

>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 = 32.3 bits (73), Expect = 0.001
 Identities = 13/57 (22%), Positives = 22/57 (38%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           I + N+  + K+ E+++   A        L   +  S   RG  FV F   + A  
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.6 bits (71), Expect = 0.002
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV 79
          + I V N+    ++++++ELF+ FG +  +    K   +G  +GF F+ F  + +A R 
Sbjct: 9  ATIRVTNLSEDTRETDLQELFRPFGSISRIY-LAKDKTTGQSKGFAFISFHRREDAARA 66

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.2 bits (70), Expect = 0.002
 Identities = 8/55 (14%), Positives = 21/55 (38%), Gaps = 7/55 (12%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 75
          +K+ + N+       ++ +LF         ++           G+ FV++  +N 
Sbjct: 2  NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNW 49

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.7 bits (71), Expect = 0.003
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 76
                + +R +PF   + E+ + F     +            G   G  FV+F ++  A
Sbjct: 12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIA 70

Query: 77 KRV 79
          ++ 
Sbjct: 71 EKA 73

>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 = 31.6 bits (71), Expect = 0.003
 Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           ++ VRN+ + + + ++E+LF A+G L  +  P   +     +GF FV F+    A +
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKK-PKGFAFVTFMFPEHAVK 65

>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 = 31.2 bits (70), Expect = 0.003
 Identities = 13/71 (18%), Positives = 36/71 (50%), Gaps = 6/71 (8%)

Query: 8  VKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 67
          ++   ++   +    +L +N+ F   + E++E+F+   E++ V         G  +G  +
Sbjct: 4  LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQD------GKSKGIAY 57

Query: 68 VEFITKNEAKR 78
          +EF ++ +A++
Sbjct: 58 IEFKSEADAEK 68

>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 = 31.2 bits (70), Expect = 0.003
 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 3/57 (5%)

Query: 22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 78
           + V N+     +  + +LF   G  K  +    +     +  + FVEF    +A  
Sbjct: 10 TLYVGNLSRDVTEVLILQLFSQIGPCKSCK---MITEHTSNDPYCFVEFYEHRDAAA 63

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.9 bits (69), Expect = 0.004
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 12 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 71
           S + K       + N+P+   +  ++E F+       VRLP++       +GFG+ EF 
Sbjct: 7  GSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNI-SAVRLPREPSNPERLKGFGYAEFE 65

Query: 72 TKNEAKRV 79
            +     
Sbjct: 66 DLDSLLSA 73

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	79
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.88
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.87
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.87
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.86
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.86
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.86
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.85
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.84
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.84
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.83
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.83
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.81
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.81
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.8
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.79
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.76
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.76
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.76
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.75
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.74
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.73
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.73
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.72
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.72
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.71
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.67
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.66
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.61
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.61
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.6
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.46
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.43
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.19
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.08
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.09
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.41
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	94.76
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	87.77

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=8.4e-23  Score=104.14  Aligned_cols=62  Identities=31%  Similarity=0.666  Sum_probs=57.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|..++++.++ .+|.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~srG~aFV~f~~~~~a~~a   66 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDL-KTGHSKGFGFVRFTEYETQVKV   66 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHH
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCC-CCcccCCEEEEEECCHHHHHHH
Confidence            3457899999999999999999999999999999999987 7899999999999999999764

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.8e-22  Score=101.75  Aligned_cols=61  Identities=21%  Similarity=0.445  Sum_probs=56.5

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|++|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~kG~afV~f~~~~~a~~a   64 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP-NTKRSRGFGFVTYATVEEVDAA   64 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccc-cCCCcccEEEEEEcCHHHHHHH
Confidence            345799999999999999999999999999999999987 7899999999999999998764

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.1e-22  Score=100.68  Aligned_cols=57  Identities=28%  Similarity=0.582  Sum_probs=54.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+++++++|+++|++||.|..++++.++ .+++++|||||+|.+.++|++|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~-~t~~~rG~~FV~f~~~~~a~~a   57 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN-KTNKRRGFCFITFKEEEPVKKI   57 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCT-TTCCTTCCEEEEESSSHHHHHH
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccc-cccccccEEEEEECCHHHHHHH
Confidence            58999999999999999999999999999999987 8899999999999999998764

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.4e-22  Score=103.57  Aligned_cols=62  Identities=26%  Similarity=0.567  Sum_probs=57.2

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +...++|||+|||+.+++++|+++|++||.|.++.++.++ .+|.++|||||+|.+.++|++|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~kg~afV~f~~~~~A~~A   68 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDR-QTGKSRGYGFVTMADRAAAERA   68 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCS-SSCCCCSEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccc-cccccCCeEEEEECCHHHHHHH
Confidence            4456789999999999999999999999999999999987 7899999999999999999865

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1e-22  Score=106.05  Aligned_cols=61  Identities=21%  Similarity=0.454  Sum_probs=56.3

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+++++++|+++|.+||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        18 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~-~~~~~kg~aFV~f~~~~~a~~a   78 (103)
T d1x4ba1          18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP-ASKRSRGFGFVTFSSMAEVDAA   78 (103)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCT-TTSSCCSEEEEECSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccc-cCCCccCeEEEEECCHHHHHHH
Confidence            345899999999999999999999999999999999987 7889999999999999999864

>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=99.87  E-value=5.3e-22  Score=100.71  Aligned_cols=63  Identities=27%  Similarity=0.482  Sum_probs=57.5

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++++|||+|||+++++++|+++|++||.|..++++.++ .+|.++|||||+|.+.++|++|
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~-~tg~~~g~afV~f~~~~~A~~A   65 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAA   65 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTSSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccc-cccccccceeEEECCHHHHHHH
Confidence            34568899999999999999999999999999999999987 7899999999999999999865

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3.5e-22  Score=98.72  Aligned_cols=57  Identities=26%  Similarity=0.549  Sum_probs=54.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+++++++|+++|++||.|..+.++.++ .+++++|||||+|.+.++|++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~-~t~~~kg~afV~f~~~~~a~~A   57 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDP-ITGRSRGFGFVLFKESESVDKV   57 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBT-TTTBCCSEEEEEESSHHHHHHH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCC-CCCCcCceEEEEECCHHHHHHH
Confidence            58999999999999999999999999999999987 8899999999999999998865

>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=99.86  E-value=6.5e-22  Score=101.28  Aligned_cols=63  Identities=25%  Similarity=0.497  Sum_probs=57.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..+.++|||+|||+.+++++|+++|++||.|.+++++.++ .+|.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~-~tg~~kg~afV~f~~~~~A~~A   67 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-VTGQHQGYGFVEFLSEEDADYA   67 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCSBCSCEEEEESSHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecc-cccccccceEEEECCHHHHHHH
Confidence            34456899999999999999999999999999999999987 7899999999999999999865

>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=99.86  E-value=4.3e-22  Score=99.73  Aligned_cols=59  Identities=24%  Similarity=0.577  Sum_probs=55.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +++|||+|||+++++++|+++|++||.|..++++.++ .+|.++|||||+|.++++|++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~~g~~~g~afV~f~~~~~A~~a   60 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-KTGYSYGYAFVDFTSEMDSQRA   60 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET-TTTEECSEEEEEESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec-ccCCccccceEEECCHHHHHHH
Confidence            5789999999999999999999999999999999887 7899999999999999999865

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=7.3e-23  Score=101.73  Aligned_cols=58  Identities=29%  Similarity=0.551  Sum_probs=54.8

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |+|||+|||+++++++|+++|++||.|..+.++.++ .+|+++|||||+|.+.++|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~kG~aFV~f~~~~~a~~a   58 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP-LTKRSRGFGFVTFMDQAGVDKV   58 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCC-CSSSCSSEEEECCCCTTHHHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeeccc-CCCCccceEEEEECCHHHHHHH
Confidence            689999999999999999999999999999999987 8899999999999999998764

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8.1e-22  Score=99.43  Aligned_cols=60  Identities=28%  Similarity=0.542  Sum_probs=56.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+++|||+|||+.+++++|+++|++||.|.+++++.++ .+|.++|||||+|.+.++|++|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~g~~kg~afV~f~~~~~a~~A   64 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ-VTGVSRGVGFIRFDKRIEAEEA   64 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccccc-ccccCCCeeEEEEcCHHHHHHH
Confidence            46789999999999999999999999999999999987 7899999999999999999865

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.86  E-value=8.2e-22  Score=99.37  Aligned_cols=61  Identities=20%  Similarity=0.444  Sum_probs=56.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+++++++|+++|++||.|..++++.++ .+|.++|||||+|.+.++|++|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~-~~g~~~g~afV~f~~~~~A~~A   64 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK-LTGRPRGVAFVRYNKREEAQEA   64 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeeccc-ccccCceeEEEEECCHHHHHHH
Confidence            456789999999999999999999999999999999987 7899999999999999999865

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=6.3e-22  Score=99.37  Aligned_cols=60  Identities=23%  Similarity=0.382  Sum_probs=55.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+.+++++|+++|++||.|.++.++.++ .++.++|||||+|.+.++|++|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~-~~~~~~g~afV~f~~~~~A~~A   67 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-QSRRSRGFAFVYFENVDDAKEA   67 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECS-SSSSEEEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccc-cccccccceEEEECCHHHHHHH
Confidence            46789999999999999999999999999999999887 7899999999999999999865

>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=99.86  E-value=1.6e-21  Score=100.02  Aligned_cols=63  Identities=75%  Similarity=1.166  Sum_probs=56.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|..++++.+...+|.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~A   67 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA   67 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHH
Confidence            446788999999999999999999999999999999887535789999999999999999865

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=3.5e-22  Score=103.68  Aligned_cols=60  Identities=18%  Similarity=0.389  Sum_probs=55.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+.+++++|+++|+.||.|..++++.++ .+|+++|||||+|.+.++|++|
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~-~tg~~kG~afV~F~~~e~a~~A   76 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR-NSRRSKGIAYVEFCEIQSVPLA   76 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSC-CSSSCCCCEEEEESCGGGHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecC-CCccccceEEEEECCHHHHHHH
Confidence            35789999999999999999999999999999999987 7899999999999999998764

>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=99.85  E-value=1.7e-21  Score=99.71  Aligned_cols=61  Identities=23%  Similarity=0.431  Sum_probs=56.9

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+++++++|+++|++||.|.++.++.++ .++.++|||||+|.+.++|+.|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~-~~~~~kg~afV~f~~~~~A~~A   65 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKKTACGFCFVEYYSRADAENA   65 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceecccccc-ccccccceEEEEECCHHHHHHH
Confidence            457899999999999999999999999999999999987 7899999999999999999865

>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=99.85  E-value=2.1e-21  Score=96.89  Aligned_cols=57  Identities=19%  Similarity=0.348  Sum_probs=53.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .|||+|||+.+++++|+++|++||.|.+++++.++ .+|.++|||||+|.++++|..|
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~-~tg~~~g~aFV~f~~~~~a~~a   58 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM-ITRRSLGYAYVNFQQPADAERA   58 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecc-cccCCCCceEEEECCHHHHHHH
Confidence            69999999999999999999999999999999987 7899999999999999999764

>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=99.85  E-value=1.2e-21  Score=99.72  Aligned_cols=62  Identities=27%  Similarity=0.607  Sum_probs=57.1

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||.++++++|+++|++||.|..++++.++ .+|.++|||||+|.+.++|++|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~-~t~~~rg~afV~f~~~~~A~~A   66 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-TTGQSKGFAFISFHRREDAARA   66 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECS-SSCSEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccc-cccccccceeEEECCHHHHHHH
Confidence            4456799999999999999999999999999999999987 7899999999999999999865

>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=99.85  E-value=3.9e-21  Score=96.14  Aligned_cols=59  Identities=27%  Similarity=0.576  Sum_probs=54.9

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+++++++|+++|++||.|..++++.+. .++.++|||||+|.+.++|++|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~-~~~~~~g~afv~f~~~~~a~~a   60 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-ITGQSLGYGFVNYIDPKDAEKA   60 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeec-cCCCceeeEEEEECCHHHHHHH
Confidence            4679999999999999999999999999999999886 7889999999999999999865

>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=99.84  E-value=9.8e-22  Score=99.86  Aligned_cols=60  Identities=25%  Similarity=0.468  Sum_probs=56.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||.|.++.++.++ .+|.++|||||+|.+.++|++|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~~~~~kg~afV~f~~~~~A~~a   63 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAA   63 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCS-SSCCCSSEEEECCSSHHHHHHH
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEeccccccc-ccccccceeEEEECCHHHHHHH
Confidence            45799999999999999999999999999999999987 7899999999999999998864

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=4.7e-21  Score=98.56  Aligned_cols=63  Identities=25%  Similarity=0.618  Sum_probs=57.2

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+++++++|+++|++||.+..+.++.++ .++.++|||||+|.+.++|.+|
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~-~~~~~~g~afV~F~~~~~a~~a   66 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP-DTEHSKGCAFAQFMTQEAAQKC   66 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCS-SSCCBCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeecccc-ccccccceEEEEEcCHHHHHHH
Confidence            34567899999999999999999999999999999998886 7888999999999999998764

>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=99.84  E-value=4.8e-21  Score=99.45  Aligned_cols=61  Identities=18%  Similarity=0.420  Sum_probs=56.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +++++|||+|||+++++++|+++|++||.|..+.++.++ .+|.++|||||+|.+.++|+.|
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~-~~g~~kG~afV~f~~~~~A~~A   76 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK-QTNLSKCFGFVSYDNPVSAQAA   76 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECS-SSCSEEEEEEEECSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeec-ccCCCccceEEEeCCHHHHHHH
Confidence            456889999999999999999999999999999998887 7899999999999999999864

>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=99.84  E-value=5.1e-21  Score=98.80  Aligned_cols=61  Identities=26%  Similarity=0.565  Sum_probs=56.2

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|.+||.|..++++.++ .+++++|||||+|.+.++|++|
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~-~tg~~~g~afV~f~~~~~a~~A   66 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDS-LTKKPKGFAFVTFMFPEHAVKA   66 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCT-TTCCCCSEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccc-cccccCcceEEEECCHHHHHHH
Confidence            346689999999999999999999999999999999987 7899999999999999998764

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5e-21  Score=99.20  Aligned_cols=64  Identities=25%  Similarity=0.556  Sum_probs=57.4

Q ss_pred             cccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          14 NVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        14 ~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....+.++|||+|||+++++++|+++|++||.|..+.+..+  .++.++|||||+|.+.++|++|
T Consensus        12 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~--~~~~~~g~afV~f~~~~~A~~A   75 (101)
T d1x5oa1          12 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD--SSGTSRGVGFARMESTEKCEAV   75 (101)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSCEEEEEEEEESCHHHHHHH
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc--cccccccceeEEeCCHHHHHHH
Confidence            344556789999999999999999999999999999998887  6788999999999999999865

>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=99.84  E-value=2.3e-21  Score=97.74  Aligned_cols=58  Identities=29%  Similarity=0.607  Sum_probs=54.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+|||+|||+.+++++|+++|++||+|..++++.++ .+|.++|||||+|.++++|+.|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~-~tg~~rg~aFV~f~~~~~A~~a   59 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS-ATGLSKGYAFCEYVDINVTDQA   59 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCC-SSSCCCCEEEEEESSSHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccc-cccccceeEEEEECCHHHHHHH
Confidence            379999999999999999999999999999999987 8899999999999999999764

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.1e-21  Score=102.05  Aligned_cols=60  Identities=25%  Similarity=0.540  Sum_probs=55.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++ .+|+++|||||+|.+.++|++|
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~-~tg~~~g~afV~f~~~~~a~~a   66 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR-ETGKPKGYGFCEYQDQETALSA   66 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEET-TTTEEEEEEEEECSCHHHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcccccccccccccc-ceeccCCceEEEECCHHHHHHH
Confidence            45789999999999999999999999999999999887 7899999999999999999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.5e-21  Score=94.53  Aligned_cols=59  Identities=25%  Similarity=0.572  Sum_probs=54.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.+++++++|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~e~~~~a   60 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVDKI   60 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCC-CCcccccEEEEEEcCHHHHHHH
Confidence            4789999999999999999999999999999999887 7889999999999999988764

>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=99.83  E-value=8.3e-21  Score=103.06  Aligned_cols=60  Identities=23%  Similarity=0.512  Sum_probs=55.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||.|.++.++.++ .+|+++|||||+|.+.++|++|
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~t~~~rg~afV~f~~~~~A~~A  100 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR-ETRQSRGYGFVKFQSGSSAQQA  100 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEET-TTTEEEEEEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhcccccccccccc-ccccccceeeEEECCHHHHHHH
Confidence            34789999999999999999999999999999999887 7899999999999999999865

>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=99.83  E-value=6.4e-21  Score=96.88  Aligned_cols=61  Identities=28%  Similarity=0.559  Sum_probs=55.8

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+..+|||+|||+++++++|+++|++||.|..+.++.++ .++.++|||||+|.++++|+.|
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~-~~~~~~g~afV~f~~~~~a~~A   63 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENIDDAKDA   63 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCS-SSCSCCSEEEEECSSHHHHHHH
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeecccc-ccccccceEEEEECCHHHHHHH
Confidence            356789999999999999999999999999999988876 7899999999999999999864

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=8.1e-21  Score=95.74  Aligned_cols=59  Identities=17%  Similarity=0.327  Sum_probs=54.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.+  .++.++|||||+|.+.++|++|
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~--~~~~~kG~afV~f~~~e~a~~a   63 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT--LHKAFKGSIFVVFDSIESAKKF   63 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC--TTCCEEEEEEEEESCHHHHHHH
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee--ccCCcceEEEEEEcCHHHHHHH
Confidence            4679999999999999999999999999999999887  6889999999999999999865

>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=99.83  E-value=7.8e-21  Score=94.40  Aligned_cols=56  Identities=34%  Similarity=0.508  Sum_probs=52.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+++++++|+++|++||.|..++++.+  .+++++|||||+|.+.++|++|
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~--~~g~~~g~afV~f~~~~~A~~A   57 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD--RSGRSLGTADVHFERKADALKA   57 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCS--SCCCSCCEEEEEESCHHHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEe--eccccceeEEEEECCHHHHHHH
Confidence            6999999999999999999999999999999988  6899999999999999999865

>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=99.82  E-value=7.7e-21  Score=94.92  Aligned_cols=59  Identities=14%  Similarity=0.295  Sum_probs=47.9

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+++++++|+++|++||.|..+.++.+. .+|.++|||||+|.+.++|++|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~~g~afV~f~~~e~A~~A   59 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSL-RFNTSRRFAYIDVTSKEDARYC   59 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHH
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeeccc-ccccccceeEEEECCHHHHHHH
Confidence            3799999999999999999999999999888776665 7889999999999999999865

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.6e-20  Score=94.13  Aligned_cols=61  Identities=20%  Similarity=0.308  Sum_probs=53.8

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..++++|||+|||+++++++|+++|++||.|..+.++.++ .+  .+|||||+|.+.++|++|
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~-~~--~~~~afV~f~~~~~A~~A   64 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH-TS--NDPYCFVEFYEHRDAAAA   64 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC-CS--SCCEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeeccc-Cc--cceeeEEEECCHHHHHHH
Confidence            34567899999999999999999999999999999998874 33  379999999999999865

>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=99.81  E-value=3.4e-20  Score=93.57  Aligned_cols=62  Identities=23%  Similarity=0.464  Sum_probs=51.2

Q ss_pred             CCCCeEEEeCCCCCCC-HHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAK-QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~-~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||++++ +++|+++|++||.|..++++.+...++.++|||||+|.+.++|++|
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~A   64 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA   64 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHH
Confidence            3578999999999976 5669999999999999998764326788999999999999999865

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.3e-20  Score=94.46  Aligned_cols=60  Identities=23%  Similarity=0.321  Sum_probs=53.4

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCC-eeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGE-LKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|+|||+|||.++++++|+++|++||. |..+.++.+...+++++|||||+|.++++|..|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~A   61 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA   61 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHH
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHH
Confidence            468999999999999999999999995 899999887424688999999999999998764

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.8e-20  Score=91.02  Aligned_cols=56  Identities=16%  Similarity=0.416  Sum_probs=52.9

Q ss_pred             EEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        23 l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |||+|||+++++++|+++|++||.|..+++..++ .++.++|||||+|.+.++|++|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~-~~~~~~g~afV~f~~~~~A~~A   56 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDK-TTNKCKGYGFVDFDSPSAAQKA   56 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCS-SSCSCCSEEEEEESCHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhcccccccccccc-ccccccceeEEEECCHHHHHHH
Confidence            7999999999999999999999999999998887 7899999999999999999875

>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=99.81  E-value=5.3e-20  Score=92.55  Aligned_cols=56  Identities=27%  Similarity=0.618  Sum_probs=50.1

Q ss_pred             EEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCC---CcceEEEEEecCHHHHhcC
Q psy3346          23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG---LHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        23 l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~---~~~g~~fv~f~~~~~a~~a   79 (79)
                      |||+|||+++++++|+++|++||.|.++.++.++ .++   .++|||||+|.+.++|++|
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~~~~~~~~kG~afV~f~~~~~A~~A   59 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKK-NKAGVLLSMGFGFVEYKKPEQAQKA   59 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEE-CTTCCEEEEEEEEEEESSHHHHHHH
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceeccc-ccccccccceEEEEEECCHHHHHHH
Confidence            7999999999999999999999999999998775 333   4689999999999998864

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=4.1e-20  Score=90.93  Aligned_cols=57  Identities=30%  Similarity=0.546  Sum_probs=53.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+++++++|+++|++||.+..+.++.++ .++.++|||||+|.+.++|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~-~~~~~~~~afV~F~~~~~a~~a   57 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDK-TTNRHRGFGFVTFESEDIVEKV   57 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCT-TCTTSCCEEEEECSCHHHHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeec-cccccCceeEEEECCHHHHHHH
Confidence            58999999999999999999999999999998886 7889999999999999998764

>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=99.80  E-value=2.1e-19  Score=91.75  Aligned_cols=62  Identities=31%  Similarity=0.561  Sum_probs=54.5

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|++||.|..+.++.++   +.++|||||+|.+.++|++|
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~---~~~kg~afV~f~~~~~a~~A   67 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE---RGSKGFGFVTFENSADADRA   67 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT---TTTCCEEEEEESCHHHHHHH
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc---cCCcceeEEEECCHHHHHHH
Confidence            344567899999999999999999999999999999998873   33689999999999999865

>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=99.80  E-value=1.4e-19  Score=95.22  Aligned_cols=58  Identities=21%  Similarity=0.486  Sum_probs=52.0

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...++|||+|||+.+++++|+++|++||.|..|++..+    +.++|||||+|.+.++|..|
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~----~~~kG~afV~f~~~~~A~~A   62 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT----PETRGTAYVVYEDIFDAKNA   62 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS----TTTTTEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc----CCcCCeEEEEECCHHHHHHH
Confidence            35689999999999999999999999999999998765    45689999999999999865

>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=99.79  E-value=9.5e-20  Score=92.37  Aligned_cols=58  Identities=24%  Similarity=0.449  Sum_probs=52.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+|||+|||+++++++|+++|++||.|..++++.++   +.++|||||+|.+.++|++|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~---~~~kg~afV~f~~~~~A~~A   64 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE---NGSKGYGFVHFETQEAAERA   64 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT---TBCCSCEEEEESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec---CCCcceeEEEECCHHHHHHH
Confidence            34579999999999999999999999999999998873   44789999999999999865

>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=99.79  E-value=5.4e-20  Score=92.15  Aligned_cols=56  Identities=18%  Similarity=0.435  Sum_probs=50.6

Q ss_pred             EEEeCCCCCCCHHHHHHHhHhcCCeeEE-EeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          23 ILVRNIPFQAKQSEVEELFKAFGELKFV-RLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        23 l~v~nl~~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |||+|||+++++++|+++|++||.|..+ .++.++ .+|+++|||||+|.+.++|++|
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~-~~g~~~g~afV~f~~~~~a~~A   57 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP-DTGNSKGYAFINFASFDASDAA   57 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCT-TTCSCCSEEEEEBSSHHHHHHH
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeec-cccccCceEEEEECCHHHHHHH
Confidence            7999999999999999999999998654 677776 7899999999999999999865

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.79  E-value=1.9e-19  Score=88.77  Aligned_cols=56  Identities=25%  Similarity=0.395  Sum_probs=50.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+++++++|+++|++||.|..++++.++  . ..++||||+|.+.++|++|
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~--~-~~~~~afV~F~~~~~a~~A   56 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--K-KNFRFARIEFARYDGALAA   56 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT--T-SSSEEEEEEESSHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeec--c-ccceEEEEEEcchHHhHHH
Confidence            589999999999999999999999999999998874  3 3458999999999999875

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.8e-19  Score=92.80  Aligned_cols=61  Identities=21%  Similarity=0.512  Sum_probs=52.5

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+++++++|+++|++|| +..+.++.+...++.++|||||+|.+.++|++|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~   73 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA   73 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHH
Confidence            3468999999999999999999999998 777777765425788999999999999998753

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.78  E-value=1.2e-20  Score=96.22  Aligned_cols=61  Identities=15%  Similarity=0.278  Sum_probs=54.8

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||+++++++|+++|++||.|..+.++.+  .+|+++|||||+|.+.++|++|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~--~~g~~kg~afv~F~~~e~a~~A   70 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV--RTGTNRKFGYVDFESAEDLEKA   70 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE--EEETTTTEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec--CCCCccEEeEEeeCCHHHHHHH
Confidence            445679999999999999999999999999988888765  6899999999999999998865

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.6e-19  Score=92.05  Aligned_cols=64  Identities=17%  Similarity=0.256  Sum_probs=53.9

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +...+..+|||+|||+++++++|+++|..+|.+....++... .++.++|||||+|.++++|++|
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~-~~~~~kG~afV~F~~~e~a~~a   73 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKA   73 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHH
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeC-CCCCcceEEEEEeCCHHHHHHH
Confidence            334566789999999999999999999999988775444444 7889999999999999999764

>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=99.78  E-value=3.2e-19  Score=92.04  Aligned_cols=64  Identities=19%  Similarity=0.277  Sum_probs=54.3

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCee--------EEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK--------FVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.++|||+|||+.+++++|+++|++||.|.        .+.+..++ .+|.++|||||+|.+.++|++|
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~-~~~~~~g~afV~f~~~~~a~~A   74 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK-ETGKPKGDATVSYEDPPTAKAA   74 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCT-TTCSBCSEEEEEBSSHHHHHHH
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeecc-ccccccceeeEEecCHHHHHHH
Confidence            3456688999999999999999999999999874        34555555 6789999999999999998864

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.6e-18  Score=88.69  Aligned_cols=60  Identities=25%  Similarity=0.491  Sum_probs=52.3

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.+..+    +.++|||||+|.+.++|+.|
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~----~~~~g~afV~f~~~e~a~~A   69 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR----RGGPPFAFVEFEDPRDAEDA   69 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS----SSSSCCEEEEESCHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc----ccccceEEEEECCHHHHHHH
Confidence            3556789999999999999999999999999999887554    45679999999999999864

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.7e-19  Score=94.81  Aligned_cols=64  Identities=23%  Similarity=0.374  Sum_probs=53.5

Q ss_pred             ccCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          15 VAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        15 ~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ......++|||+|||+.+++++|+++|+.||.+..+.++.+. .+|.++|||||+|.+.++|++|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~-~~g~~~G~afVeF~~~e~a~~a   76 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-PNGKATGEGFVEFRNEADYKAA   76 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-TTSSEEEEEEEEBSSSHHHHHH
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecC-cccceeeEEEEEECCHHHHHHH
Confidence            334567899999999999999999999999987664444333 6899999999999999999764

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.76  E-value=2e-18  Score=86.39  Aligned_cols=57  Identities=25%  Similarity=0.428  Sum_probs=50.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++.++|||+|||..+++++|.++|++||.|..+++..+      .+|||||+|.+.++|++|
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~------~~g~afV~f~~~~~A~~A   61 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN------RHDIAFVEFTTELQSNAA   61 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT------TCSCEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc------cceeEEEecCCHHHHHHH
Confidence            344689999999999999999999999999999998665      258999999999999865

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=7.7e-19  Score=90.95  Aligned_cols=61  Identities=23%  Similarity=0.372  Sum_probs=53.5

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+.+|||+|||+++++++|+++|..|| +..+.++.+  .++.++|||||+|.+.++|++|
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~--~~g~~~G~afVeF~~~~~a~~A   71 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG--PDGRVTGEADVEFATHEDAVAA   71 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES--SSSCEEEEEEEECSSSHHHHHH
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe--cCCcceEEEEEEECCHHHHHHH
Confidence            345678999999999999999999999998 557777777  5789999999999999999865

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=6e-19  Score=89.44  Aligned_cols=61  Identities=20%  Similarity=0.311  Sum_probs=52.1

Q ss_pred             CCCCeEEEeCCCCCCCHHHH---HHHhHhcCCeeEEEeecccCCCCC---cceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEV---EELFKAFGELKFVRLPKKMVGSGL---HRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l---~~~f~~~g~i~~~~~~~~~~~~~~---~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+.+++++|   .++|++||.|..+.++.++ .++.   .+|||||+|.+.++|++|
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~-~~~~~~~~~g~aFV~f~~~~~A~~A   72 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNST-SYAGSQGPSASAYVTYIRSEDALRA   72 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCS-SCCSSSCCCEEEEEEESSHHHHHHH
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeecc-CcCCCCCcceEEEEecccchhHHHH
Confidence            35678999999999999999   6789999999999998876 4433   459999999999999875

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.3e-18  Score=88.31  Aligned_cols=55  Identities=20%  Similarity=0.410  Sum_probs=50.3

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..++|||+|||..+++++|+++|++||.|.+++++.+       +|||||+|.+.++|++|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-------kg~afV~f~~~~~A~~A   70 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-------KGYSFVRFSTHESAAHA   70 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-------ceEEEEEECCHHHHHHH
Confidence            44689999999999999999999999999999999876       48999999999999865

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.2e-18  Score=88.10  Aligned_cols=55  Identities=27%  Similarity=0.472  Sum_probs=49.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++||.|..++++.      .++|||||+|.+.++|++|
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~------~~~gfafV~f~~~~~a~~a   58 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK------PFRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS------SCCSCCEEECSCHHHHHHT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee------ccCceEEEEECCHHHHHHH
Confidence            467999999999999999999999999999987644      3578999999999999876

>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=99.74  E-value=3.8e-19  Score=91.93  Aligned_cols=61  Identities=23%  Similarity=0.347  Sum_probs=55.2

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||.++++++|+++|.+||.|..+.+..+. .+|.++|||||+|.+.++|++|
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~g~~~g~~fV~f~~~~~A~~A   76 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM-MTGRMRGQAFITFPNKEIAWQA   76 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEE-ECSSSCSEEEEECSSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeeccc-ccccccccceEEeccHHHHHHH
Confidence            456899999999999999999999999999888887765 6789999999999999999865

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=1e-18  Score=90.54  Aligned_cols=60  Identities=18%  Similarity=0.309  Sum_probs=52.1

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....+|||+|||+++++++|+++|..||.+.. +.++.+  .+|+++|+|||+|.+.++|++|
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~--~~g~~~G~afV~F~s~~~a~~A   66 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD--NNGQGLGQALVQFKNEDDARKS   66 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCC--TTSSCSSCEEEECSSHHHHHHH
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeC--CCCCcCccEEEEECCHHHHHHH
Confidence            34578999999999999999999999998866 455555  6899999999999999999865

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=2.1e-18  Score=90.21  Aligned_cols=54  Identities=33%  Similarity=0.515  Sum_probs=48.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+.+++++|+++|++||.|..+.+...       +|||||+|.+.++|++|
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~-------kg~afV~f~~~~~A~~A   62 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-------GITAIVEFLEPLEARKA   62 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-------SSCEEEEESCHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeecc-------CceEEEEEcCHHHHHHH
Confidence            4579999999999999999999999999999987443       58999999999999865

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.4e-18  Score=87.42  Aligned_cols=60  Identities=25%  Similarity=0.398  Sum_probs=51.7

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeE-EEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..+.|||+|||+++++++|+++|..||.+.. +.+..+  .++.++|+|||+|.+.++|++|
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~--~~g~~~G~afV~f~~~e~a~~A   67 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN--EKGMPTGEAMVAFESRDEATAA   67 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC--SSSCEEEEEEEEESCHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC--CCCCcceEEEEEEcCcHHHHHH
Confidence            34668999999999999999999999998765 445555  6899999999999999999865

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.2e-17  Score=85.95  Aligned_cols=56  Identities=18%  Similarity=0.510  Sum_probs=49.7

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|++||.|..+.+..+        |||||+|.+.++|++|
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~--------g~afV~f~~~~~a~~A   66 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--------GMGMVEYLRKEDMEYA   66 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT--------TEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc--------ceEEEEECCHHHHHHH
Confidence            3446788999999999999999999999999999987543        8999999999999865

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.7e-18  Score=84.81  Aligned_cols=57  Identities=21%  Similarity=0.329  Sum_probs=50.9

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..+.++|||+|||+.+++++|+++|++||.|..+.+..+       ++||||+|.+.++|++|
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-------~~~afV~f~~~e~A~~a   60 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-------KNQAFLELATEEAAITM   60 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-------ceEEEEEeCCHHHHHHH
Confidence            3556789999999999999999999999999999988765       38999999999998764

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.8e-18  Score=89.55  Aligned_cols=56  Identities=14%  Similarity=0.240  Sum_probs=50.4

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+|||+|||+.+++++|+++|++||.|..+.+..++     ++|||||+|.+.++|++|
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~-----~~g~aFV~f~~~e~A~~A   61 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHA   61 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET-----TEEEEEEEESCHHHHHHH
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC-----CCCeEEEEECCHHHHHHH
Confidence            45689999999999999999999999999999987762     479999999999999875

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.6e-18  Score=85.30  Aligned_cols=54  Identities=30%  Similarity=0.565  Sum_probs=49.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||.|.++.+..+       +|||||+|.+.++|++|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-------k~~afV~f~~~~~A~~A   60 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-------KGFGFIRLETRTLAEIA   60 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-------TTEEEEECSSSHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-------cceEEEEECCHHHHHHH
Confidence            4578999999999999999999999999999998766       48999999999999865

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3.6e-18  Score=86.15  Aligned_cols=50  Identities=18%  Similarity=0.482  Sum_probs=46.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          22 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        22 ~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +|||+|||+.+++++|+++|++||.|..+.+..+        |||||+|.+.++|++|
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~--------g~afV~f~~~~~a~~A   51 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--------GTGVVEFVRKEDMTYA   51 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--------SEEEEEESSHHHHHHH
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc--------ceeeEEeCCHHHHHHH
Confidence            6999999999999999999999999999987654        8999999999999865

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=9e-18  Score=84.73  Aligned_cols=56  Identities=16%  Similarity=0.204  Sum_probs=48.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+++++++|+++|++||.|..+.+..+     +++|||||+|.+.++|.+|
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~-----~~~~~afV~f~~~~~A~~A   64 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ-----KDRKMALIQMGSVEEAVQA   64 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS-----SSTTCEEEEESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee-----cccceeEEEECCHHHHHHH
Confidence            4679999999999999999999999999988766443     3568999999999999865

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=9.4e-18  Score=87.45  Aligned_cols=54  Identities=20%  Similarity=0.313  Sum_probs=48.3

Q ss_pred             CCeEEEeCCCC-CCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPF-QAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+ .+++++|+++|++||.|..+.++.++      +|||||+|.+.++|++|
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~------kg~afV~f~~~~~A~~a   56 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK------KENALVQMADGNQAQLA   56 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT------SCCEEEEESCHHHHHHH
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc------cceEEEEECCHHHHHHH
Confidence            47899999965 59999999999999999999998762      68999999999999865

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=2.2e-17  Score=85.60  Aligned_cols=56  Identities=20%  Similarity=0.292  Sum_probs=50.3

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+..+|||+|||+.+++++|.++|++||.|..+.+..+       +++|||+|.+.++|++|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-------k~~AfV~f~~~e~A~~a   67 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-------KRQALVEFENIDSAKEC   67 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-------TTEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-------ceeEEEEeCCHHHHHHH
Confidence            445789999999999999999999999999999988665       48999999999999864

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=2.2e-17  Score=84.71  Aligned_cols=55  Identities=13%  Similarity=0.344  Sum_probs=49.4

Q ss_pred             CCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          18 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        18 ~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+.++|||+|||+++++++|+++|++||.|..+++..+       ++||||+|.+.++|+.|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-------~~~afV~f~~~~~A~~A   69 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-------DSFAYIQYESLDAAQAA   69 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-------SCCEEEEESSHHHHHHH
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-------ccEEEeccCCHHHHHHH
Confidence            44689999999999999999999999999999988655       48999999999999864

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=6.6e-18  Score=85.75  Aligned_cols=57  Identities=23%  Similarity=0.388  Sum_probs=48.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHH----HhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEE----LFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|||+|||+.+++++|++    +|++||.|.++.+..+    +.++|||||+|.+.++|.+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~----~~~~g~afV~F~~~~~A~~A   62 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS----LKMRGQAFVIFKEVSSATNA   62 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH----HHHTTCEEEEESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee----ccCCCceEEEECCHHHHHHH
Confidence            468999999999999998864    5799999999887553    56789999999999999865

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.4e-17  Score=93.11  Aligned_cols=59  Identities=22%  Similarity=0.450  Sum_probs=54.9

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .++|||+|||+.+++++|+++|++||.|..+.++.+. .++.++|||||+|.+.++|++|
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a   64 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP-NTKRSRGFGFVTYATVEEVDAA   64 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESSHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecc-cCCCccCceecccCCHHHHHHH
Confidence            4799999999999999999999999999999999886 7899999999999999998764

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=5.3e-17  Score=90.66  Aligned_cols=63  Identities=27%  Similarity=0.557  Sum_probs=57.5

Q ss_pred             cCCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|||+|||+.+++++|+++|+.||.|..+.++.++ .++.++|||||+|.+.++|++|
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~-~~~~~~g~~fV~f~~~e~A~~A  155 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTFDDHDSVDKI  155 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TTCCEEEEEEEEESCHHHHHHH
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccc-ccCccceeEEEEECCHHHHHHH
Confidence            34556899999999999999999999999999999999886 7889999999999999999865

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.69  E-value=8e-18  Score=86.18  Aligned_cols=57  Identities=23%  Similarity=0.554  Sum_probs=48.9

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+.++|||+|||+++++++|+++|++||.|..+.      .++.++|||||+|.+.++|++|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~------~~~~~~~~afV~f~~~~~A~~A   69 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS------QDGKSKGIAYIEFKSEADAEKN   69 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE------ETTEEEEEEEEEESSHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee------ecCccccEEEEEeCCHHHHHHH
Confidence            34568999999999999999999999999875543      3577899999999999999865

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=3.2e-17  Score=84.41  Aligned_cols=56  Identities=25%  Similarity=0.419  Sum_probs=49.5

Q ss_pred             CCCCCeEEEeCCCCC-CCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ...+++|||+|||.. +++++|.++|++||.|..+.+..+       +|+|||+|.+.++|.+|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-------k~~afV~f~~~~~A~~A   71 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-------KSQAFIEMETREDAMAM   71 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-------TTEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-------CCcEEEEecchHHHHHH
Confidence            455789999999985 899999999999999999998765       48999999999998764

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.9e-18  Score=86.92  Aligned_cols=58  Identities=22%  Similarity=0.401  Sum_probs=49.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeec-----ccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPK-----KMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~-----~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ++|||+|||+.+++++|+++|++||.+..+.+..     +. .++.++|||||+|.+.++|++|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~-~~~~~kg~afV~f~~~e~a~~a   64 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAV-QINQDKNFAFLEFRSVDETTQA   64 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEEC-CEETTTTEEEEEESSCTTTTTG
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeec-ccCCCceEEEEEeCCHHHHHHH
Confidence            6899999999999999999999999876655432     22 5677899999999999998865

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.4e-17  Score=82.81  Aligned_cols=52  Identities=19%  Similarity=0.289  Sum_probs=45.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+|||+|||+++++++|+++|++||.+..+.+..       .+|||||+|.+.++|++|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-------~rg~aFV~f~~~~~A~~A   53 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRA   53 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-------ccceEEEEECCHHHHHHH
Confidence            4799999999999999999999999876654443       469999999999999865

>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=99.66  E-value=8e-17  Score=82.75  Aligned_cols=54  Identities=26%  Similarity=0.668  Sum_probs=46.8

Q ss_pred             CCCCCeEEEeCCC-CCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIP-FQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+||| ..+++.+|+++|++||.|..+.+         ++|||||+|.+.++|++|
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i---------~rg~aFV~f~~~~~A~~A   66 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---------HKGFAFVQYVNERNARAA   66 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE---------ETEEEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE---------eCCeEEEEECCHHHHHHH
Confidence            4456789999997 57888999999999999999887         258999999999999875

>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=99.66  E-value=2.6e-16  Score=78.94  Aligned_cols=54  Identities=22%  Similarity=0.377  Sum_probs=47.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++||.+..+.+..       ++|||||+|.+.++|.+|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-------~rg~afV~f~~~~~A~~A   60 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-------IRDYAFVHFSNREDAVEA   60 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-------CSSEEEEEESSHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-------ccEEEEEEeCCHHHHHHH
Confidence            347899999999999999999999999987776533       468999999999999865

>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=99.65  E-value=1.1e-16  Score=79.29  Aligned_cols=54  Identities=17%  Similarity=0.313  Sum_probs=47.5

Q ss_pred             CCCCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +..+++|||+|++  +++++|+++|++||.|..+.+..+       +|||||+|.+.++|.+|
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-------~~~afV~f~~~~~A~~A   55 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-------RNCAFVTYEKMESADQA   55 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-------TTEEEEECSSHHHHHHH
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-------CCEEEEEEcccHHHHHH
Confidence            3467899999996  899999999999999999988655       48999999999999764

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.6e-16  Score=79.55  Aligned_cols=56  Identities=16%  Similarity=0.249  Sum_probs=49.5

Q ss_pred             CCCCCeEEEeCCCCC-CCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ....++|||+|||.. +++++|.++|++||.|..+.+..++       ++|||+|.+.++|..|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k-------~~afV~f~~~~~A~~A   61 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI-------NEAFIEMATTEDAQAA   61 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS-------SCEEEEESSHHHHHHH
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc-------eEEEEEEcchhhHHHH
Confidence            456789999999986 7899999999999999999987763       7899999999999764

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=1.2e-15  Score=79.97  Aligned_cols=52  Identities=23%  Similarity=0.362  Sum_probs=44.8

Q ss_pred             CCC-eEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCH-HHHh
Q psy3346          19 TGS-KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITK-NEAK   77 (79)
Q Consensus        19 ~~~-~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~-~~a~   77 (79)
                      .++ .+||+|||+.+|+++|+.+|++||.|.+|.++.+       +|||||.|.++ ++|.
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-------kg~gfV~F~~~~~~A~   62 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-------AKEGIILFKEKAKEAL   62 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-------CSEEEEEESSCHHHHH
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-------CceEEEEecCcHHHHH
Confidence            344 5699999999999999999999999999999765       49999999986 4554

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=9.2e-16  Score=79.12  Aligned_cols=56  Identities=16%  Similarity=0.359  Sum_probs=48.8

Q ss_pred             CCCCCeEEEeC--CCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRN--IPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~n--l~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..+..+++|.|  ||..+++++|+++|++||.|..+.+..+       ++||||+|.+.++|.+|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-------k~~aFV~f~~~e~A~~A   72 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-------KPYSFARYRTTEESKRA   72 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-------CSCEEEEESSHHHHHHH
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-------ccEEEEEECCHHHHHHH
Confidence            34567888865  9999999999999999999999988765       47999999999999865

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=3.6e-16  Score=78.86  Aligned_cols=53  Identities=28%  Similarity=0.527  Sum_probs=44.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+|||+++++++|+++|++|| +..+.+       +.++|||||+|.+.++|++|
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~-------~~~kg~afV~f~~~~~A~~A   56 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-------DRNKRTAFVTLLNGEQAQNA   56 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE-------EGGGTEEEECCSCHHHHHHH
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee-------eccCCceEEEECCHHHHHHH
Confidence            357899999999999999999999999 323322       34579999999999999875

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=1.5e-15  Score=74.47  Aligned_cols=49  Identities=27%  Similarity=0.532  Sum_probs=42.1

Q ss_pred             EEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          23 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        23 l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      |||+|||+++++++|+++|++|| +..+.+       ++++|||||+|.+.++|++|
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-------~~~~g~afv~f~~~~~A~~A   49 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-------DKYKGTAFVTLLNGEQAEAA   49 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-------ETTTTEEEEEESSHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-------cccceeEEEEECCHHHHHHH
Confidence            79999999999999999999999 544443       34579999999999999875

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.7e-15  Score=78.44  Aligned_cols=57  Identities=14%  Similarity=0.170  Sum_probs=51.3

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.++|.+++..+++++|+++|++||.|.++.++.+  .++.++|+|||+|.+.++|.+|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~--~~~~~~G~~fV~f~~~~~A~~A   84 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN--LGDHLVGNVYVKFRREEDAEKA   84 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS--SSSSSEEEEEEEESCHHHHHHH
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC--CCCCEeeEEEEEEechhHHHHH
Confidence            45777888888899999999999999999999877  6899999999999999999875

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=8.5e-14  Score=69.05  Aligned_cols=53  Identities=11%  Similarity=0.215  Sum_probs=44.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+.|+|.++|++.+++.| +.|++||.|.++++..+       ++||||+|.++++|++|
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-------~~~~fV~f~~~~~A~~A   55 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-------GNWMHIRYQSKLQARKA   55 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-------SSEEEEEESSHHHHHHH
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-------CCEEEEEEcccHHHHHH
Confidence            4567999999999986555 57999999999876543       59999999999999875

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.41  E-value=5.1e-14  Score=72.80  Aligned_cols=54  Identities=13%  Similarity=0.090  Sum_probs=46.0

Q ss_pred             CCCeEEEeCCCCCC-CH----HHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNIPFQA-KQ----SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl~~~~-~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      ..++|||+||+.++ ++    ++|+++|++||.|..+.+...       ++||||+|.+.++|.+|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-------~~~afV~f~~~~~A~~A   62 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-------FKRVRINFSNPLSAADA   62 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-------TTEEEEECSSTTHHHHH
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-------CCEEEEEECCHHHHHHH
Confidence            46789999999986 33    568999999999999988654       58999999999999875

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.2e-11  Score=63.08  Aligned_cols=59  Identities=17%  Similarity=0.335  Sum_probs=47.1

Q ss_pred             cCCCCCeEEEeCC--CCCCC---------HHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          16 AKQTGSKILVRNI--PFQAK---------QSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        16 ~~~~~~~l~v~nl--~~~~~---------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .....++|+|.||  |.+..         .++|++.|++||.|..+.+..+     ..+|++||+|.+.++|.+|
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~-----~~~G~~fV~f~~~e~A~~A   73 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR-----HPDGVASVSFRDPEEADYC   73 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT-----CTTCEEEEECSCHHHHHHH
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC-----CCccEEEEEECCHHHHHHH
Confidence            3456789999998  55421         2678899999999999987654     3569999999999999875

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=6.3e-11  Score=60.84  Aligned_cols=61  Identities=18%  Similarity=0.265  Sum_probs=47.0

Q ss_pred             CCCeEEEeCC--CCCCC--------HHHHHHHhHhcCCeeEEEeecccC-CCCCcceEEEEEecCHHHHhcC
Q psy3346          19 TGSKILVRNI--PFQAK--------QSEVEELFKAFGELKFVRLPKKMV-GSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        19 ~~~~l~v~nl--~~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      +.+.|.|.||  |....        .++|++.|++||.|.++.++.++. ......|++||+|.+.++|.+|
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A   74 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKA   74 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHH
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHH
Confidence            4678999998  55443        256899999999999999987640 1233568999999999999875

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=9.4e-06  Score=40.24  Aligned_cols=56  Identities=14%  Similarity=0.289  Sum_probs=44.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCC--cceEEEEEecCHHHHh
Q psy3346          21 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGL--HRGFGFVEFITKNEAK   77 (79)
Q Consensus        21 ~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~--~~g~~fv~f~~~~~a~   77 (79)
                      ++|-|+.||+..+++++.+.+...|.+........+ .+.+  .-.-|||.|.+.++..
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk-~s~~~~~~SRAYi~F~~~~~v~   59 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND-TSLYPHMYARAYINFKNQEDII   59 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESC-CSSTTCCCEEEEEEESSSHHHH
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCC-cCCCCCcceEEEEEeCCHHHHH
Confidence            578999999999999999999999988887766554 2222  2356999999988754

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.41  E-value=0.0062  Score=30.17  Aligned_cols=50  Identities=22%  Similarity=0.357  Sum_probs=38.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          20 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        20 ~~~l~v~nl~~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      ..-+|.-..|......+|.++|++||.| .|.++.+        --|||...+.++|+.
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIdd--------TSa~V~L~~~e~~~~   64 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD--------TSAFVSLSQPEQVQI   64 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET--------TEEEEECSCHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCce-EEEEecC--------ceEEEEecCHHHHHH
Confidence            3457888899999999999999999975 3334444        258999888888754

>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=94.76  E-value=0.015  Score=28.35  Aligned_cols=54  Identities=17%  Similarity=0.269  Sum_probs=37.6

Q ss_pred             CCCCCeEEEeCCCCCC------CH---HHHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhcC
Q psy3346          17 KQTGSKILVRNIPFQA------KQ---SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRV   79 (79)
Q Consensus        17 ~~~~~~l~v~nl~~~~------~~---~~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~a   79 (79)
                      .+..-+|.|.=..++.      .+   .+|.+.|..||+|.-++++.+.         -+|+|.+-++|.+|
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~---------mwVTF~dG~SAL~a   74 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ---------MLVTFADSHSALSV   74 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE---------EEEECSCSHHHHHH
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe---------EEEEECCcHHHHHH
Confidence            3445666665443332      22   3578888999999999988763         78999998887653

>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=87.77  E-value=0.68  Score=21.25  Aligned_cols=39  Identities=21%  Similarity=0.164  Sum_probs=28.3

Q ss_pred             HHHHHhHhcCCeeEEEeecccCCCCCcceEEEEEecCHHHHhc
Q psy3346          36 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR   78 (79)
Q Consensus        36 ~l~~~f~~~g~i~~~~~~~~~~~~~~~~g~~fv~f~~~~~a~~   78 (79)
                      .|...|.+++.|.++.+...  ..+.  -.|-|...+.++|.-
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~--~dg~--~~A~V~v~~~q~A~~   50 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPH--TDYQ--LKAVVQMENLQDAIG   50 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSC--CSTT--CCEEEEESSHHHHHH
T ss_pred             HHHHHHHhheeEEEEEEEec--cCCc--EEEEEEcCCHHHHHH
Confidence            45677789999999887554  2333  458888888888753