Citrus Sinensis ID: 032280

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140----
Protein Sequence
MAEYYPPPAGLHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMAM
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccccEEEEEEcccccccEEEEEEccHHHHHHHHHHHcccccccccccEEccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccHHHHHHHHcccccccEEEEEEccccccEEEEEEEccHHHHHHHHHHHcccEEccccccEcccccccc
Coil and Loop (DISEMBL)
maeyypppaglhygyyqtppppppppppggvvapptqpympqpqppplgsysasfpaygsydEVRTLFVaglpedvkpreIYNLfrefpgyesshlrsstqnsqpfaFAVFSDQQSALGAMYAlnnfapsdsacsllfphsmam
Flexible Loop (DISEMBL)
maeyypppAGLHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMAM
Low Complexity Region (SEG)
MAEYYPPPAGLHYGYYqtppppppppppggvvapptqpympqpqpppLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMAM
Disordered region (IsUnstruct)
******************************************************FPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGY**************FAFAVFSDQQSALGAMYALNNFAP***ACSLL*******
Disordered Region (DISOPRED)
*****************************************************************TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMA*
Disordered Region (DISEMBL)
MAEYYPPPAGLHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGY**********NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMAM
Disordered Region (DISPRO)
**EYYPPPAGLHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLG***********YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAEYYPPPAGLHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMAM
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	144	2.2.26 [Sep-21-2011]
Q8VC52	206	RNA-binding protein with	yes	no	0.444	0.310	0.5	8e-12
Q6ZRY4	209	RNA-binding protein with	yes	no	0.444	0.306	0.5	2e-11
Q9W6I1	200	RNA-binding protein with	yes	no	0.444	0.32	0.5	3e-11
Q93062	196	RNA-binding protein with	no	no	0.444	0.326	0.5	3e-11
Q9WVB0	197	RNA-binding protein with	no	no	0.444	0.324	0.5	4e-11
Q9YGP5	196	RNA-binding protein with	N/A	no	0.430	0.316	0.5	1e-10
Q01617	738	Protein couch potato OS=D	no	no	0.437	0.085	0.469	5e-10

>sp|Q8VC52|RBPS2_MOUSE RNA-binding protein with multiple splicing 2 OS=Mus musculus GN=Rbpms2 PE=1 SV=1

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 44/66 (66%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F +F  +  A  A 
Sbjct: 22  EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSR--QPVGFVIFDSRAGAEAAK 79

Query: 122 YALNNF 127
            ALN  
Sbjct: 80  NALNGI 85

Mus musculus (taxid: 10090)

>sp|Q6ZRY4|RBPS2_HUMAN RNA-binding protein with multiple splicing 2 OS=Homo sapiens GN=RBPMS2 PE=2 SV=1

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ + +  QP  F +F  +  A  A 
Sbjct: 28  EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTAR--QPVGFVIFDSRAGAEAAK 85

Query: 122 YALNNF 127
            ALN  
Sbjct: 86  NALNGI 91

Homo sapiens (taxid: 9606)

>sp|Q9W6I1|RBPMS_CHICK RNA-binding protein with multiple splicing OS=Gallus gallus GN=RBPMS PE=2 SV=1

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A 
Sbjct: 19  EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDSRAGAEAAK 76

Query: 122 YALNNF 127
            ALN  
Sbjct: 77  NALNGI 82

Acts as a coactivator of transcriptional activity. Binds RNA.

Gallus gallus (taxid: 9031)

>sp|Q93062|RBPMS_HUMAN RNA-binding protein with multiple splicing OS=Homo sapiens GN=RBPMS PE=1 SV=1

 Score = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A 
Sbjct: 21  EEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVSFDSRSEAEAAK 78

Query: 122 YALNNF 127
            ALN  
Sbjct: 79  NALNGI 84

Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins. Binds to poly(A) RNA.

Homo sapiens (taxid: 9606)

>sp|Q9WVB0|RBPMS_MOUSE RNA-binding protein with multiple splicing OS=Mus musculus GN=Rbpms PE=2 SV=2

 Score = 67.0 bits (162), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 43/66 (65%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A 
Sbjct: 21  EEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVSFDSRSEAEAAK 78

Query: 122 YALNNF 127
            ALN  
Sbjct: 79  NALNGI 84

Acts as a coactivator of transcriptional activity. Required to increase TGFB1/Smad-mediated transactivation. Acts through SMAD2, SMAD3 and SMAD4 to increase transcriptional activity. Increases phosphorylation of SMAD2 and SMAD3 on their C-terminal SSXS motif, possibly through recruitment of TGFBR1. Promotes the nuclear accumulation of SMAD2, SMAD3 and SMAD4 proteins. Binds to poly(A) RNA.

Mus musculus (taxid: 10090)

>sp|Q9YGP5|RBPMS_XENLA RNA-binding protein with multiple splicing OS=Xenopus laevis GN=rbpms PE=2 SV=1

 Score = 65.1 bits (157), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 42/64 (65%), Gaps = 2/64 (3%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           VRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F ++  A  A  A
Sbjct: 19  VRTLFVSGLPIDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDNRAGAEAAKNA 76

Query: 124 LNNF 127
           LN  
Sbjct: 77  LNGI 80

Acts as a coactivator of transcriptional activity. Binds RNA.

Xenopus laevis (taxid: 8355)

>sp|Q01617|CPO_DROME Protein couch potato OS=Drosophila melanogaster GN=cpo PE=2 SV=3

 Score = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 41/66 (62%), Gaps = 3/66 (4%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ---PFAFAVFSDQQSAL 118
           +EVRTLFV+GLP D KPRE+Y LFR + GYE S L+ +++N +   P  F  F  +  A 
Sbjct: 448 EEVRTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTASPVGFVTFHTRAGAE 507

Query: 119 GAMYAL 124
            A   L
Sbjct: 508 AAKQDL 513

May play a role in the development or function of the peripheral nervous system by regulating the processing of nervous system-specific transcripts.

Drosophila melanogaster (taxid: 7227)

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	144
449525690	306	PREDICTED: U2 small nuclear ribonucleopr	0.701	0.330	0.631	8e-27
296082378	333	unnamed protein product [Vitis vinifera]	0.479	0.207	0.840	2e-26
225438787	336	PREDICTED: uncharacterized protein LOC10	0.479	0.205	0.840	3e-26
147802946	335	hypothetical protein VITISV_021557 [Viti	0.479	0.205	0.826	6e-26
224094288	323	predicted protein [Populus trichocarpa]	0.506	0.226	0.753	1e-24
297824185	289	hypothetical protein ARALYDRAFT_903572 [	0.694	0.346	0.572	4e-24
356541768	338	PREDICTED: uncharacterized protein LOC10	0.590	0.251	0.652	6e-24
28207150	277	hypothetical protein [Arabidopsis thalia	0.472	0.245	0.782	8e-24
2673920	158	putative RNA-binding protein [Arabidopsi	0.472	0.430	0.782	9e-24
186507399	289	RNA recognition motif-containing protein	0.472	0.235	0.782	1e-23

>gi|449525690|ref|XP_004169849.1| PREDICTED: U2 small nuclear ribonucleoprotein B''-like, partial [Cucumis sativus]

 Score =  125 bits (313), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 65/103 (63%), Positives = 76/103 (73%), Gaps = 2/103 (1%)

Query: 37  QPYMPQPQPPPLGSYSA-SFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH 95
           Q Y+ Q  P    SY+    P   S +EVRTLF+AGLPEDVKPREIYNLFREFPGYESSH
Sbjct: 40  QHYLSQ-HPSTFASYALPLLPHTTSINEVRTLFIAGLPEDVKPREIYNLFREFPGYESSH 98

Query: 96  LRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF 138
           LR+ TQ +QPFAFAVFSDQQSA+GAM+A+N         S+L+
Sbjct: 99  LRTPTQTTQPFAFAVFSDQQSAVGAMHAVNGMVFDLEKQSVLY 141

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296082378|emb|CBI21383.3| unnamed protein product [Vitis vinifera]

 Score =  123 bits (309), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 62/69 (89%)

Query: 60  SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALG 119
           S DEVRTLF+AGLPEDVKPREIYNLFREFPGYESSHLRS +QNSQPFAFAVF DQQSA+ 
Sbjct: 73  SVDEVRTLFIAGLPEDVKPREIYNLFREFPGYESSHLRSPSQNSQPFAFAVFLDQQSAIA 132

Query: 120 AMYALNNFA 128
           AM+ALN   
Sbjct: 133 AMHALNGMV 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225438787|ref|XP_002283118.1| PREDICTED: uncharacterized protein LOC100247532 [Vitis vinifera]

 Score =  123 bits (308), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 58/69 (84%), Positives = 62/69 (89%)

Query: 60  SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALG 119
           S DEVRTLF+AGLPEDVKPREIYNLFREFPGYESSHLRS +QNSQPFAFAVF DQQSA+ 
Sbjct: 76  SVDEVRTLFIAGLPEDVKPREIYNLFREFPGYESSHLRSPSQNSQPFAFAVFLDQQSAIA 135

Query: 120 AMYALNNFA 128
           AM+ALN   
Sbjct: 136 AMHALNGMV 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147802946|emb|CAN64038.1| hypothetical protein VITISV_021557 [Vitis vinifera]

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 57/69 (82%), Positives = 61/69 (88%)

Query: 60  SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALG 119
           S DEVRTLF+AGLPEDVKPREIYNLFREFPGYESSHLRS +QNSQPFAFAVF DQQSA+ 
Sbjct: 73  SVDEVRTLFIAGLPEDVKPREIYNLFREFPGYESSHLRSPSQNSQPFAFAVFLDQQSAIA 132

Query: 120 AMYALNNFA 128
            M+ALN   
Sbjct: 133 TMHALNGMV 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224094288|ref|XP_002310126.1| predicted protein [Populus trichocarpa] gi|222853029|gb|EEE90576.1| predicted protein [Populus trichocarpa]

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 55/73 (75%), Positives = 65/73 (89%)

Query: 53  ASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFS 112
            S PAY  +D+VRTLFVAGLP+D+KPRE+YNLFREFPGYESSHLR+ +QNSQPFAFA F+
Sbjct: 61  VSVPAYVPHDQVRTLFVAGLPDDIKPREMYNLFREFPGYESSHLRTPSQNSQPFAFATFT 120

Query: 113 DQQSALGAMYALN 125
           DQ SA+ AM+ALN
Sbjct: 121 DQPSAVAAMHALN 133

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824185|ref|XP_002879975.1| hypothetical protein ARALYDRAFT_903572 [Arabidopsis lyrata subsp. lyrata] gi|297325814|gb|EFH56234.1| hypothetical protein ARALYDRAFT_903572 [Arabidopsis lyrata subsp. lyrata]

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 67/117 (57%), Positives = 76/117 (64%), Gaps = 17/117 (14%)

Query: 15  YYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAY---GSYDEVRTLFVAG 71
           YY  P   PPP P    VAP           P   ++S   P +   G+ DEVRTLFVAG
Sbjct: 8   YYNLPAIVPPPQPG---VAPI----------PITSAHSVFLPTHVSIGARDEVRTLFVAG 54

Query: 72  LPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFA 128
           LPEDVKPREIYNLFREFPGYE+SHLRSS   ++PFAFAVFSD QSA+  M+ALN   
Sbjct: 55  LPEDVKPREIYNLFREFPGYETSHLRSS-DGAKPFAFAVFSDLQSAVTVMHALNGMV 110

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356541768|ref|XP_003539345.1| PREDICTED: uncharacterized protein LOC100780983 [Glycine max]

 Score =  115 bits (288), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 62/95 (65%), Positives = 70/95 (73%), Gaps = 10/95 (10%)

Query: 38  PYMPQPQPPPLGSYSASFPAYG----SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYES 93
           PY+ Q Q        A F +YG    S  EVRTLFVAGLPEDVKPREIYNLFREFPGYES
Sbjct: 54  PYVAQHQQ------QAVFGSYGAPQSSTHEVRTLFVAGLPEDVKPREIYNLFREFPGYES 107

Query: 94  SHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFA 128
           SHLRS + +SQPFAFAVF+ Q+SA+ AM+ALN   
Sbjct: 108 SHLRSPSNSSQPFAFAVFASQKSAILAMHALNGLV 142

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|28207150|gb|AAO37215.1| hypothetical protein [Arabidopsis thaliana]

 Score =  115 bits (287), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 54/69 (78%), Positives = 61/69 (88%), Gaps = 1/69 (1%)

Query: 57  AYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQS 116
           + G+ DEVRTLFVAGLPEDVKPREIYNLFREFPGYE+SHLRSS   ++PFAFAVFSD QS
Sbjct: 27  SIGARDEVRTLFVAGLPEDVKPREIYNLFREFPGYETSHLRSS-DGAKPFAFAVFSDLQS 85

Query: 117 ALGAMYALN 125
           A+  M+ALN
Sbjct: 86  AVAVMHALN 94

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2673920|gb|AAB88654.1| putative RNA-binding protein [Arabidopsis thaliana]

 Score =  114 bits (286), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 54/69 (78%), Positives = 61/69 (88%), Gaps = 1/69 (1%)

Query: 57  AYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQS 116
           + G+ DEVRTLFVAGLPEDVKPREIYNLFREFPGYE+SHLRSS   ++PFAFAVFSD QS
Sbjct: 27  SIGARDEVRTLFVAGLPEDVKPREIYNLFREFPGYETSHLRSS-DGAKPFAFAVFSDLQS 85

Query: 117 ALGAMYALN 125
           A+  M+ALN
Sbjct: 86  AVAVMHALN 94

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186507399|ref|NP_001118504.1| RNA recognition motif-containing protein [Arabidopsis thaliana] gi|330255001|gb|AEC10095.1| RNA recognition motif-containing protein [Arabidopsis thaliana]

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 54/69 (78%), Positives = 61/69 (88%), Gaps = 1/69 (1%)

Query: 57  AYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQS 116
           + G+ DEVRTLFVAGLPEDVKPREIYNLFREFPGYE+SHLRSS   ++PFAFAVFSD QS
Sbjct: 42  SIGARDEVRTLFVAGLPEDVKPREIYNLFREFPGYETSHLRSS-DGAKPFAFAVFSDLQS 100

Query: 117 ALGAMYALN 125
           A+  M+ALN
Sbjct: 101 AVAVMHALN 109

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	144
TAIR|locus:2060015	302	AT2G42240 [Arabidopsis thalian	0.513	0.245	0.733	5.3e-24
UNIPROTKB|E2QU21	214	RBPMS2 "Uncharacterized protei	0.472	0.317	0.486	3.9e-12
MGI|MGI:1919223	206	Rbpms2 "RNA binding protein wi	0.472	0.330	0.486	3.9e-12
UNIPROTKB|Q6ZRY4	209	RBPMS2 "RNA-binding protein wi	0.472	0.325	0.486	5e-12
ZFIN|ZDB-GENE-040426-741	200	rbpms2b "RNA binding protein w	0.472	0.34	0.486	5e-12
UNIPROTKB|F1N2U8	203	RBPMS2 "Uncharacterized protei	0.465	0.330	0.492	6.4e-12
UNIPROTKB|Q9W6I1	200	RBPMS "RNA-binding protein wit	0.472	0.34	0.486	8.2e-12
UNIPROTKB|Q9YGP5	196	rbpms "RNA-binding protein wit	0.472	0.346	0.486	8.2e-12
ZFIN|ZDB-GENE-040718-106	199	rbpms2a "RNA binding protein w	0.430	0.311	0.515	8.2e-12
UNIPROTKB|F1S0B2	195	RBPMS2 "Uncharacterized protei	0.493	0.364	0.466	1e-11

TAIR|locus:2060015 AT2G42240 [Arabidopsis thaliana (taxid:3702)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 55/75 (73%), Positives = 63/75 (84%)

Query:    51 YSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAV 110
             Y  +  + G+ DEVRTLFVAGLPEDVKPREIYNLFREFPGYE+SHLRSS   ++PFAFAV
Sbjct:    36 YLPTHVSIGARDEVRTLFVAGLPEDVKPREIYNLFREFPGYETSHLRSS-DGAKPFAFAV 94

Query:   111 FSDQQSALGAMYALN 125
             FSD QSA+  M+ALN
Sbjct:    95 FSDLQSAVAVMHALN 109

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|E2QU21 RBPMS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 35/72 (48%), Positives = 47/72 (65%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F +F  +  A  A 
Sbjct:    32 EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSR--QPVGFVIFDSRAGAEAAK 89

Query:   122 YALNN--FAPSD 131
              ALN   F P +
Sbjct:    90 NALNGIRFDPEN 101

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1919223 Rbpms2 "RNA binding protein with multiple splicing 2" [Mus musculus (taxid:10090)]

 Score = 163 (62.4 bits), Expect = 3.9e-12, P = 3.9e-12
 Identities = 35/72 (48%), Positives = 47/72 (65%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F +F  +  A  A 
Sbjct:    22 EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSR--QPVGFVIFDSRAGAEAAK 79

Query:   122 YALNN--FAPSD 131
              ALN   F P +
Sbjct:    80 NALNGIRFDPEN 91

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|Q6ZRY4 RBPMS2 "RNA-binding protein with multiple splicing 2" [Homo sapiens (taxid:9606)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 35/72 (48%), Positives = 46/72 (63%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ + +  QP  F +F  +  A  A 
Sbjct:    28 EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTAR--QPVGFVIFDSRAGAEAAK 85

Query:   122 YALNN--FAPSD 131
              ALN   F P +
Sbjct:    86 NALNGIRFDPEN 97

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-040426-741 rbpms2b "RNA binding protein with multiple splicing 2b" [Danio rerio (taxid:7955)]

 Score = 162 (62.1 bits), Expect = 5.0e-12, P = 5.0e-12
 Identities = 35/72 (48%), Positives = 46/72 (63%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A 
Sbjct:    17 EEVRTLFVSGLPTDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDSRSGAEAAK 74

Query:   122 YALNN--FAPSD 131
              ALN   F P +
Sbjct:    75 NALNGVRFDPEN 86

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|F1N2U8 RBPMS2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 35/71 (49%), Positives = 46/71 (64%)

Query:    63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F +F  +  A  A  
Sbjct:    23 EVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSR--QPVGFVIFDSRAGAEAAKN 80

Query:   123 ALNN--FAPSD 131
             ALN   F P +
Sbjct:    81 ALNGIRFDPEN 91

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9W6I1 RBPMS "RNA-binding protein with multiple splicing" [Gallus gallus (taxid:9031)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 35/72 (48%), Positives = 46/72 (63%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A 
Sbjct:    19 EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDSRAGAEAAK 76

Query:   122 YALNN--FAPSD 131
              ALN   F P +
Sbjct:    77 NALNGIRFDPEN 88

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISS

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

UNIPROTKB|Q9YGP5 rbpms "RNA-binding protein with multiple splicing" [Xenopus laevis (taxid:8355)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 35/72 (48%), Positives = 47/72 (65%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F ++  A  A 
Sbjct:    17 EEVRTLFVSGLPIDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDNRAGAEAAK 74

Query:   122 YALNN--FAPSD 131
              ALN   F P +
Sbjct:    75 NALNGIRFDPEN 86

GO:0003713 "transcription coactivator activity" evidence=ISS

GO:0008143 "poly(A) RNA binding" evidence=ISS

GO:0010862 "positive regulation of pathway-restricted SMAD protein phosphorylation" evidence=ISS

GO:0060391 "positive regulation of SMAD protein import into nucleus" evidence=ISS

ZFIN|ZDB-GENE-040718-106 rbpms2a "RNA binding protein with multiple splicing 2a" [Danio rerio (taxid:7955)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 33/64 (51%), Positives = 43/64 (67%)

Query:    62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +EVRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A 
Sbjct:    17 EEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDSRSGAEAAK 74

Query:   122 YALN 125
              ALN
Sbjct:    75 NALN 78

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|F1S0B2 RBPMS2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 35/75 (46%), Positives = 47/75 (62%)

Query:    59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSAL 118
             G   +VRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F +F  +  A 
Sbjct:    10 GLCPQVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSR--QPVGFVIFDSRAGAE 67

Query:   119 GAMYALNN--FAPSD 131
              A  ALN   F P +
Sbjct:    68 AAKNALNGIRFDPEN 82

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00019542001 SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (336 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	144
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	9e-24
smart00360	73	smart00360, RRM, RNA recognition motif	1e-12
cd12684	83	cd12684, RRM_cpo, RNA recognition motif in Drosoph	1e-12
cd12683	76	cd12683, RRM_RBPMS2, RNA recognition motif in vert	4e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-11
cd12682	76	cd12682, RRM_RBPMS, RNA recognition motif in verte	3e-11
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	1e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-06
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	5e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	1e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	4e-05
COG5178	2365	COG5178, PRP8, U5 snRNP spliceosome subunit [RNA p	7e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	1e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	2e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	6e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.001
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	0.001
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	0.001
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	0.002
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	0.002
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.002
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.002
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.003
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.003
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.003
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.003
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.004
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.004
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.004
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.004

>gnl|CDD|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 87.3 bits (217), Expect = 9e-24
 Identities = 34/66 (51%), Positives = 40/66 (60%), Gaps = 3/66 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN---SQPFAFAVFSDQQSALGAM 121
           RTLFV+GLP DVK RE+ +LFR FPGYE+S L    +     QP  F  FS  Q A  AM
Sbjct: 1   RTLFVSGLPSDVKERELAHLFRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAAM 60

Query: 122 YALNNF 127
            AL  +
Sbjct: 61  DALQGY 66

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 59.1 bits (144), Expect = 1e-12
 Identities = 25/64 (39%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAMYA 123
           TLFV  LP D    E+  LF +F   ES  L     T  S+ FAF  F  ++ A  A+ A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 124 LNNF 127
           LN  
Sbjct: 61  LNGK 64

Length = 73

>gnl|CDD|241128 cd12684, RRM_cpo, RNA recognition motif in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins

 Score = 59.3 bits (143), Expect = 1e-12
 Identities = 30/64 (46%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN---SQPFAFAVFSDQQSALGA 120
           VRTLFV+GLP D KPRE+Y LFR + GYE S L+ +++N   + P  F  F  +  A  A
Sbjct: 1   VRTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFETRAGAEAA 60

Query: 121 MYAL 124
              L
Sbjct: 61  KQDL 64

This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS). . Length = 83

>gnl|CDD|241127 cd12683, RRM_RBPMS2, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2)

 Score = 57.7 bits (139), Expect = 4e-12
 Identities = 32/62 (51%), Positives = 41/62 (66%), Gaps = 2/62 (3%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           VRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A  A
Sbjct: 1   VRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVTFDSRAGAEAAKNA 58

Query: 124 LN 125
           LN
Sbjct: 59  LN 60

This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 56.4 bits (137), Expect = 1e-11
 Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           LFV  LP D    ++ +LF +F   ES  + R  T  S+ FAF  F D++ A  A+ ALN
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 126 NF 127
             
Sbjct: 61  GK 62

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

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           LFV  LP D    ++  LF +F   ES  + R     S+ FAF  F   + A  A+ ALN
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 126 NF 127
             
Sbjct: 61  GK 62

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|241126 cd12682, RRM_RBPMS, RNA recognition motif in vertebrate RNA-binding protein with multiple splicing (RBP-MS)

 Score = 55.4 bits (133), Expect = 3e-11
 Identities = 32/62 (51%), Positives = 41/62 (66%), Gaps = 2/62 (3%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           VRTLFV+GLP D+KPRE+Y LFR F GYE S ++ +++  QP  F  F  +  A  A  A
Sbjct: 1   VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSK--QPVGFVSFDSRSEAEAAKNA 58

Query: 124 LN 125
           LN
Sbjct: 59  LN 60

This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. . Length = 76

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 5/62 (8%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           TLFVA L  +    E+  LF   PG+    L+   +   P  F  F D      A  ALN
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGF--RRLKMHNKGGGPVCFVEFEDVSF---ATQALN 58

Query: 126 NF 127
           + 
Sbjct: 59  SL 60

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 42.9 bits (102), Expect = 1e-06
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGY-ESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           L+V  LP  V   ++   F  + G  E   L  +    + FAF  F+  + A  A+  LN
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPY-GKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLN 59

Query: 126 N 126
            
Sbjct: 60  G 60

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

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

 Score = 45.7 bits (107), Expect = 2e-06
 Identities = 27/94 (28%), Positives = 41/94 (43%), Gaps = 2/94 (2%)

Query: 36  TQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH 95
            + Y  + +     S  +      S +E  TLFV  LP DV   ++  LF++F   +   
Sbjct: 87  ERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR 146

Query: 96  LRSS--TQNSQPFAFAVFSDQQSALGAMYALNNF 127
           L     T  S+ FAF  F  ++SA  A+  LN  
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGK 180

Length = 306

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

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 28/85 (32%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS-----------------------STQ 101
           RT+FV  LP   K +++  LF++F   ES   RS                          
Sbjct: 1   RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 102 NSQPFAFAVFSDQQSALGAMYALNN 126
           N    A+ VF +++SA  A+  LN 
Sbjct: 61  N----AYVVFKEEESAEKAL-KLNG 80

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

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

 Score = 41.0 bits (97), Expect = 1e-05
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQSALGAMYA 123
           T+ V  L ED    ++  LFR F      +L     T  S+ FAF  F  ++ A  A+  
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 124 LNNFA 128
           LN F 
Sbjct: 61  LNGFG 65

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS---QPFAFAVFSDQQSALGAM 121
            T+FV  +PE V    I  L  +  G   S  R    ++   + F F  F D + AL A+
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKC-GKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRAL 59

Query: 122 YALNNF 127
             LN  
Sbjct: 60  RLLNGL 65

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

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

 Score = 39.1 bits (92), Expect = 4e-05
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           + LF+  LPE+     +  LF +FPG++   L          AF  F  ++ A  A+ AL
Sbjct: 3   KILFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPRRG----IAFVEFETEEQATVALQAL 58

Query: 125 NNF 127
             F
Sbjct: 59  QGF 61

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|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and modification]

 Score = 41.1 bits (96), Expect = 7e-05
 Identities = 20/33 (60%), Positives = 21/33 (63%), Gaps = 8/33 (24%)

Query: 19 PP--PPPPPPPPGGVVAPPTQPYMPQPQPPPLG 49
          PP  PPPPPPPPG    PP+QP    P PPP G
Sbjct: 5  PPGNPPPPPPPPG--FEPPSQP----PPPPPPG 31

Length = 2365

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 8/59 (13%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRS-STQNSQPFAFAV--FSDQQSALGAM 121
           T+ V  LP+D    +I   F+     +   +R      S+    AV  F  +  AL A+
Sbjct: 2   TVKVKNLPKDTTENKIRQFFK-----DCGEIREVKIVESEGGLVAVIEFETEDEALAAL 55

This subfamily corresponds to the RRM1 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 = 71

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

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPG-YESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           +F+  LP D+   E+  L  +    YE   +     N++ +AF  FS++Q A  A+  LN
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63

Query: 126 NF 127
           N+
Sbjct: 64  NY 65

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 37.5 bits (87), Expect = 2e-04
 Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
           ++V  LP DV+ +++ +LF ++       L++  +   PFAF  F D + A  A++  N 
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNR-RGLVPFAFVRFEDPRDAEDAVFGRNG 60

Query: 127 F 127
           +
Sbjct: 61  Y 61

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that 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. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

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

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           L+V GL E+V  + ++  F  F   +     L   TQ  + FAF  F + + A  A+  +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 125 NNF 127
           N  
Sbjct: 61  NES 63

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|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPG--YESSHLR-SSTQNSQPFAFAVFSDQQSALGAMYA 123
           LFV  LP+     ++  LF E+ G   E + +R   T  S+  AF  FS ++ A  A+ A
Sbjct: 2   LFVGQLPKTATEEDVRALFEEY-GNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 124 LNN 126
           L+ 
Sbjct: 61  LHG 63

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           + TL+V GL E V  +++ + F +F    S  +    Q     AF  F+ +++A  A   
Sbjct: 1   ITTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC----AFVTFTTREAAEKAAER 56

Query: 124 LNN 126
           L N
Sbjct: 57  LFN 59

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 35.8 bits (83), Expect = 6e-04
 Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
            ++V  LP D++ R+I +LF ++   ++  L++  +   PFAF  F D + A  A+   +
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNR-RRGPPFAFVEFEDPRDAEDAVRGRD 59

Query: 126 NF 127
            +
Sbjct: 60  GY 61

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|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF protein family

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 7/67 (10%)

Query: 66  TLFVAGLPEDVKPRE----IYNLFREF-PGYESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
           TL++  L E +K  E    +Y LF +F P  +    ++     Q  AF VF D +SA  A
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTLKMRGQ--AFVVFKDVESATNA 58

Query: 121 MYALNNF 127
           + AL  F
Sbjct: 59  LRALQGF 65

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 4/65 (6%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAMY 122
            L+V  LP +V   ++ +LF +F    S+ +   R + + S+ F F      + A  A+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGR-SRGFGFVEMETAEEANAAIE 59

Query: 123 ALNNF 127
            LN  
Sbjct: 60  KLNGT 64

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.4 bits (82), Expect = 0.001
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 81  IYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYALNNF 127
           ++ LF   PG E   L+    T  S+ FA+  +S+  SA+ A   LN F
Sbjct: 16  LHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGF 64

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 7/61 (11%)

Query: 66  TLFVAGL-PEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           TLFV G  P   +  +I  LF  F       +R      + FAF  F D + A  A+ AL
Sbjct: 1   TLFVVGFDPGTTREEDIEKLFEPFGPLVRCDIR------KTFAFVEFEDSEDATKALEAL 54

Query: 125 N 125
           +
Sbjct: 55  H 55

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

>gnl|CDD|240687 cd12241, RRM_SF3B14, RNA recognition motif found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLR-SSTQNSQPFAFAVFSDQQSALGAMYA 123
           R L+V  LP  +   E+Y+LF ++ G     +R  +T+ ++  AF V+ D   A  A   
Sbjct: 3   RILYVRNLPFKISSEELYDLFGKY-G-AIRQIRIGNTKETRGTAFVVYEDIYDAKNACDH 60

Query: 124 LNNF 127
           L+ F
Sbjct: 61  LSGF 64

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is 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 has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           RTLFV  +  +V+  E+  LF +F G +   L ++ ++ + F    + D ++A  A  AL
Sbjct: 2   RTLFVRNINSNVEDEELRALFEQF-G-DIRTLYTACKH-RGFIMVSYYDIRAARRAKRAL 58

Query: 125 NN 126
             
Sbjct: 59  QG 60

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

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAMYAL 124
           +FV  L  +V    ++  F  FP    + +     +  S+ + F  F  QQ A  A+  +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 125 N 125
           N
Sbjct: 62  N 62

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

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           T++    P      ++  LF          + S T   QP AF  F + ++A  A+  LN
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTV--QPHAFITFENLEAAQLAIETLN 58

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

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 34.5 bits (80), Expect = 0.002
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           LF+  LP +   +++Y LF  F    S+ +    +T  S+ F F  + + +SA  A+ A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 125 NNF 127
           N F
Sbjct: 61  NGF 63

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

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 34.7 bits (79), Expect = 0.002
 Identities = 17/60 (28%), Positives = 29/60 (48%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           TL+V  L  DV    I  LF +    +S  + +   ++ P+ F  F + + A  A+ A+N
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 60

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 16/62 (25%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           +FV  +P D+   E+  LF +  P YE   +   +  ++ +AF  ++++++A  A+  L+
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKQLH 63

Query: 126 NF 127
           N+
Sbjct: 64  NY 65

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

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMY 122
             L V  LP+D+   E+ +LF      ES  +     T  S  + F  + D+  A  A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 123 ALNNF 127
            LN F
Sbjct: 61  TLNGF 65

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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 34.1 bits (79), Expect = 0.003
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           +F+ GLP  +   ++  L   F   ++ +L   S+T  S+ +AF  + D      A+  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 125 NN 126
           N 
Sbjct: 63  NG 64

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

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREF--PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           T++V  LP++     +  +F ++    Y S      T + + FAF  F   + A  A   
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 124 LNNF 127
           LNN 
Sbjct: 61  LNNP 64

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|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 = 33.8 bits (78), Expect = 0.004
 Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           LFV  LP      E+  LF  F      HL     T+ S+ FAF  F   + A+ A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 125 NN 126
           + 
Sbjct: 62  DG 63

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

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 21/103 (20%), Positives = 37/103 (35%), Gaps = 12/103 (11%)

Query: 37  QPYMPQPQPPP----------LGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFR 86
             Y+P PQ  P            +      +    D    +++  LP  +   +I  L  
Sbjct: 258 HDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLE 317

Query: 87  EFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
            F   ++ +L    +T  S+ +AF  + D      A+ ALN  
Sbjct: 318 SFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGK 360

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

 Score = 34.1 bits (79), Expect = 0.004
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPG---YESSHLRSSTQNSQPFAFAVFSDQQSA 117
           RT+F+  LP D    E+  LF +F G   Y        T +S+  AF  F  ++SA
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQF-GEVKYARIVKDKLTGHSKGTAFVKFKTKESA 55

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

 Score = 34.0 bits (78), Expect = 0.004
 Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           + V  LP +   +++  LF  +   +S  + +   Q+++ FAF  FS  + AL AM AL 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNALK 62

Query: 126 N 126
           +
Sbjct: 63  D 63

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	144
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.82
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.77
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.77
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.76
KOG0122	270	consensus Translation initiation factor 3, subunit	99.75
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.75
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.75
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.73
PLN03120	260	nucleic acid binding protein; Provisional	99.73
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.71
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.69
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.68
PLN03121	243	nucleic acid binding protein; Provisional	99.67
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.66
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.66
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.66
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.65
smart00362	72	RRM_2 RNA recognition motif.	99.65
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.65
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.64
PLN03213	759	repressor of silencing 3; Provisional	99.64
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.62
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.61
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.61
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.61
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.61
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.6
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.6
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.59
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.59
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.58
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.57
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.56
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.56
smart00360	71	RRM RNA recognition motif.	99.55
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.55
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.54
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.53
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.53
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.52
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.52
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.5
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.5
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.5
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.47
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.45
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.43
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.41
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.38
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.38
smart00361	70	RRM_1 RNA recognition motif.	99.38
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.35
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.33
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.33
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.32
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.32
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.32
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.28
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.28
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.26
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.26
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.21
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.16
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.14
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.14
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.14
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.14
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.11
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.09
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.08
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.06
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.04
KOG0151	877	consensus Predicted splicing regulator, contains R	99.02
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.98
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.98
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.96
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.94
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.94
KOG0226	290	consensus RNA-binding proteins [General function p	98.83
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.83
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.76
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.72
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.71
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.56
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.55
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.5
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.37
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.27
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.26
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.25
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.23
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.22
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.22
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.08
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.01
KOG2314	698	consensus Translation initiation factor 3, subunit	98.0
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.94
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.93
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.9
KOG4210	285	consensus Nuclear localization sequence binding pr	97.85
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.78
KOG3152	278	consensus TBP-binding protein, activator of basal	97.76
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.72
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.71
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.69
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.69
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.64
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.54
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.52
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.52
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.5
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	97.39
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.37
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.32
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	97.29
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.24
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.16
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.06
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	97.04
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.0
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.0
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.94
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.77
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.71
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.62
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.6
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.51
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.45
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.45
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.3
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.24
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.97
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.82
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.65
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.65
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.38
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.29
KOG2318	650	consensus Uncharacterized conserved protein [Funct	95.22
KOG2135	526	consensus Proteins containing the RNA recognition	95.17
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.13
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	93.87
KOG4210	285	consensus Nuclear localization sequence binding pr	92.57
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	91.81
KOG4660	549	consensus Protein Mei2, essential for commitment t	91.5
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	90.36
COG5178	2365	PRP8 U5 snRNP spliceosome subunit [RNA processing	87.14
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	86.5
KOG2891	445	consensus Surface glycoprotein [General function p	85.7
KOG2295	648	consensus C2H2 Zn-finger protein [General function	84.15
PF08544	85	GHMP_kinases_C: GHMP kinases C terminal ; InterPro	84.13
PHA01732	94	proline-rich protein	83.57
PF09707	86	Cas_Cas2CT1978: CRISPR-associated protein (Cas_Cas	83.08
KOG3671	569	consensus Actin regulatory protein (Wiskott-Aldric	81.86
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	80.01

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

Probab=99.82  E-value=1.3e-19  Score=131.31  Aligned_cols=80  Identities=15%  Similarity=0.228  Sum_probs=71.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+++++|++|+++|++||.|++|+++.++.++  ++||||+|++.++|++|++.|||..|+  |+.|+|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~--Gr~l~V  108 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELN--GRHIRV  108 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC--CEEEEE
Confidence            3456789999999999999999999999999999999886544  449999999999999999999999995  889999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|..
T Consensus       109 ~~a~  112 (144)
T PLN03134        109 NPAN  112 (144)
T ss_pred             EeCC
Confidence            9874

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.77  E-value=3.6e-18  Score=137.94  Aligned_cols=79  Identities=16%  Similarity=0.285  Sum_probs=71.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ..+++|||+||+.++++++|+++|++||.|++|+|+++..+  .++||||+|++.++|.+|++.|||..|+  |+.|+|+
T Consensus       267 ~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~--gr~i~V~  344 (352)
T TIGR01661       267 GAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLG--NRVLQVS  344 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEE
Confidence            45668999999999999999999999999999999988533  4459999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |..
T Consensus       345 ~~~  347 (352)
T TIGR01661       345 FKT  347 (352)
T ss_pred             Ecc
Confidence            963

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.77  E-value=2e-18  Score=108.45  Aligned_cols=69  Identities=28%  Similarity=0.433  Sum_probs=61.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeec-CCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-TQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~-~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      |||+|||.++++++|+++|++||.+..+.+..+ .+..++||||+|++.++|++|++.|||..+.  |+.||
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~--~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKIN--GRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEEC--ccCcC
Confidence            799999999999999999999999999999886 3333449999999999999999999999994  77765

(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=99.76  E-value=4.6e-18  Score=137.35  Aligned_cols=78  Identities=21%  Similarity=0.265  Sum_probs=70.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...+|||+|||.+++|++|+++|++||.|.+|+|++++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|+|
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~--g~~i~v~~   79 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQ--NKTIKVSY   79 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEEC--CeeEEEEe
Confidence            35789999999999999999999999999999999886543  449999999999999999999999994  88899988


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        80 a~   81 (352)
T TIGR01661        80 AR   81 (352)
T ss_pred             ec
Confidence            64

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

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

Probab=99.75  E-value=8.2e-18  Score=129.43  Aligned_cols=82  Identities=26%  Similarity=0.358  Sum_probs=75.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ..++..||-|.||+++++|++|++||..||.|..|.|.+|+.++.+  ||||+|+++++|.+||+.|||.-++  ..+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd--~LILr  262 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYD--NLILR  262 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccc--eEEEE
Confidence            4456778999999999999999999999999999999999877655  9999999999999999999999996  88999


Q ss_pred             EEeecC
Q 032280          138 FPHSMA  143 (144)
Q Consensus       138 v~~s~~  143 (144)
                      ||||..
T Consensus       263 vEwskP  268 (270)
T KOG0122|consen  263 VEWSKP  268 (270)
T ss_pred             EEecCC
Confidence            999974

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

Probab=99.75  E-value=3e-18  Score=120.76  Aligned_cols=78  Identities=15%  Similarity=0.226  Sum_probs=70.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+.|||||||++.++|++|.+||+++|.|..|.+-.|+-++.+  ||||+|.+.++|+.|++.+||+.++  .+.|+|+|
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLd--dr~ir~D~  112 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLD--DRPIRIDW  112 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccc--ccceeeec
Confidence            4679999999999999999999999999999999888655544  9999999999999999999999996  78899998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      .-
T Consensus       113 D~  114 (153)
T KOG0121|consen  113 DA  114 (153)
T ss_pred             cc
Confidence            64

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.75  E-value=9.8e-18  Score=136.85  Aligned_cols=79  Identities=23%  Similarity=0.344  Sum_probs=70.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||++++||++|+++|++||.|++|+|+.+..++  ++||||+|.|.++|++|++.|||..+.  ++.|+|+
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~--gr~i~V~  182 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVR--NKRLKVS  182 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccC--Cceeeee
Confidence            356799999999999999999999999999999999885543  349999999999999999999999994  7889998


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       183 ~a~  185 (346)
T TIGR01659       183 YAR  185 (346)
T ss_pred             ccc
Confidence            864

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).

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

Probab=99.73  E-value=1.2e-17  Score=132.94  Aligned_cols=81  Identities=16%  Similarity=0.232  Sum_probs=74.3

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...+.-++|+|+|||+...|-||+.+|++||.|.+|+|+.+.+++++||||+|++.+||++|.++|+|+.+.  |++|.|
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VE--GRkIEV  168 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVE--GRKIEV  168 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceee--ceEEEE
Confidence            344566899999999999999999999999999999999999988899999999999999999999999994  888888


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      ...
T Consensus       169 n~A  171 (376)
T KOG0125|consen  169 NNA  171 (376)
T ss_pred             ecc
Confidence            754

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.73  E-value=3.5e-17  Score=127.97  Aligned_cols=75  Identities=23%  Similarity=0.263  Sum_probs=68.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++||||||+++++|++|+++|+.||.|++|+|.+++.. ++||||+|++.++|+.|+ .|||..|.  |+.|+|+++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~-~GfAFVtF~d~eaAe~Al-lLnG~~l~--gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENER-SQIAYVTFKDPQGAETAL-LLSGATIV--DQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC-CCEEEEEeCcHHHHHHHH-HhcCCeeC--CceEEEEecc
Confidence            689999999999999999999999999999999887643 349999999999999999 59999994  8889998764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.71  E-value=8.8e-17  Score=131.25  Aligned_cols=79  Identities=20%  Similarity=0.337  Sum_probs=70.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+||+.+++|++|+++|++||.|++|+|+.++.+++  .||||+|++.++|++||+.|||..+++.++.|+|.|.
T Consensus       193 ~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a  272 (346)
T TIGR01659       193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLA  272 (346)
T ss_pred             cceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEEC
Confidence            45799999999999999999999999999999998865443  4999999999999999999999999766678888775


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       273 ~  273 (346)
T TIGR01659       273 E  273 (346)
T ss_pred             C
Confidence            3

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).

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

Probab=99.69  E-value=3.2e-16  Score=119.67  Aligned_cols=82  Identities=51%  Similarity=0.788  Sum_probs=74.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC---cEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ---PFAFAVFSDQQSALGAMYALNNFAP-SDSACSL  136 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~---~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l  136 (144)
                      .+++|||||++||.|+...||+.||+.|-+.+.+.|++..+.++   ++|||+|.+..+|.+|+++|||.+| .+.+.+|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            46799999999999999999999999999999999988755543   4999999999999999999999999 5679999


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +||+.+
T Consensus       111 hiElAK  116 (284)
T KOG1457|consen  111 HIELAK  116 (284)
T ss_pred             Eeeehh
Confidence            999865

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

Probab=99.68  E-value=1.2e-16  Score=117.84  Aligned_cols=75  Identities=20%  Similarity=0.263  Sum_probs=67.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeecC
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMA  143 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~~  143 (144)
                      .++||||||..++++.||+.+|..||.|.+|-|..+   .-+||||||+|..+|+.|+..|||+.|  +|..|+||.|..
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn---PPGfAFVEFed~RDA~DAvr~LDG~~~--cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN---PPGFAFVEFEDPRDAEDAVRYLDGKDI--CGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec---CCCceEEeccCcccHHHHHhhcCCccc--cCceEEEEeecC
Confidence            568999999999999999999999999999888653   222999999999999999999999999  599999999864

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.67  E-value=4.2e-16  Score=120.53  Aligned_cols=74  Identities=16%  Similarity=0.179  Sum_probs=65.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+..||||+||++++||++|+++|+.||.|++|+|+++++.+ +||||+|++.++|+.|+ .|||..|.  ++.|.|.
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~-gfAfVtF~d~~aaetAl-lLnGa~l~--d~~I~It   76 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYA-CTAYVTFKDAYALETAV-LLSGATIV--DQRVCIT   76 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcc-eEEEEEECCHHHHHHHH-hcCCCeeC--CceEEEE
Confidence            346899999999999999999999999999999999885544 49999999999999999 89999995  5667665

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

Probab=99.66  E-value=5.5e-16  Score=133.85  Aligned_cols=78  Identities=18%  Similarity=0.316  Sum_probs=71.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..++|||+||+.++++++|+++|+.||.|++|++.+++.+  .++||||+|++.++|.+|++.|||..|  +|+.|+|.+
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~el--gGr~LrV~k  280 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDL--GGQYLRVGK  280 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCee--CCeEEEEEe
Confidence            4579999999999999999999999999999999988543  345999999999999999999999999  499999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       281 Ai  282 (612)
T TIGR01645       281 CV  282 (612)
T ss_pred             cC
Confidence            75

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

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

Probab=99.66  E-value=4.5e-16  Score=133.46  Aligned_cols=75  Identities=20%  Similarity=0.293  Sum_probs=68.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      +||||||+.++||++|+++|++||.|++|++.+|+.++  .+||||+|.+.++|++|++.||+..+.  |+.|+|.|+.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~--gk~i~i~~s~   78 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLG--GKPIRIMWSQ   78 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CeeEEeeccc
Confidence            79999999999999999999999999999999886543  349999999999999999999999994  8889999974

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

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

Probab=99.66  E-value=2.2e-16  Score=117.68  Aligned_cols=78  Identities=27%  Similarity=0.553  Sum_probs=68.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||||||-++.|+||++||.+||.|..|.|+. ..+.-+||||+|+|..+|+.||..-||..++  |+.|+|||-
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~-r~g~ppfafVeFEd~RDAeDAiygRdGYdyd--g~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKN-RPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD--GCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEecc-CCCCCCeeEEEecCccchhhhhhcccccccC--cceEEEEec
Confidence            3467899999999999999999999999999999863 3333449999999999999999999999996  899999985


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        81 r   81 (241)
T KOG0105|consen   81 R   81 (241)
T ss_pred             c
Confidence            3

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.65  E-value=1.2e-15  Score=96.59  Aligned_cols=69  Identities=26%  Similarity=0.405  Sum_probs=59.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      |||+|||.++++++|+++|+.+|.|..+++..++.+ .+++|||+|.+.++|.+|++.++|..|+  |+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~--g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEID--GRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEEC--CEEcC
Confidence            799999999999999999999999999999987552 2239999999999999999999999994  76664

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

>smart00362 RRM_2 RNA recognition motif

Probab=99.65  E-value=1.7e-15  Score=93.78  Aligned_cols=71  Identities=35%  Similarity=0.481  Sum_probs=63.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      +|||+||+.++++++|+++|++||.+..+++..+.+...++|||+|.+.++|++|++.++|..+.  |+.|+|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~--~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLG--GRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEEC--CEEEee
Confidence            58999999999999999999999999999988766334459999999999999999999999994  777765

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

Probab=99.65  E-value=1.3e-15  Score=120.16  Aligned_cols=85  Identities=16%  Similarity=0.208  Sum_probs=74.5

Q ss_pred             CCCCCCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCC
Q 032280           55 FPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDS  132 (144)
Q Consensus        55 ~~~~~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~  132 (144)
                      .+++...+.-+||||+.|+++++|+.|++.|+.||.|+.|+|+.|+.++++  ||||+|++..+...|.+..+|..|+  
T Consensus        92 ~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Id--  169 (335)
T KOG0113|consen   92 NDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKID--  169 (335)
T ss_pred             CCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceec--
Confidence            344555677899999999999999999999999999999999999766555  9999999999999999999999997  


Q ss_pred             CCeEEEEee
Q 032280          133 ACSLLFPHS  141 (144)
Q Consensus       133 g~~l~v~~s  141 (144)
                      |+.|-|++.
T Consensus       170 grri~VDvE  178 (335)
T KOG0113|consen  170 GRRILVDVE  178 (335)
T ss_pred             CcEEEEEec
Confidence            666666654

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

Probab=99.64  E-value=8.6e-16  Score=132.65  Aligned_cols=78  Identities=14%  Similarity=0.198  Sum_probs=69.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++||||||+++++|++|+++|++||.|++|++++|+.+  .++||||+|++.++|++|++.|||..|+  |+.|+|.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~--GR~IkV~  182 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG--GRNIKVG  182 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEe--cceeeec
Confidence            34578999999999999999999999999999999988544  3449999999999999999999999995  8888887


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      +.
T Consensus       183 rp  184 (612)
T TIGR01645       183 RP  184 (612)
T ss_pred             cc
Confidence            64

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.64  E-value=1.2e-15  Score=127.44  Aligned_cols=76  Identities=18%  Similarity=0.246  Sum_probs=67.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCH--HHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQ--QSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~--~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ....+||||||++++++++|+++|+.||.|.+|.|++.+  +++||||+|.+.  .++.+||+.|||..+  +|+.|+|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET--GRGFAFVEMssdddaEeeKAISaLNGAEW--KGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK--GRSFAYIDFSPSSTNSLTKLFSTYNGCVW--KGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc--CCceEEEEecCCcHHHHHHHHHHhcCCee--cCceeEEe
Confidence            345689999999999999999999999999999999544  467999999987  789999999999999  58999997


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      -.
T Consensus        84 KA   85 (759)
T PLN03213         84 KA   85 (759)
T ss_pred             ec
Confidence            54

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

Probab=99.62  E-value=2.5e-15  Score=129.32  Aligned_cols=80  Identities=23%  Similarity=0.263  Sum_probs=68.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +...+|||+||+.+++|++|+++|++||.|.+|+|++|.. .+++||||+|.+.++|++||+.|||..+. .++.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~-~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIR-PGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeec-CCccccccc
Confidence            3457899999999999999999999999999999998832 33459999999999999999999999984 366777766


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      |.
T Consensus       135 S~  136 (578)
T TIGR01648       135 SV  136 (578)
T ss_pred             cc
Confidence            54

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.

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

Probab=99.62  E-value=2.9e-15  Score=128.95  Aligned_cols=74  Identities=24%  Similarity=0.305  Sum_probs=67.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcC--CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREF--PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~--G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.+++|++|+++|++|  |.|++|++++  +    ||||+|++.++|++|++.|||..|+  |+.|+|+
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--g----fAFVeF~s~e~A~kAi~~lnG~~i~--Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--D----YAFVHFEDREDAVKAMDELNGKELE--GSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--C----eEEEEeCCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            346899999999999999999999999  9999998753  2    9999999999999999999999995  8999999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      |+..
T Consensus       303 ~Akp  306 (578)
T TIGR01648       303 LAKP  306 (578)
T ss_pred             EccC
Confidence            9853

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=99.61  E-value=5.3e-15  Score=124.99  Aligned_cols=78  Identities=21%  Similarity=0.296  Sum_probs=69.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +..++||||||+.++++++|+++|+.||.|..+.++.+..+  .++||||+|.+.++|..|++.|||..|.  |+.|+|.
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~--~~~l~v~  370 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTG--DNKLHVQ  370 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEE
Confidence            45689999999999999999999999999999999887433  3459999999999999999999999995  7788888


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      ++
T Consensus       371 ~a  372 (509)
T TIGR01642       371 RA  372 (509)
T ss_pred             EC
Confidence            85

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

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

Probab=99.61  E-value=4.7e-15  Score=125.56  Aligned_cols=79  Identities=18%  Similarity=0.149  Sum_probs=69.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ...+|||+||++++++++|+++|+.||.|++|.+.++++  ..+|||+|++.++|.+|++.|||..|.+.++.|+|+||.
T Consensus        95 ~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~--~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk  172 (481)
T TIGR01649        95 KVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN--VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAK  172 (481)
T ss_pred             ceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC--ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEec
Confidence            345899999999999999999999999999999876443  248999999999999999999999997566899999986


Q ss_pred             C
Q 032280          143 A  143 (144)
Q Consensus       143 ~  143 (144)
                      .
T Consensus       173 ~  173 (481)
T TIGR01649       173 P  173 (481)
T ss_pred             C
Confidence            3

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).

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

Probab=99.61  E-value=7.1e-15  Score=100.35  Aligned_cols=76  Identities=21%  Similarity=0.350  Sum_probs=66.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +..+.|||.|||+++|.++..+||.+||.|..|++-..+.+. +-|||.|+|..+|.+|++.|+|..++  ++-|.|-|
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~Tr-GTAFVVYedi~dAk~A~dhlsg~n~~--~ryl~vly   91 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETR-GTAFVVYEDIFDAKKACDHLSGYNVD--NRYLVVLY   91 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcC-ceEEEEehHhhhHHHHHHHhcccccC--CceEEEEe
Confidence            557899999999999999999999999999999997555444 48999999999999999999999995  77777654

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

Probab=99.61  E-value=4.2e-15  Score=124.18  Aligned_cols=76  Identities=22%  Similarity=0.384  Sum_probs=69.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+||+.++++++|+++|++||.|.+|.+..+..+  .++||||+|.+.++|.+|++.|||..|.  |+.|+|.|.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~--g~~i~v~~a  263 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELA--GRPIKVGYA  263 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEEC--CEEEEEEEc
Confidence            689999999999999999999999999999999887654  3349999999999999999999999994  889999984

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

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

Probab=99.60  E-value=5.8e-15  Score=126.61  Aligned_cols=79  Identities=20%  Similarity=0.257  Sum_probs=70.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....+|||+||+.++++++|+++|++||.|++|++..+. +..++||||+|++.++|.+|++.|||..|.  |+.|+|.|
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~--gk~l~V~~  360 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLG--GKPLYVAL  360 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeC--CceeEEEe
Confidence            345689999999999999999999999999999998874 334459999999999999999999999994  88899988


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      ..
T Consensus       361 a~  362 (562)
T TIGR01628       361 AQ  362 (562)
T ss_pred             cc
Confidence            54

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

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

Probab=99.60  E-value=4.4e-15  Score=125.73  Aligned_cols=73  Identities=18%  Similarity=0.172  Sum_probs=65.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHh--cCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL--NNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~l--nG~~~~~~g~~l~v~~s  141 (144)
                      +++|||+||+++++|++|+++|++||.|++|+++.++    +||||+|++.++|++|++.|  ||..+  .|+.|+|+||
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k----~~afVef~~~e~A~~Ai~~~~~~~~~l--~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGK----RQALVEFEDEESAKACVNFATSVPIYI--RGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCC----CEEEEEeCchHHHHHHHHHhhcCCceE--cCeEEEEEec
Confidence            5899999999999999999999999999999998643    39999999999999999875  67777  4889999998


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        76 ~   76 (481)
T TIGR01649        76 T   76 (481)
T ss_pred             C
Confidence            4

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).

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

Probab=99.59  E-value=9.5e-15  Score=122.07  Aligned_cols=78  Identities=21%  Similarity=0.321  Sum_probs=68.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...+||||+||+.++++++|+++|++||.|.+|+++.++.++  ++||||+|.+.++|.+|| .|||..|.  |+.|.|.
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al-~l~g~~~~--g~~i~v~  163 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL-ALTGQMLL--GRPIIVQ  163 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHH-HhCCCEEC--CeeeEEe
Confidence            346899999999999999999999999999999999885443  449999999999999999 59999994  7888887


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus       164 ~~~  166 (457)
T TIGR01622       164 SSQ  166 (457)
T ss_pred             ecc
Confidence            753

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.

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

Probab=99.59  E-value=2e-16  Score=117.43  Aligned_cols=78  Identities=21%  Similarity=0.393  Sum_probs=72.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .++.-||||||+++.||.||--+|++||+|++|.|++|++++++  |||+.|+|..+..-|+..|||..|.  |+.|||+
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~--gRtirVD  110 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKIL--GRTIRVD  110 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceec--ceeEEee
Confidence            45667999999999999999999999999999999999877655  9999999999999999999999994  9999999


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      +.
T Consensus       111 Hv  112 (219)
T KOG0126|consen  111 HV  112 (219)
T ss_pred             ec
Confidence            85

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

Probab=99.58  E-value=5.1e-15  Score=113.46  Aligned_cols=64  Identities=19%  Similarity=0.352  Sum_probs=57.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhc
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ....+||||||+|++..++|++.|++||+|++..++.|+.++++  ||||+|.|.++|.+||+.-|
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~   75 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN   75 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC
Confidence            34568999999999999999999999999999999999766554  99999999999999998765

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

Probab=99.57  E-value=1.8e-14  Score=108.96  Aligned_cols=76  Identities=30%  Similarity=0.410  Sum_probs=69.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++||||||+.++++++|+++|.+||.+..+++..++  +..++||||+|.+.++|..|++.+||..|.  |+.|+|++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~--~~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELE--GRPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeEC--CceeEeecc
Confidence            5899999999999999999999999999999998885  334459999999999999999999999994  888999874

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

Probab=99.57  E-value=1.4e-14  Score=113.29  Aligned_cols=76  Identities=13%  Similarity=0.213  Sum_probs=70.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..+..+|||||+...++|++|++.|+.||.|.+||+..+++    |+||.|++.|+|.+||..+||+++  .|..+|..|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qG----YaFVrF~tkEaAahAIv~mNntei--~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQG----YAFVRFETKEAAAHAIVQMNNTEI--GGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccc----eEEEEecchhhHHHHHHHhcCcee--CceEEEEec
Confidence            45568999999999999999999999999999999987766    999999999999999999999999  489999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      .+
T Consensus       235 GK  236 (321)
T KOG0148|consen  235 GK  236 (321)
T ss_pred             cc
Confidence            64

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

Probab=99.56  E-value=1.1e-14  Score=113.53  Aligned_cols=77  Identities=21%  Similarity=0.292  Sum_probs=71.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...|.|.-||.++|+|||+.||+..|+|++|+|++|+-++++  ||||.|.+.++|++|+..|||.++  ..++|+|.|.
T Consensus        41 kTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrL--Q~KTIKVSyA  118 (360)
T KOG0145|consen   41 KTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRL--QNKTIKVSYA  118 (360)
T ss_pred             cceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceee--ccceEEEEec
Confidence            346889999999999999999999999999999999877665  999999999999999999999999  5889999986


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       119 R  119 (360)
T KOG0145|consen  119 R  119 (360)
T ss_pred             c
Confidence            5

>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=99.56  E-value=7.2e-14  Score=86.80  Aligned_cols=73  Identities=34%  Similarity=0.474  Sum_probs=64.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +|+|+||+.++++++|+++|+.+|.+..+.+..+..+ ..++|||+|.+.++|..|++.++|..+.  |+.++|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~--~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELG--GRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeEC--CeEEEEeC
Confidence            5899999999999999999999999999999876433 2349999999999999999999999984  78888764

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).

>smart00360 RRM RNA recognition motif

Probab=99.55  E-value=4.5e-14  Score=86.92  Aligned_cols=69  Identities=33%  Similarity=0.431  Sum_probs=60.3

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC--CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           69 VAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ--NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        69 VgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~--~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      |+||+.++++++|+++|++||.|..+.+..++.  ..+++|||+|.+.++|.+|++.|+|..+.  |+.|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~--~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELD--GRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeC--CcEEEeC
Confidence            689999999999999999999999999987643  23349999999999999999999999994  7777763

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

Probab=99.55  E-value=5.7e-15  Score=116.34  Aligned_cols=69  Identities=19%  Similarity=0.397  Sum_probs=64.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .||||||+.++++.+|+.||++||+|.+|.|++|      ||||+.+|...|+.||+.|+|..|+  |..|+||-|+
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN------YgFVHiEdktaaedairNLhgYtLh--g~nInVeaSk   72 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN------YGFVHIEDKTAAEDAIRNLHGYTLH--GVNINVEASK   72 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc------cceEEeecccccHHHHhhcccceec--ceEEEEEecc
Confidence            5999999999999999999999999999999864      9999999999999999999999995  8889998775

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

Probab=99.54  E-value=5.5e-15  Score=112.82  Aligned_cols=82  Identities=20%  Similarity=0.304  Sum_probs=73.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....||||||+|-.+|+|.-|...|-.||.|.+|.+..|-  .+.++||||+|+..++|.+||..||+.+|  .|++|||
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL--~GrtirV   84 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESEL--FGRTIRV   84 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhh--cceeEEE
Confidence            3567999999999999999999999999999999998873  34455999999999999999999999999  5999999


Q ss_pred             EeecCC
Q 032280          139 PHSMAM  144 (144)
Q Consensus       139 ~~s~~~  144 (144)
                      .+.+.+
T Consensus        85 N~AkP~   90 (298)
T KOG0111|consen   85 NLAKPE   90 (298)
T ss_pred             eecCCc
Confidence            997653

>PF13893 RRM_5: RNA recognition motif

Probab=99.53  E-value=7e-14  Score=85.26  Aligned_cols=56  Identities=23%  Similarity=0.325  Sum_probs=49.5

Q ss_pred             HHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           81 IYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        81 L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      |+++|++||.|.++++..++   +.+|||+|++.++|++|++.|||..|  .|+.|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~---~~~a~V~f~~~~~A~~a~~~l~~~~~--~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK---RGFAFVEFASVEDAQKAIEQLNGRQF--NGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS---TTEEEEEESSHHHHHHHHHHHTTSEE--TTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCEE--CCcEEEEEEC
Confidence            78999999999999986544   34999999999999999999999999  4889999997

(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 ....

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

Probab=99.53  E-value=2.8e-14  Score=119.14  Aligned_cols=76  Identities=21%  Similarity=0.323  Sum_probs=71.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      +++||||++++++|++|.++|+..|.|.+++++.|+.+++.  |||++|.+.++|++|++.|||.++  .|+.|+|+|..
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~--~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEF--NGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCccc--CCceEEeeccc
Confidence            88999999999999999999999999999999999766654  999999999999999999999999  59999999864

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

Probab=99.52  E-value=5.3e-14  Score=115.99  Aligned_cols=79  Identities=25%  Similarity=0.312  Sum_probs=72.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..-||||.||.|+.|+||..||++.|+|-+++|.+|.  +.+++||||+|.+.++|++|++.||+++|. .|+.|+|+-|
T Consensus        83 G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir-~GK~igvc~S  161 (506)
T KOG0117|consen   83 GCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIR-PGKLLGVCVS  161 (506)
T ss_pred             CceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcccc-CCCEeEEEEe
Confidence            4679999999999999999999999999999999984  445569999999999999999999999995 5999999998


Q ss_pred             cC
Q 032280          142 MA  143 (144)
Q Consensus       142 ~~  143 (144)
                      ++
T Consensus       162 va  163 (506)
T KOG0117|consen  162 VA  163 (506)
T ss_pred             ee
Confidence            75

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

Probab=99.52  E-value=3.6e-14  Score=116.97  Aligned_cols=73  Identities=23%  Similarity=0.354  Sum_probs=65.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...+.|||.||..++||+.|+++|++||.|+.|+.++|      ||||+|.++++|.+||+.|||+.|+  |..|.|...
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD------YaFVHf~eR~davkAm~~~ngkeld--G~~iEvtLA  328 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD------YAFVHFAEREDAVKAMKETNGKELD--GSPIEVTLA  328 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc------eeEEeecchHHHHHHHHHhcCceec--CceEEEEec
Confidence            35689999999999999999999999999999887644      9999999999999999999999996  777777654


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      +
T Consensus       329 K  329 (506)
T KOG0117|consen  329 K  329 (506)
T ss_pred             C
Confidence            3

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

Probab=99.50  E-value=4.7e-14  Score=100.52  Aligned_cols=79  Identities=19%  Similarity=0.279  Sum_probs=71.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+...|||.++....+|++|.+.|..||+|++++|-.|++++.  +||.|+|++...|++|+++|||..|.  +..|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll--~q~v~VD  147 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELL--GQNVSVD  147 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhh--CCceeEE
Confidence            3567899999999999999999999999999999988877664  39999999999999999999999995  7889999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |..
T Consensus       148 w~F  150 (170)
T KOG0130|consen  148 WCF  150 (170)
T ss_pred             EEE
Confidence            864

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

Probab=99.50  E-value=2.4e-14  Score=117.66  Aligned_cols=79  Identities=27%  Similarity=0.356  Sum_probs=69.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~v~~  140 (144)
                      +.++||||-|+..++|.|++++|++||.|++|.|.++. +.+++||||.|++++.|..||++|||..- .|+...|.|.|
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            35789999999999999999999999999999999974 44566999999999999999999999864 66777788877


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      .
T Consensus       203 A  203 (510)
T KOG0144|consen  203 A  203 (510)
T ss_pred             c
Confidence            4

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

Probab=99.50  E-value=4.4e-14  Score=106.92  Aligned_cols=79  Identities=19%  Similarity=0.279  Sum_probs=70.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .+...+|-|-||-+.++.++|+.+|++||.|.+|.|-+|..++.  +||||.|.+..+|+.|+++|+|..||  |+.|+|
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ld--gRelrV   87 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLD--GRELRV   87 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeec--cceeee
Confidence            35567899999999999999999999999999999988865544  49999999999999999999999997  778887


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      .+.
T Consensus        88 q~a   90 (256)
T KOG4207|consen   88 QMA   90 (256)
T ss_pred             hhh
Confidence            653

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

Probab=99.47  E-value=1.2e-13  Score=102.65  Aligned_cols=80  Identities=23%  Similarity=0.272  Sum_probs=70.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ..+...|||||||+..++++.|+++|-+.|.|+++++-+++.+.  ++||||+|.++++|+-|++.||+.++-  |+.|+
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLY--grpIr   82 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLY--GRPIR   82 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhc--CceeE
Confidence            34567899999999999999999999999999999998875443  449999999999999999999988884  88888


Q ss_pred             EEee
Q 032280          138 FPHS  141 (144)
Q Consensus       138 v~~s  141 (144)
                      |.-+
T Consensus        83 v~ka   86 (203)
T KOG0131|consen   83 VNKA   86 (203)
T ss_pred             EEec
Confidence            8654

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

Probab=99.45  E-value=3.4e-13  Score=110.97  Aligned_cols=80  Identities=18%  Similarity=0.277  Sum_probs=68.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAP-SDSACSLLF  138 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~v  138 (144)
                      .+.-+||||-+|+.++|+||+++|++||.|.+|.|++|+.++..  ||||.|.++++|.+|+.+|+..+. .|....|+|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            34557999999999999999999999999999999999766543  999999999999999999998654 666667776


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      .|.
T Consensus       112 k~A  114 (510)
T KOG0144|consen  112 KYA  114 (510)
T ss_pred             ccc
Confidence            653

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

Probab=99.43  E-value=2.9e-13  Score=105.88  Aligned_cols=77  Identities=13%  Similarity=0.236  Sum_probs=69.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +-.+|||.|..+++-++||+.|..||+|.++++++|..+.  ++||||.|-+.++|+.||..|||.=|  .++.||-.|+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl--G~R~IRTNWA  139 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL--GRRTIRTNWA  139 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee--ccceeecccc
Confidence            4579999999999999999999999999999999995443  44999999999999999999999999  4889999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       140 T  140 (321)
T KOG0148|consen  140 T  140 (321)
T ss_pred             c
Confidence            4

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

Probab=99.41  E-value=7.3e-13  Score=111.66  Aligned_cols=78  Identities=18%  Similarity=0.238  Sum_probs=71.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc-EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP-FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~-~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..+|.|.|||+.+.+.+|+.+|++||.|.+|.|.+...++.+ ||||.|.+..+|.+|++.+||..|+  |+.|.|+|.+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~--gR~VAVDWAV  194 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKID--GRPVAVDWAV  194 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceec--CceeEEeeec
Confidence            457999999999999999999999999999999876655555 9999999999999999999999996  8999999986


Q ss_pred             C
Q 032280          143 A  143 (144)
Q Consensus       143 ~  143 (144)
                      .
T Consensus       195 ~  195 (678)
T KOG0127|consen  195 D  195 (678)
T ss_pred             c
Confidence            4

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

Probab=99.38  E-value=1.6e-12  Score=109.84  Aligned_cols=73  Identities=25%  Similarity=0.402  Sum_probs=58.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcC------------CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCc
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREF------------PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFA  128 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~------------G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~  128 (144)
                      ....++||||||+.++|+++|+++|+++            +.|..+.+..    .++||||+|.+.++|..|| .|||..
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~----~kg~afVeF~~~e~A~~Al-~l~g~~  246 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK----EKNFAFLEFRTVEEATFAM-ALDSII  246 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC----CCCEEEEEeCCHHHHhhhh-cCCCeE
Confidence            3456899999999999999999999975            2344444432    2339999999999999999 699999


Q ss_pred             cCCCCCeEEEEe
Q 032280          129 PSDSACSLLFPH  140 (144)
Q Consensus       129 ~~~~g~~l~v~~  140 (144)
                      |.  |..|+|..
T Consensus       247 ~~--g~~l~v~r  256 (509)
T TIGR01642       247 YS--NVFLKIRR  256 (509)
T ss_pred             ee--CceeEecC
Confidence            95  77788753

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

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

Probab=99.38  E-value=6.9e-13  Score=107.17  Aligned_cols=77  Identities=18%  Similarity=0.291  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..|||-.|+.-+++++|+-||+.||.|.+|.++++++++-.  ||||+|++.+++++|.-.|++..|+  .+.|+|+||.
T Consensus       240 NVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLID--DrRIHVDFSQ  317 (479)
T KOG0415|consen  240 NVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLID--DRRIHVDFSQ  317 (479)
T ss_pred             ceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeec--cceEEeehhh
Confidence            68999999999999999999999999999999999877665  9999999999999999999999996  7889999986


Q ss_pred             C
Q 032280          143 A  143 (144)
Q Consensus       143 ~  143 (144)
                      .
T Consensus       318 S  318 (479)
T KOG0415|consen  318 S  318 (479)
T ss_pred             h
Confidence            4

>smart00361 RRM_1 RNA recognition motif

Probab=99.38  E-value=2.7e-12  Score=81.89  Aligned_cols=59  Identities=12%  Similarity=0.102  Sum_probs=50.0

Q ss_pred             HHHHHHHhh----cCCCeEEEE-EeecC----CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           78 PREIYNLFR----EFPGYESSH-LRSST----QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        78 e~~L~~~F~----~~G~v~~v~-l~~~~----~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      +++|+++|+    +||.|.+|. +..++    +..++||||+|.+.++|.+|++.|||..+.  |+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~--gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFD--GRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEe
Confidence            678999999    999999995 65554    334559999999999999999999999995  777875

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

Probab=99.35  E-value=7.8e-12  Score=97.74  Aligned_cols=78  Identities=18%  Similarity=0.272  Sum_probs=70.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....|||-||..+.+|.-|.++|..||.|.+|++++|-.+++  +||||+..+-++|.-||..|||+.+.  +++|.|.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg--~rvLQVs  353 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLG--DRVLQVS  353 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCcccc--ceEEEEE
Confidence            3467899999999999999999999999999999999955444  49999999999999999999999994  8889998


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |-
T Consensus       354 FK  355 (360)
T KOG0145|consen  354 FK  355 (360)
T ss_pred             Ee
Confidence            74

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

Probab=99.33  E-value=1.8e-12  Score=109.09  Aligned_cols=73  Identities=22%  Similarity=0.357  Sum_probs=65.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .||||||+++++|++|+.+|+.||.|+.|.+.+|.  +..++||||+|.+.++|.+|++.|||.++  .|+.|+|..
T Consensus       280 rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfel--AGr~ikV~~  354 (549)
T KOG0147|consen  280 RLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFEL--AGRLIKVSV  354 (549)
T ss_pred             hhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhcccee--cCceEEEEE
Confidence            49999999999999999999999999999999884  44455999999999999999999999888  488888754

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

Probab=99.33  E-value=5.9e-12  Score=103.71  Aligned_cols=70  Identities=23%  Similarity=0.429  Sum_probs=63.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .|||.||+.+++.++|+++|+.||.|++|++..+..+.++| ||+|++.++|.+|++.|||..+.  ++.|-|
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~--~kki~v  147 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLN--GKKIYV  147 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccC--CCeeEE
Confidence            39999999999999999999999999999999987777778 99999999999999999999994  555544

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

Probab=99.32  E-value=6.6e-12  Score=95.82  Aligned_cols=76  Identities=24%  Similarity=0.313  Sum_probs=66.0

Q ss_pred             cceEEEcCCCCCCCHHHHHH----HhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           64 VRTLFVAGLPEDVKPREIYN----LFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~----~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ..||||.||++.+..++|++    ||++||+|.+|......+ -++-|||.|.+.+.|..|+++|+|..|-  |+.++|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~K-mRGQA~VvFk~~~~As~A~r~l~gfpFy--gK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPK-MRGQAFVVFKETEAASAALRALQGFPFY--GKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCC-ccCceEEEecChhHHHHHHHHhcCCccc--Cchhhee
Confidence            34999999999999999888    999999999998764322 3347999999999999999999999995  7889998


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        86 yA~   88 (221)
T KOG4206|consen   86 YAK   88 (221)
T ss_pred             ccc
Confidence            864

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

Probab=99.32  E-value=4.2e-12  Score=110.44  Aligned_cols=74  Identities=28%  Similarity=0.420  Sum_probs=67.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeecC
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMA  143 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~~  143 (144)
                      +||||||+|+.+++|.||.++|+.||.|.+|.++.+.+    ||||....+.+|++|+..|+...+  .++.|+|.|.+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~----cAfI~M~~RqdA~kalqkl~n~kv--~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRG----CAFIKMVRRQDAEKALQKLSNVKV--ADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCc----eeEEEEeehhHHHHHHHHHhcccc--cceeeEEeeecc
Confidence            48999999999999999999999999999999976555    999999999999999999998888  478899999753

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

Probab=99.32  E-value=7.8e-12  Score=105.55  Aligned_cols=80  Identities=21%  Similarity=0.265  Sum_probs=67.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHh-----cC-CccCCC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYAL-----NN-FAPSDS  132 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~l-----nG-~~~~~~  132 (144)
                      ....+||||.||++++||++|++.|++||.|..+.|+.++.++.+  .|||.|.+..+|..||+..     .| ..+  .
T Consensus       289 ~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll--~  366 (678)
T KOG0127|consen  289 ITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLL--D  366 (678)
T ss_pred             ccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEE--e
Confidence            345689999999999999999999999999999999988766554  9999999999999999887     23 334  4


Q ss_pred             CCeEEEEeec
Q 032280          133 ACSLLFPHSM  142 (144)
Q Consensus       133 g~~l~v~~s~  142 (144)
                      |+.|+|...+
T Consensus       367 GR~Lkv~~Av  376 (678)
T KOG0127|consen  367 GRLLKVTLAV  376 (678)
T ss_pred             ccEEeeeecc
Confidence            8888887543

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

Probab=99.28  E-value=1.2e-11  Score=99.49  Aligned_cols=78  Identities=19%  Similarity=0.254  Sum_probs=65.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+..++|||||||...++|.+|++.|.+||+|+++++...++    +|||+|.++++|+.|.+.+-...+ -+|..|+|-
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~----CAFv~ftTR~aAE~Aae~~~n~lv-I~G~Rl~i~  298 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKG----CAFVTFTTREAAEKAAEKSFNKLV-INGFRLKIK  298 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccc----cceeeehhhHHHHHHHHhhcceee-ecceEEEEE
Confidence            345678999999999999999999999999999999875444    999999999999998866655333 258889999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       299 Wg~  301 (377)
T KOG0153|consen  299 WGR  301 (377)
T ss_pred             eCC
Confidence            975

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

Probab=99.28  E-value=1.2e-11  Score=101.81  Aligned_cols=72  Identities=18%  Similarity=0.184  Sum_probs=67.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..||||   .++||..|+++|+.+|.|+++++.+|. ++-+||||.|.+..+|++||++||...+  +|+.+||.||.
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-tslgy~yvnf~~~~da~~A~~~~n~~~~--~~~~~rim~s~   73 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-TSLGYAYVNFQQPADAERALDTMNFDVL--KGKPIRIMWSQ   73 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-CccceEEEecCCHHHHHHHHHHcCCccc--CCcEEEeehhc
Confidence            369999   999999999999999999999999998 6555999999999999999999999999  59999999985

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

Probab=99.26  E-value=1.4e-11  Score=96.66  Aligned_cols=79  Identities=27%  Similarity=0.372  Sum_probs=68.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~v~~  140 (144)
                      +.|+||||-|...-+|||++++|..||.|++|.+.+.. +..++||||.|.+..+|..||+.|+|.+- .+....|.|.|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK~   97 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVKF   97 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEEe
Confidence            56899999999999999999999999999999998763 34455999999999999999999999765 65666777766


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      .
T Consensus        98 A   98 (371)
T KOG0146|consen   98 A   98 (371)
T ss_pred             c
Confidence            3

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

Probab=99.26  E-value=6.9e-12  Score=99.08  Aligned_cols=73  Identities=16%  Similarity=0.244  Sum_probs=66.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..+.+|+||||...++..||+..|++||.|.+|++++|      |+||.|+-.++|..|++.|||++|+  |+.++|..|
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd------y~fvh~d~~eda~~air~l~~~~~~--gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD------YAFVHFDRAEDAVEAIRGLDNTEFQ--GKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc------eeEEEEeeccchHHHHhcccccccc--cceeeeeee
Confidence            34568999999999999999999999999999999754      9999999999999999999999996  777888766


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       148 t  148 (346)
T KOG0109|consen  148 T  148 (346)
T ss_pred             c
Confidence            3

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

Probab=99.21  E-value=4.1e-11  Score=103.48  Aligned_cols=74  Identities=26%  Similarity=0.274  Sum_probs=65.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-----SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-----~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      |||.||+++++.++|+.+|+..|.|.++.|...++.     +.+||||+|.+.++|++|++.|||+.++  |+.|.|.+|
T Consensus       518 lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvld--GH~l~lk~S  595 (725)
T KOG0110|consen  518 LFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLD--GHKLELKIS  595 (725)
T ss_pred             hhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceec--CceEEEEec
Confidence            999999999999999999999999999998664332     2259999999999999999999999997  777888776


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            4

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

Probab=99.16  E-value=2.7e-11  Score=92.84  Aligned_cols=67  Identities=28%  Similarity=0.463  Sum_probs=59.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      ...|.||||.||..+++|++|+.+|+.|.+....+|.  .+++.+.||++|++.+.|..||..|+|..+
T Consensus       207 ~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~--~~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  207 ARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR--ARGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             chhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe--cCCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            3457799999999999999999999999998777764  356677999999999999999999999998

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

Probab=99.14  E-value=4.2e-11  Score=97.41  Aligned_cols=73  Identities=15%  Similarity=0.213  Sum_probs=65.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+||||.+.+++.|+.||..|..||.|++|.+.+|.-+  .++||||+|+-.+.|.-|++.|||..+.  |++|+|.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlG--GRNiKVg  188 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLG--GRNIKVG  188 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhcccccc--Ccccccc
Confidence            47999999999999999999999999999999888433  3449999999999999999999999994  7778875

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

Probab=99.14  E-value=1e-10  Score=99.50  Aligned_cols=77  Identities=16%  Similarity=0.289  Sum_probs=69.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..|+|||++|+..+...+|++||++||+|+..+++.+.++  .+|||||++.+..+|.+||+.|+-+.|  +|+.|.|+-
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTEL--HGrmISVEk  481 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTEL--HGRMISVEK  481 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhh--cceeeeeee
Confidence            3579999999999999999999999999999999988654  456999999999999999999999999  488888875


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      .
T Consensus       482 a  482 (940)
T KOG4661|consen  482 A  482 (940)
T ss_pred             c
Confidence            4

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

Probab=99.14  E-value=5.6e-11  Score=93.31  Aligned_cols=76  Identities=25%  Similarity=0.353  Sum_probs=66.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+..+|||-.||.+..+.||-.+|-.||.|++.++..|+.++  ++||||.|++..+|+.||.+|||..|.  =+.|+|.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIG--MKRLKVQ  360 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIG--MKRLKVQ  360 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhh--hhhhhhh
Confidence            456789999999999999999999999999999998886554  559999999999999999999999993  3445554

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

Probab=99.14  E-value=1.8e-10  Score=95.44  Aligned_cols=75  Identities=20%  Similarity=0.315  Sum_probs=65.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhh-cCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFR-EFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~-~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ..|.+||.|||+++.+.+|++||+ +.|+|+-|.|..|..++ +.||.|||++.+.+++|++.||-..+  +|+.|+|.
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~--~GR~l~vK  119 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEV--NGRELVVK  119 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccc--cCceEEEe
Confidence            346799999999999999999997 77999999999985544 44999999999999999999999988  47777764

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

Probab=99.11  E-value=1.9e-10  Score=85.65  Aligned_cols=77  Identities=18%  Similarity=0.274  Sum_probs=64.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEE-EEeecCC--CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESS-HLRSSTQ--NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v-~l~~~~~--~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      -..+||||||..+++|..|.++|+.||.+.+. ++.++..  ..++||||.|++.+.+.+|++.|||..+  +++.+.|+
T Consensus        95 vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l--~nr~itv~  172 (203)
T KOG0131|consen   95 VGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYL--CNRPITVS  172 (203)
T ss_pred             ccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchh--cCCceEEE
Confidence            34689999999999999999999999998653 4445533  4445999999999999999999999999  46777777


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |.
T Consensus       173 ya  174 (203)
T KOG0131|consen  173 YA  174 (203)
T ss_pred             EE
Confidence            64

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

Probab=99.09  E-value=5.6e-10  Score=84.41  Aligned_cols=75  Identities=23%  Similarity=0.308  Sum_probs=64.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcC-CCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~-G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...+||+.++..+.+.++..+|++| |.+..+++.+++++|.+  ||||+|++.+.|.-|-+.||++-|.  ++.|.+.+
T Consensus        49 ~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~--e~lL~c~v  126 (214)
T KOG4208|consen   49 EGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLM--EHLLECHV  126 (214)
T ss_pred             ccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhh--hheeeeEE
Confidence            3468999999999999999999999 66788888788766554  9999999999999999999999984  77777654

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

Probab=99.08  E-value=5.3e-11  Score=90.97  Aligned_cols=69  Identities=22%  Similarity=0.184  Sum_probs=63.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      +..|||||+||...|+|+-|.++|-+.|.|.+|.|..++.++..||||.|+++.+..-|++.|||..+.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~   75 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLE   75 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhc
Confidence            456999999999999999999999999999999987776666669999999999999999999999884

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

Probab=99.06  E-value=4e-10  Score=93.96  Aligned_cols=78  Identities=19%  Similarity=0.310  Sum_probs=61.7

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ......+|||+|||.++++++|+++|.+||.|+...|....  .+..+||||+|++.+++..||++-   .+.-.++.|.
T Consensus       284 ~~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As---p~~ig~~kl~  360 (419)
T KOG0116|consen  284 PRADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS---PLEIGGRKLN  360 (419)
T ss_pred             eeecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC---ccccCCeeEE
Confidence            34455679999999999999999999999999888775432  222269999999999999999765   3322578888


Q ss_pred             EEe
Q 032280          138 FPH  140 (144)
Q Consensus       138 v~~  140 (144)
                      ||-
T Consensus       361 Vee  363 (419)
T KOG0116|consen  361 VEE  363 (419)
T ss_pred             EEe
Confidence            874

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

Probab=99.04  E-value=5.6e-10  Score=90.92  Aligned_cols=78  Identities=18%  Similarity=0.322  Sum_probs=67.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...+|||..++.|.+|+||+.+|+.||+|+.|.|.++.  ++.++|||++|.+..+...|+..||=..+  .|.-|||-.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDL--GGQyLRVGk  286 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDL--GGQYLRVGK  286 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhc--ccceEeccc
Confidence            34689999999999999999999999999999998873  34455999999999999999999997777  588898876


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      ++
T Consensus       287 ~v  288 (544)
T KOG0124|consen  287 CV  288 (544)
T ss_pred             cc
Confidence            54

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

Probab=99.02  E-value=5.2e-10  Score=96.92  Aligned_cols=81  Identities=16%  Similarity=0.229  Sum_probs=70.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-----CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-----QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-----~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ...++||||||+..++|+.|...|..||.|.++++..-+     .....||||.|-++.+|++|++.|||..+  .+..+
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv--~~~e~  249 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIV--MEYEM  249 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceee--eeeee
Confidence            446789999999999999999999999999999997642     23334999999999999999999999999  47889


Q ss_pred             EEEeecCC
Q 032280          137 LFPHSMAM  144 (144)
Q Consensus       137 ~v~~s~~~  144 (144)
                      ++-|+.|+
T Consensus       250 K~gWgk~V  257 (877)
T KOG0151|consen  250 KLGWGKAV  257 (877)
T ss_pred             eecccccc
Confidence            99999764

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

Probab=98.98  E-value=5e-10  Score=94.68  Aligned_cols=70  Identities=21%  Similarity=0.233  Sum_probs=60.4

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           58 YGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        58 ~~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      .+.+...++|+|-||+..|++++|+++|+.||+|++|+.-.+   +.+..||+|.|..+|++|+++||+.++-
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~---~~~~~~v~FyDvR~A~~Alk~l~~~~~~  138 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN---KRGIVFVEFYDVRDAERALKALNRREIA  138 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc---cCceEEEEEeehHhHHHHHHHHHHHHhh
Confidence            344556789999999999999999999999999999765433   2338999999999999999999999984

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

Probab=98.98  E-value=4.1e-10  Score=86.29  Aligned_cols=70  Identities=19%  Similarity=0.394  Sum_probs=61.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..+|||+|++.+.+++|+++|..||.+.++.+..  +    |+||+|+|..+|+.|+..|||.+|.  +..+.+||..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--g----f~fv~fed~rda~Dav~~l~~~~l~--~e~~vve~~r   71 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--G----FGFVEFEDPRDADDAVHDLDGKELC--GERLVVEHAR   71 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--c----cceeccCchhhhhcccchhcCceec--ceeeeeeccc
Confidence            3589999999999999999999999999888742  2    9999999999999999999999995  5558888764

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

Probab=98.96  E-value=3.3e-09  Score=82.76  Aligned_cols=74  Identities=19%  Similarity=0.183  Sum_probs=64.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+|+|.||++.|+++||+++|.+||.+..+-+.++..+. .+.|-|.|...++|++|++.+||..++  |..++++.
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ld--G~~mk~~~  158 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALD--GRPMKIEI  158 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccC--CceeeeEE
Confidence            579999999999999999999999999988888875443 348999999999999999999997776  66677764

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

Probab=98.94  E-value=8.5e-10  Score=95.43  Aligned_cols=79  Identities=22%  Similarity=0.295  Sum_probs=68.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ..+..|+|.||++..+-++++.||..||.+.+|+|....  ...++||||+|-+..+|.+|+++|.++.|.  |+.|.++
T Consensus       611 k~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHly--GRrLVLE  688 (725)
T KOG0110|consen  611 KKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLY--GRRLVLE  688 (725)
T ss_pred             cccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhccccee--chhhhee
Confidence            346789999999999999999999999999999996542  223459999999999999999999999996  8889999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |..
T Consensus       689 wA~  691 (725)
T KOG0110|consen  689 WAK  691 (725)
T ss_pred             hhc
Confidence            863

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

Probab=98.94  E-value=2.4e-09  Score=88.83  Aligned_cols=73  Identities=14%  Similarity=0.121  Sum_probs=63.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +..+|||.|||.++|+..|++-|..||.|..+.|.-+   ++.-+.|.|.+.++|++||..|||.+++  |+.|+|.|
T Consensus       535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~---GkskGVVrF~s~edAEra~a~Mngs~l~--Gr~I~V~y  607 (608)
T KOG4212|consen  535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMEN---GKSKGVVRFFSPEDAERACALMNGSRLD--GRNIKVTY  607 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhcc---CCccceEEecCHHHHHHHHHHhccCccc--Cceeeeee
Confidence            4457999999999999999999999999998888432   2225699999999999999999999996  88898876

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

Probab=98.83  E-value=4.7e-09  Score=81.79  Aligned_cols=73  Identities=16%  Similarity=0.360  Sum_probs=64.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .-+||.|.|..+++++.|-+.|++|-.....++++++++++.  |+||.|.|..++..|+++|||..+.  .+.|++
T Consensus       190 DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVg--srpikl  264 (290)
T KOG0226|consen  190 DFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVG--SRPIKL  264 (290)
T ss_pred             cceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccc--cchhHh
Confidence            357999999999999999999999999988889988776655  9999999999999999999999984  444444

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

Probab=98.83  E-value=3.9e-09  Score=85.13  Aligned_cols=61  Identities=18%  Similarity=0.356  Sum_probs=53.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHH
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYA  123 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~  123 (144)
                      +..+||||+|+++++++.|++.|++||+|.+|.+.+|..+++  +|+||+|++.+...+++..
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~   67 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA   67 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc
Confidence            667899999999999999999999999999999998855444  4999999998888887754

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

Probab=98.76  E-value=1.8e-08  Score=78.34  Aligned_cols=79  Identities=14%  Similarity=0.100  Sum_probs=67.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.+.+||||+.+.++-++++..|+.||.+..+.+..++..+  ++|+||+|.+.+.++.|++ |||..|.  +..+.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~--~~~i~v  174 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIP--GPAIEV  174 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccc--ccccee
Confidence            3456889999999999999999999999999988887775443  4499999999999999998 9999995  777877


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      .+-+
T Consensus       175 t~~r  178 (231)
T KOG4209|consen  175 TLKR  178 (231)
T ss_pred             eeee
Confidence            7643

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

Probab=98.72  E-value=7.9e-08  Score=77.72  Aligned_cols=75  Identities=17%  Similarity=0.169  Sum_probs=62.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEE--------EEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYES--------SHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSAC  134 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~--------v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~  134 (144)
                      ...|||+|||.++|.+|+.++|++||.|..        |+|-++..+ -++=|.++|...++.+-|++.|++..|  +|+
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~--rg~  211 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDEL--RGK  211 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccc--cCc
Confidence            456999999999999999999999998843        555555433 233799999999999999999999999  599


Q ss_pred             eEEEEe
Q 032280          135 SLLFPH  140 (144)
Q Consensus       135 ~l~v~~  140 (144)
                      .|+|+-
T Consensus       212 ~~rVer  217 (382)
T KOG1548|consen  212 KLRVER  217 (382)
T ss_pred             EEEEeh
Confidence            999974

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

Probab=98.71  E-value=2.1e-08  Score=80.97  Aligned_cols=58  Identities=24%  Similarity=0.495  Sum_probs=52.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHH
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAM  121 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~  121 (144)
                      .+++|||+|+.++++++|++.|++||.|..+.+.+|..+.+.  |+||+|.+.+++++++
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~  156 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVT  156 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceec
Confidence            568999999999999999999999999999999998665544  9999999999999887

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

Probab=98.56  E-value=3.4e-07  Score=70.15  Aligned_cols=77  Identities=22%  Similarity=0.422  Sum_probs=67.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ....+||+.|||..++.+.|..+|++|.+.++++++..+   ...|||+|.+...|..|...|+|..+. +...++|.++
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~---~~iAfve~~~d~~a~~a~~~lq~~~it-~~~~m~i~~a  219 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR---SGIAFVEFLSDRQASAAQQALQGFKIT-KKNTMQITFA  219 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC---CceeEEecchhhhhHHHhhhhccceec-cCceEEeccc
Confidence            345899999999999999999999999999999997532   228999999999999999999999995 3778888876


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       220 ~  220 (221)
T KOG4206|consen  220 K  220 (221)
T ss_pred             C
Confidence            4

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

Probab=98.55  E-value=3.6e-07  Score=75.42  Aligned_cols=74  Identities=24%  Similarity=0.257  Sum_probs=66.7

Q ss_pred             cceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ...|-|+||.++ ||.+-|..+|+-||.|.+|+|.++++.   -|.|.+.|...|+-|++.|+|..+-  |+.|||.+|+
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd---~ALIQmsd~~qAqLA~~hL~g~~l~--gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKD---NALIQMSDGQQAQLAMEHLEGHKLY--GKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCc---ceeeeecchhHHHHHHHHhhcceec--CceEEEeecc
Confidence            457889999876 899999999999999999999987652   6999999999999999999999994  7999999985

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

Probab=98.50  E-value=1.3e-06  Score=57.69  Aligned_cols=67  Identities=21%  Similarity=0.194  Sum_probs=46.1

Q ss_pred             ceEEEcCCCCCCCHHH----HHHHhhcCCC-eEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           65 RTLFVAGLPEDVKPRE----IYNLFREFPG-YESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~----L~~~F~~~G~-v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ..|||.|||.+.+...    |++|+..+|+ |.+|.    .    +-|.|.|.+.+.|++|.+.|+|..+-  |..|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----~----~tAilrF~~~~~A~RA~KRmegEdVf--G~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----G----GTAILRFPNQEFAERAQKRMEGEDVF--GNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------T----T-EEEEESSHHHHHHHHHHHTT--SS--SS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----C----CEEEEEeCCHHHHHHHHHhhcccccc--cceEEEE
Confidence            4699999999998765    6678889987 33321    1    27999999999999999999999874  7778887


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |+
T Consensus        73 ~~   74 (90)
T PF11608_consen   73 FS   74 (90)
T ss_dssp             SS
T ss_pred             Ec
Confidence            76

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

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

Probab=98.37  E-value=7.3e-07  Score=73.66  Aligned_cols=77  Identities=19%  Similarity=0.161  Sum_probs=64.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .-++.|+|+-+-|+-|-|..+|++||.|.+|.-.. |..+. -|.|.|.|.+.|..|..+|+|..|.+.-|+|||+||.
T Consensus       150 vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~-Knn~F-QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  150 VLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFT-KNNGF-QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             eEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEe-cccch-hhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            34677999999999999999999999998775432 22221 5999999999999999999999996567899999985

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

Probab=98.27  E-value=4e-06  Score=57.71  Aligned_cols=58  Identities=19%  Similarity=0.256  Sum_probs=38.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCC
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF  127 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~  127 (144)
                      .|+|.++...++-++|+++|++||.|.-|.+..    +..-|||.|.+.++|++|++.+.-.
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~----G~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSR----GDTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--T----T-SEEEEEESS---HHHHHHHHHHT
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecC----CCCEEEEEECCcchHHHHHHHHHhc
Confidence            588999999999999999999999988887743    2228999999999999999877655

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

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

Probab=98.26  E-value=2.9e-07  Score=78.03  Aligned_cols=79  Identities=20%  Similarity=0.266  Sum_probs=68.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      +.+.||+|+--|..++++.+|+++|+.+|.|..|+++.|+...  ++.|||+|.|.++...|+ .|.|..+.  |..|.|
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrll--g~pv~v  252 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLL--GVPVIV  252 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCccc--CceeEe
Confidence            3456899999999999999999999999999999999985443  449999999999999999 89999985  777777


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      ..+.
T Consensus       253 q~sE  256 (549)
T KOG0147|consen  253 QLSE  256 (549)
T ss_pred             cccH
Confidence            6553

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

Probab=98.25  E-value=1.6e-06  Score=73.81  Aligned_cols=77  Identities=25%  Similarity=0.365  Sum_probs=66.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC--CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ--NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~--~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      -+....+|||+|+..+++++++++...||.+...+++.|..  .+++|||.+|-|......|+..|||+.+.  ++.|.+
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lg--d~~lvv  363 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLG--DKKLVV  363 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhc--CceeEe
Confidence            34567899999999999999999999999999999988754  34559999999999999999999999994  455655


Q ss_pred             E
Q 032280          139 P  139 (144)
Q Consensus       139 ~  139 (144)
                      .
T Consensus       364 q  364 (500)
T KOG0120|consen  364 Q  364 (500)
T ss_pred             e
Confidence            4

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

Probab=98.23  E-value=2.5e-05  Score=53.11  Aligned_cols=76  Identities=17%  Similarity=0.201  Sum_probs=58.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcC--CCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCC--CCCeEEE
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREF--PGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSD--SACSLLF  138 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~--G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~--~g~~l~v  138 (144)
                      +||-|.|||...|.++|.+++...  |...-+-|..|-  +.+.+||||-|.+.++|.+-.+.++|..+..  ..++..|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            589999999999999999988743  444445555553  3344599999999999999999999999832  2444455


Q ss_pred             Ee
Q 032280          139 PH  140 (144)
Q Consensus       139 ~~  140 (144)
                      .|
T Consensus        82 ~y   83 (97)
T PF04059_consen   82 SY   83 (97)
T ss_pred             eh
Confidence            54

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

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

Probab=98.22  E-value=1.1e-06  Score=67.57  Aligned_cols=72  Identities=21%  Similarity=0.191  Sum_probs=60.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ......|.|.||..++.+.+|++.|+++|.+....+      ...++||+|++.++|.+|++.|+|..+.  ++.|.+..
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~------~~~~~~v~Fs~~~da~ra~~~l~~~~~~--~~~l~~~~  167 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA------RRNFAFVEFSEQEDAKRALEKLDGKKLN--GRRISVEK  167 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh------hccccceeehhhhhhhhcchhccchhhc--Cceeeecc
Confidence            344567889999999999999999999999855443      1228999999999999999999999994  77777643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.22  E-value=3.6e-06  Score=68.35  Aligned_cols=74  Identities=14%  Similarity=0.243  Sum_probs=59.7

Q ss_pred             cceEEEcCCCCCCCHHH----H--HHHhhcCCCeEEEEEeecCCCC-----Cc-E-EEEEeCCHHHHHHHHHHhcCCccC
Q 032280           64 VRTLFVAGLPEDVKPRE----I--YNLFREFPGYESSHLRSSTQNS-----QP-F-AFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~----L--~~~F~~~G~v~~v~l~~~~~~~-----~~-~-aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ..-+||-+|+..+-.++    |  .++|.+||+|..|.+  ++++.     .. + -||+|.+.++|.+||.+.+|..+|
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvv--Nkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVV--NKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEe--cccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            34679999999988777    3  479999999998877  33321     11 2 399999999999999999999997


Q ss_pred             CCCCeEEEEee
Q 032280          131 DSACSLLFPHS  141 (144)
Q Consensus       131 ~~g~~l~v~~s  141 (144)
                        |+.|+..|.
T Consensus       192 --Gr~lkatYG  200 (480)
T COG5175         192 --GRVLKATYG  200 (480)
T ss_pred             --CceEeeecC
Confidence              899998875

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

Probab=98.08  E-value=1.5e-05  Score=67.13  Aligned_cols=65  Identities=15%  Similarity=0.217  Sum_probs=50.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      +..-|-+.+|||.+|++||.++|+.++ |+++.+.+..++..+-|||+|.+.+++++|++ .|-..+
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~m   73 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALK-KDRESM   73 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHH-hhHHHh
Confidence            344566789999999999999999995 67766655534444489999999999999995 344443

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

Probab=98.01  E-value=2e-05  Score=47.70  Aligned_cols=52  Identities=17%  Similarity=0.327  Sum_probs=41.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHH
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM  121 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~  121 (144)
                      +.|-|.+.+.+..+. +...|.+||+|+++.+-    .+..+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~----~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP----ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC----CCCcEEEEEECCHHHHHhhC
Confidence            567788888776654 55689999999998873    22339999999999999985

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

Probab=98.00  E-value=2.5e-05  Score=66.99  Aligned_cols=74  Identities=12%  Similarity=0.158  Sum_probs=58.0

Q ss_pred             ceEEEcCCCCCCCH------HHHHHHhhcCCCeEEEEEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           65 RTLFVAGLPEDVKP------REIYNLFREFPGYESSHLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        65 ~tLfVgnLp~~vte------~~L~~~F~~~G~v~~v~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ..|+|.|+|---..      .-|..+|+++|++++..+..+. ++.++|.|++|.+..+|+.|++.|||+.|+ +.+++.
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ld-knHtf~  137 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLD-KNHTFF  137 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceec-ccceEE
Confidence            46889998863222      2366799999999988887663 344559999999999999999999999996 566766


Q ss_pred             EE
Q 032280          138 FP  139 (144)
Q Consensus       138 v~  139 (144)
                      +.
T Consensus       138 v~  139 (698)
T KOG2314|consen  138 VR  139 (698)
T ss_pred             ee
Confidence            54

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

Probab=97.94  E-value=2e-05  Score=64.09  Aligned_cols=77  Identities=16%  Similarity=0.194  Sum_probs=61.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEE--------EEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYES--------SHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~--------v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      .....||||-+|+..+++++|.++|.++|.|..        |.|-+++++...  -|.|+|+|...|+.|+.-++|..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            445568999999999999999999999998743        333334433332  8999999999999999999999994


Q ss_pred             CCCCeEEEE
Q 032280          131 DSACSLLFP  139 (144)
Q Consensus       131 ~~g~~l~v~  139 (144)
                        +.+|+|.
T Consensus       143 --gn~ikvs  149 (351)
T KOG1995|consen  143 --GNTIKVS  149 (351)
T ss_pred             --CCCchhh
Confidence              6666653

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.93  E-value=5.1e-05  Score=66.54  Aligned_cols=77  Identities=18%  Similarity=0.213  Sum_probs=63.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCe-EEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGY-ESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v-~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...++.|-+.|+|++++-+||-++|..|--+ .+|+++++.++. .+-|-|.|++.++|.+|...|+|..|  ..+++.+
T Consensus       864 ~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i--~nr~V~l  941 (944)
T KOG4307|consen  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKI--RNRVVSL  941 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcc--cceeEEE
Confidence            4456789999999999999999999999766 567777664432 33899999999999999999999999  4666666


Q ss_pred             E
Q 032280          139 P  139 (144)
Q Consensus       139 ~  139 (144)
                      +
T Consensus       942 ~  942 (944)
T KOG4307|consen  942 R  942 (944)
T ss_pred             E
Confidence            4

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.90  E-value=1.3e-05  Score=66.81  Aligned_cols=74  Identities=22%  Similarity=0.250  Sum_probs=57.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeecC
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMA  143 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~~  143 (144)
                      ..||||||...++.++|+.+|....--.+-.++.    +.+|+||.+.|...|.+|++.++|+.-. .|..+.+++|+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~----k~gyafvd~pdq~wa~kaie~~sgk~el-qGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV----KSGYAFVDCPDQQWANKAIETLSGKVEL-QGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee----ecceeeccCCchhhhhhhHHhhchhhhh-cCceeeccchhh
Confidence            3699999999999999999998552111112221    1229999999999999999999998643 688999999873

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.85  E-value=1.1e-05  Score=64.59  Aligned_cols=75  Identities=19%  Similarity=0.208  Sum_probs=61.9

Q ss_pred             cceEE-EcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           64 VRTLF-VAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        64 ~~tLf-VgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..++| |+||++++++++|+..|..+|.|..+++..+..++.+  ||||+|.+...+..++.. ++..+.  ++.+++++
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~--~~~~~~~~  260 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIG--GRPLRLEE  260 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCccc--Cccccccc
Confidence            34555 9999999999999999999999999998776555544  999999999999999877 666663  66677766


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      .
T Consensus       261 ~  261 (285)
T KOG4210|consen  261 D  261 (285)
T ss_pred             C
Confidence            4

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

Probab=97.78  E-value=2.9e-05  Score=64.60  Aligned_cols=66  Identities=18%  Similarity=0.167  Sum_probs=55.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-------CC-C-------CcEEEEEeCCHHHHHHHHHHhcC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-------QN-S-------QPFAFAVFSDQQSALGAMYALNN  126 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-------~~-~-------~~~aFV~F~~~~~A~~A~~~lnG  126 (144)
                      -.+|||.+-||+.+-.-+.|.+||+.+|.|.+|+|..-.       +. +       +-+|+|+|+..+.|.+|.+.||-
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            368999999999999999999999999999999996530       11 1       12899999999999999988864


Q ss_pred             C
Q 032280          127 F  127 (144)
Q Consensus       127 ~  127 (144)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            3

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.76  E-value=2.1e-05  Score=61.61  Aligned_cols=67  Identities=12%  Similarity=0.221  Sum_probs=56.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC----------CCc----EEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN----------SQP----FAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~----------~~~----~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ..||++|||..++-.-|++||++||.|-.|-|......          +..    -|.|+|.+...|.++.+.|||..|.
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            57999999999999999999999999999888543211          111    3999999999999999999999995


Q ss_pred             C
Q 032280          131 D  131 (144)
Q Consensus       131 ~  131 (144)
                      |
T Consensus       155 g  155 (278)
T KOG3152|consen  155 G  155 (278)
T ss_pred             C
Confidence            4

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

Probab=97.72  E-value=5.7e-05  Score=67.61  Aligned_cols=77  Identities=14%  Similarity=0.148  Sum_probs=67.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....+.+|||+|..++....|...|..||.|..|.+    ..+..|++|.|++...++.|++.|-|..|.+-.+.|+|+|
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy----~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY----RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeec----ccCCcceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            345678999999999999999999999999999877    3345599999999999999999999999966667788877


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      .
T Consensus       528 a  528 (975)
T KOG0112|consen  528 A  528 (975)
T ss_pred             c
Confidence            4

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

Probab=97.71  E-value=0.00011  Score=62.40  Aligned_cols=63  Identities=27%  Similarity=0.358  Sum_probs=51.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhh-cCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHH
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFR-EFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYA  123 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~-~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~  123 (144)
                      -+..||||||+||.-++.+||..+|+ -||+|+-+-|=.|.+-+-  +=|-|+|++..+-.+||.+
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            45678999999999999999999999 899998887744422222  2689999999999999864

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

Probab=97.69  E-value=0.00019  Score=59.10  Aligned_cols=72  Identities=14%  Similarity=0.086  Sum_probs=60.0

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeecC
Q 032280           69 VAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMA  143 (144)
Q Consensus        69 VgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~~  143 (144)
                      |-|-=+-+|-+-|+.+....|+|..|.|..  + +.--|.|||++.+.|++|.++|||..|-..=++|+|||.+.
T Consensus       127 IlNp~YpItvDVly~Icnp~GkVlRIvIfk--k-ngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP  198 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGKVLRIVIFK--K-NGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKP  198 (494)
T ss_pred             eecCccccchhhhhhhcCCCCceEEEEEEe--c-cceeeEEeechhHHHHHHHhhcccccccccceeEEEEecCc
Confidence            345556789999999999999999988754  2 22279999999999999999999999955578999999753

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

Probab=97.69  E-value=9.2e-06  Score=72.53  Aligned_cols=70  Identities=19%  Similarity=0.300  Sum_probs=60.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ....+|||+|||...+++.+|+..|..+|.|.+|.+..-. ++...||||.|.+...+-+|+..+.|..|.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~  439 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIG  439 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccc
Confidence            3456899999999999999999999999999999986542 333449999999999999999999998884

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

Probab=97.64  E-value=0.00018  Score=61.40  Aligned_cols=58  Identities=14%  Similarity=0.122  Sum_probs=46.0

Q ss_pred             HHHHhhcCCCeEEEEEeec-C----CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           81 IYNLFREFPGYESSHLRSS-T----QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        81 L~~~F~~~G~v~~v~l~~~-~----~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ++.-+++||.|.+|.+-+. -    .-+-+.-||+|.+.+++++|+++|+|.+|.  ++++...|
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~--nRtVvtsY  488 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFA--NRTVVASY  488 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeC--CcEEEEEe
Confidence            4445679999999998665 1    112227899999999999999999999994  88887776

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

Probab=97.54  E-value=0.00012  Score=63.25  Aligned_cols=77  Identities=14%  Similarity=0.143  Sum_probs=62.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCe-EEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGY-ESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v-~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~v~  139 (144)
                      ..+..|||.||=.-.|..+|+.|+.+-|++ ++.  -.|+-.  .-|||.|.+.++|.+.+.+|+|..+ .++++.|.++
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDkIK--ShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDKIK--SHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHH--HHHHhh--cceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            456789999999999999999999966654 433  223322  2799999999999999999999999 7789999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |..
T Consensus       518 f~~  520 (718)
T KOG2416|consen  518 FVR  520 (718)
T ss_pred             ecc
Confidence            864

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

Probab=97.52  E-value=0.0003  Score=59.48  Aligned_cols=60  Identities=22%  Similarity=0.196  Sum_probs=46.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEE-EEEeecCCCCCc-EEEEEeCCHHHHHHHHHH
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYES-SHLRSSTQNSQP-FAFAVFSDQQSALGAMYA  123 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~-v~l~~~~~~~~~-~aFV~F~~~~~A~~A~~~  123 (144)
                      ...|-+.+||+.||++||.++|+-.--+.. +.+..+.+...+ -|||.|++.+.|++|+..
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r  164 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR  164 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH
Confidence            456788999999999999999986654433 445555443322 899999999999999853

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

Probab=97.52  E-value=0.0002  Score=60.87  Aligned_cols=60  Identities=28%  Similarity=0.468  Sum_probs=43.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeE-EEEEeecC------CCCCcEEEEEeCCHHHHHHHHHH
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYE-SSHLRSST------QNSQPFAFAVFSDQQSALGAMYA  123 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~-~v~l~~~~------~~~~~~aFV~F~~~~~A~~A~~~  123 (144)
                      ++.||||+|+++++|++|.+.|..||.+. +.-.+.+.      ++..+|.|+.|+++.+...-+.+
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            47899999999999999999999999863 21111111      12223999999999887754433

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

Probab=97.50  E-value=0.0016  Score=53.80  Aligned_cols=76  Identities=20%  Similarity=0.175  Sum_probs=64.4

Q ss_pred             CCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .....+.|-+|... ++-+.|-++|-.||.|+.|++++.+.   +-|.|+..|..+.++|+..||+..+-  |.+|.|..
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~---gtamVemgd~~aver~v~hLnn~~lf--G~kl~v~~  359 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP---GTAMVEMGDAYAVERAVTHLNNIPLF--GGKLNVCV  359 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc---ceeEEEcCcHHHHHHHHHHhccCccc--cceEEEee
Confidence            44567889999886 67788999999999999999875432   27999999999999999999999883  88888888


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      |.
T Consensus       360 Sk  361 (494)
T KOG1456|consen  360 SK  361 (494)
T ss_pred             cc
Confidence            75

>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=97.39  E-value=0.0026  Score=44.10  Aligned_cols=69  Identities=14%  Similarity=0.002  Sum_probs=55.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCC-eEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~-v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      ......+.+...+..++.++|..+.+.+-. |..++++++...++-.+.+.|.+.++|+.-.+.+||+.|
T Consensus        10 ~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~F   79 (110)
T PF07576_consen   10 ERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPF   79 (110)
T ss_pred             CCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCcc
Confidence            344556667888888888888877766644 678899887666665799999999999999999999999

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

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

Probab=97.37  E-value=0.00083  Score=54.78  Aligned_cols=74  Identities=8%  Similarity=0.061  Sum_probs=55.2

Q ss_pred             CcceEEEcCCCC----CCC-------HHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           63 EVRTLFVAGLPE----DVK-------PREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        63 ~~~tLfVgnLp~----~vt-------e~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      ..+||-+.||=.    +.+       +++|++-.++||.|.+|.|. ++.. .+.+-|.|.+.++|+.||+.|+|+-|+ 
T Consensus       264 ~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d~hP-dGvvtV~f~n~eeA~~ciq~m~GR~fd-  340 (382)
T KOG1548|consen  264 ADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-DRHP-DGVVTVSFRNNEEADQCIQTMDGRWFD-  340 (382)
T ss_pred             CCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-ccCC-CceeEEEeCChHHHHHHHHHhcCeeec-
Confidence            446888888632    223       24566667899999998764 3332 338999999999999999999999996 


Q ss_pred             CCCeEEEEe
Q 032280          132 SACSLLFPH  140 (144)
Q Consensus       132 ~g~~l~v~~  140 (144)
                       |+.|..+.
T Consensus       341 -gRql~A~i  348 (382)
T KOG1548|consen  341 -GRQLTASI  348 (382)
T ss_pred             -ceEEEEEE
Confidence             77776543

>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=97.32  E-value=0.0015  Score=44.55  Aligned_cols=75  Identities=15%  Similarity=0.134  Sum_probs=47.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEE-Eeec--------CCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSH-LRSS--------TQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSAC  134 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~-l~~~--------~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~  134 (144)
                      .+.|-|=+.|.. ....+-+.|++||.|.+.. +.++        ...+..+-.|+|++..+|.+|+ .-||+.|. ...
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL-~~NG~i~~-g~~   82 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRAL-QKNGTIFS-GSL   82 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHH-TTTTEEET-TCE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHH-HhCCeEEc-CcE
Confidence            455777788887 4456778999999998764 1110        0123339999999999999999 67999994 123


Q ss_pred             eEEEEee
Q 032280          135 SLLFPHS  141 (144)
Q Consensus       135 ~l~v~~s  141 (144)
                      .+-|.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            3445554

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.

>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=97.29  E-value=0.00092  Score=49.98  Aligned_cols=79  Identities=10%  Similarity=0.143  Sum_probs=50.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhc-CCCe---EEEEEeecCCCC----CcEEEEEeCCHHHHHHHHHHhcCCcc-CCCC
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFRE-FPGY---ESSHLRSSTQNS----QPFAFAVFSDQQSALGAMYALNNFAP-SDSA  133 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~-~G~v---~~v~l~~~~~~~----~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g  133 (144)
                      +...|-|++||.++||+++.+.++. ++.-   ..+.-.......    .+-|||.|.+.++...-++.++|..| |.+|
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4458999999999999999887776 6654   333322332221    12799999999999999999999999 5555


Q ss_pred             CeE--EEEee
Q 032280          134 CSL--LFPHS  141 (144)
Q Consensus       134 ~~l--~v~~s  141 (144)
                      ...  .|+++
T Consensus        86 ~~~~~~VE~A   95 (176)
T PF03467_consen   86 NEYPAVVEFA   95 (176)
T ss_dssp             -EEEEEEEE-
T ss_pred             CCcceeEEEc
Confidence            533  44443

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.

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

Probab=97.24  E-value=0.0012  Score=53.01  Aligned_cols=61  Identities=13%  Similarity=0.018  Sum_probs=47.9

Q ss_pred             HHHHHHHhhcCCCeEEEEEeecCCC--C-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           78 PREIYNLFREFPGYESSHLRSSTQN--S-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        78 e~~L~~~F~~~G~v~~v~l~~~~~~--~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      |+++++..++||.|..|.|.-....  . ..--||+|+..++|.+|+-.|||..|.  |++++..|
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFG--Gr~v~A~F  363 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFG--GRVVSACF  363 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceec--ceeeehee
Confidence            3567788899999999887554211  1 116899999999999999999999994  88887665

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

Probab=97.16  E-value=0.0039  Score=47.21  Aligned_cols=67  Identities=12%  Similarity=0.113  Sum_probs=57.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCe
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACS  135 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~  135 (144)
                      ..+|.|++||..-++.||++...+.|.|+-..+.+|.     ++.|+|...++.+-|++.|+...+...|.+
T Consensus       115 e~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg-----~GvV~~~r~eDMkYAvr~ld~~~~~seGe~  181 (241)
T KOG0105|consen  115 EYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDG-----VGVVEYLRKEDMKYAVRKLDDQKFRSEGET  181 (241)
T ss_pred             ceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeeccc-----ceeeeeeehhhHHHHHHhhccccccCcCcE
Confidence            3468899999999999999999999999888775442     899999999999999999999888434443

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

Probab=97.06  E-value=0.00031  Score=55.08  Aligned_cols=54  Identities=15%  Similarity=0.095  Sum_probs=43.6

Q ss_pred             cCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           87 EFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        87 ~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      +||+|+++++..+.... .+-.||.|...++|++|++.|||.-|  .|+.|..+++.
T Consensus        92 kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~--~G~pi~ae~~p  146 (260)
T KOG2202|consen   92 KYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWY--NGRPIHAELSP  146 (260)
T ss_pred             HhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccc--cCCcceeeecC
Confidence            99999998776542211 12689999999999999999999999  48889888875

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=97.04  E-value=0.0013  Score=57.36  Aligned_cols=69  Identities=17%  Similarity=0.083  Sum_probs=58.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..-|+||||+...+.++-++.+...+|.|.++....       |||++|.+......|+..++-..+++.+.+.++
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            356899999999999999999999999998876532       999999999999999999988888655554444

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

Probab=97.03  E-value=0.0025  Score=46.30  Aligned_cols=51  Identities=22%  Similarity=0.324  Sum_probs=41.5

Q ss_pred             HHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           80 EIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        80 ~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +|-+.|++||.+.=+|+.-  +    --.|+|.+.++|.+|+ .++|.++  +|+.|+|.
T Consensus        52 ~ll~~~~~~GevvLvRfv~--~----~mwVTF~dg~sALaal-s~dg~~v--~g~~l~i~  102 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVG--D----TMWVTFRDGQSALAAL-SLDGIQV--NGRTLKIR  102 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEET--T----CEEEEESSCHHHHHHH-HGCCSEE--TTEEEEEE
T ss_pred             HHHHHHHhCCceEEEEEeC--C----eEEEEECccHHHHHHH-ccCCcEE--CCEEEEEE
Confidence            5778899999988777653  2    4699999999999998 7999999  58888875

; PDB: 1UFW_A 2DNR_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.00  E-value=0.0011  Score=55.04  Aligned_cols=65  Identities=20%  Similarity=0.223  Sum_probs=52.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc-----EEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP-----FAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~-----~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      .+.|-|.||...++.++++.||...|+|.+++|.-+-+....     .|||-|.|...+..|- .|.++.|
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvf   76 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVF   76 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhcccee
Confidence            347999999999999999999999999999998654222221     8999999999999886 4555555

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

Probab=97.00  E-value=0.0048  Score=38.52  Aligned_cols=54  Identities=26%  Similarity=0.380  Sum_probs=42.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcC---CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHh
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREF---PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL  124 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~---G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~l  124 (144)
                      .+|+|.|+.. ++-++|+.+|..|   .....|.-+-|.     -|-|.|.|.+.|.+|+.+|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-----ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-----SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-----cEEEEECCHHHHHHHHHcC
Confidence            4799999964 7888999999999   123566666543     5899999999999999765

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.94  E-value=0.001  Score=52.35  Aligned_cols=61  Identities=16%  Similarity=0.194  Sum_probs=52.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhc
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ..|||.||...++.+.|++-|+.||.|+...++.|.... ..=++|+|.....|.+|+...+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhc
Confidence            679999999999999999999999999887777664332 3379999999999999998874

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.77  E-value=0.00057  Score=55.38  Aligned_cols=74  Identities=12%  Similarity=0.249  Sum_probs=55.5

Q ss_pred             ceEEEcCCCCCCCHHH-HH--HHhhcCCCeEEEEEeecCC-----CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           65 RTLFVAGLPEDVKPRE-IY--NLFREFPGYESSHLRSSTQ-----NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~-L~--~~F~~~G~v~~v~l~~~~~-----~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      +-+||-+|+.++..++ |+  +.|.+||+|.+|....+..     ++.+-++|+|+..++|..||...+|..++  |+.|
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~d--g~~l  155 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDD--GRAL  155 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhh--hhhh
Confidence            4578889998875554 43  5889999999988765431     11126999999999999999999999986  5556


Q ss_pred             EEEe
Q 032280          137 LFPH  140 (144)
Q Consensus       137 ~v~~  140 (144)
                      +..+
T Consensus       156 ka~~  159 (327)
T KOG2068|consen  156 KASL  159 (327)
T ss_pred             HHhh
Confidence            5544

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

Probab=96.71  E-value=0.014  Score=38.66  Aligned_cols=54  Identities=22%  Similarity=0.380  Sum_probs=40.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ...||+ .|......||.++|+.||.|. |.-+.| .    -|||...+++.|..|++.++
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-T----SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-T----SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-T----EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-C----cEEEEeecHHHHHHHHHHhc
Confidence            346676 999999999999999999974 333422 2    69999999999999998886

; 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.

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

Probab=96.62  E-value=0.0023  Score=52.52  Aligned_cols=67  Identities=10%  Similarity=0.099  Sum_probs=51.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCC--eEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPG--YESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~--v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      ..+|||||-|++|++||.+.....|-  +.++++..++  +.+++||.|...+..+..+-++.|--+.|.+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHG  151 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHG  151 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecC
Confidence            47999999999999999988876663  3444443332  3344599999999999999999998888853

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.60  E-value=0.01  Score=51.36  Aligned_cols=55  Identities=18%  Similarity=0.260  Sum_probs=47.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhh--cCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           66 TLFVAGLPEDVKPREIYNLFR--EFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~--~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      .|.++.|++.+.+|+++.||+  .+-++.+|.+..+.     -.||+|++..||++|.+.|.
T Consensus       177 IvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-----nWyITfesd~DAQqAykylr  233 (684)
T KOG2591|consen  177 IVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-----NWYITFESDTDAQQAYKYLR  233 (684)
T ss_pred             EEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-----ceEEEeecchhHHHHHHHHH
Confidence            456799999999999999997  58889999987654     38999999999999987664

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.51  E-value=0.018  Score=41.86  Aligned_cols=71  Identities=24%  Similarity=0.301  Sum_probs=53.5

Q ss_pred             CcceEEEcCCCCCCCH-HH---HHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           63 EVRTLFVAGLPEDVKP-RE---IYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte-~~---L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .-.||.|.=|..++.. +|   +-..++.||.|.+|.+.     |+.-|.|.|+|..+|-+|+.+++...-   |..++.
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----GrqsavVvF~d~~SAC~Av~Af~s~~p---gtm~qC  156 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GRQSAVVVFKDITSACKAVSAFQSRAP---GTMFQC  156 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CCceEEEEehhhHHHHHHHHhhcCCCC---CceEEe
Confidence            3468888877776533 33   44556899999999874     222799999999999999999987654   777887


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      .|.
T Consensus       157 sWq  159 (166)
T PF15023_consen  157 SWQ  159 (166)
T ss_pred             ecc
Confidence            774

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

Probab=96.45  E-value=0.0014  Score=58.75  Aligned_cols=73  Identities=11%  Similarity=0.076  Sum_probs=60.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ..|||+|+++..|.++|+.+++.+|.+.+.+++..+.++ ++.+||.|.+..++.++....++..+..++..+.
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~  810 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQ  810 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCcccc
Confidence            478999999999999999999999999999887664432 3389999999999999998888887744443333

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=96.45  E-value=0.0086  Score=45.16  Aligned_cols=60  Identities=18%  Similarity=0.046  Sum_probs=44.1

Q ss_pred             CHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc--CCccCCCCCeEEEEeec
Q 032280           77 KPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN--NFAPSDSACSLLFPHSM  142 (144)
Q Consensus        77 te~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln--G~~~~~~g~~l~v~~s~  142 (144)
                      ..+.|+++|..++.+.+......-+    -..|.|.+.++|.+|+..|+  |..+.  |..+++-|+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr----Ri~v~f~~~~~A~~~r~~l~~~~~~~~--g~~l~~yf~~   69 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR----RIRVVFESPESAQRARQLLHWDGTSFN--GKRLRVYFGQ   69 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT----EEEEE-SSTTHHHHHHHTST--TSEET--TEE-EEE---
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC----EEEEEeCCHHHHHHHHHHhcccccccC--CCceEEEEcc
Confidence            3478999999999998887765433    68999999999999999999  89884  7778887763

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

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

Probab=96.30  E-value=0.036  Score=46.21  Aligned_cols=62  Identities=19%  Similarity=0.236  Sum_probs=45.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcC----CCeEEEEEeec-CCCCCcEEEEEeCCHHHHHHHHHH
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREF----PGYESSHLRSS-TQNSQPFAFAVFSDQQSALGAMYA  123 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~----G~v~~v~l~~~-~~~~~~~aFV~F~~~~~A~~A~~~  123 (144)
                      ...-.|-..+||+++++.|+.++|..-    |..+.|.++.. .++-.+-|||.|...++|+.|+..
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH
Confidence            334457789999999999999999632    34556655543 222233899999999999999854

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

Probab=96.24  E-value=0.009  Score=49.69  Aligned_cols=73  Identities=15%  Similarity=0.178  Sum_probs=54.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCe---EEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGY---ESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v---~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...|-..+||+..+.+||.++|..|..-   ..|+++.|..+. .+-|||+|.+.++|..|....+.+..  +.+-|.|
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~m--k~RYiEv  356 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLM--KSRYIEV  356 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhc--ccceEEE
Confidence            3467889999999999999999988753   336777774432 33899999999999998877665544  3454443

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

Probab=95.97  E-value=0.00046  Score=61.66  Aligned_cols=65  Identities=14%  Similarity=0.122  Sum_probs=54.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEee--cCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~--~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      .++||+||+..+.+.+|...|..+|.+..+++..  +++.-+++||++|.+.+++.+|+...++..+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~  734 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFF  734 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhh
Confidence            3789999999999999999999999988877652  3444455999999999999999977666655

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

Probab=95.82  E-value=0.0068  Score=54.54  Aligned_cols=74  Identities=15%  Similarity=0.126  Sum_probs=62.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeecC
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSMA  143 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~~  143 (144)
                      +.++.|+.-+.+...|..+|++||.|.+....++-.    .|.|+|.+.+.|..|+++|+|+++...|...+|.++..
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N----~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN----MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc----chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            456677777888999999999999999887765543    89999999999999999999999855677788887653

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=95.65  E-value=0.046  Score=46.27  Aligned_cols=66  Identities=12%  Similarity=0.143  Sum_probs=57.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcC-CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~-G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      ++.|+|=.+|..++-.||-.+...+ ..|.++++++|...++=...|.|.+.++|..-.+.+||+.|
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~F  140 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQF  140 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcC
Confidence            7899999999999999999888755 45789999986554443689999999999999999999998

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

Probab=95.65  E-value=0.024  Score=45.71  Aligned_cols=56  Identities=18%  Similarity=0.183  Sum_probs=41.8

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           69 VAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        69 VgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      |-+.+..-. ..|.++|++||.|++....    .+..+-+|.|.++.+|++|| ..||+.|+
T Consensus       202 VfGFppg~~-s~vL~~F~~cG~Vvkhv~~----~ngNwMhirYssr~~A~KAL-skng~ii~  257 (350)
T KOG4285|consen  202 VFGFPPGQV-SIVLNLFSRCGEVVKHVTP----SNGNWMHIRYSSRTHAQKAL-SKNGTIID  257 (350)
T ss_pred             EeccCccch-hHHHHHHHhhCeeeeeecC----CCCceEEEEecchhHHHHhh-hhcCeeec
Confidence            334444333 3577899999999876542    23339999999999999999 57999995

>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=95.38  E-value=0.06  Score=33.96  Aligned_cols=48  Identities=15%  Similarity=0.172  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           75 DVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        75 ~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      .++-++++..+++|+- ..|+.  + ++|   =||.|.|..+|++|.+..||+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~~I~~--d-~tG---fYIvF~~~~Ea~rC~~~~~~~~~   58 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-DRIRD--D-RTG---FYIVFNDSKEAERCFRAEDGTLF   58 (66)
T ss_pred             CccHHHHHHHHhcCCc-ceEEe--c-CCE---EEEEECChHHHHHHHHhcCCCEE
Confidence            4677899999999974 44432  3 222   48999999999999999999987

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

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=95.29  E-value=0.13  Score=32.81  Aligned_cols=66  Identities=20%  Similarity=0.289  Sum_probs=39.1

Q ss_pred             eEEEc-CCCCCCCHHHHHHHhhcCCCe-----EEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           66 TLFVA-GLPEDVKPREIYNLFREFPGY-----ESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        66 tLfVg-nLp~~vte~~L~~~F~~~G~v-----~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +|||. +--..++..+|-.++...+++     -+|++.  ..    |+||+-... .|+.+++.|++..+  +|+.|+|+
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~--~~----~S~vev~~~-~a~~v~~~l~~~~~--~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIF--DN----FSFVEVPEE-VAEKVLEALNGKKI--KGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE---SS-----EEEEE-TT--HHHHHHHHTT--S--SS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEe--ee----EEEEEECHH-HHHHHHHHhcCCCC--CCeeEEEE
Confidence            46662 344568899999999888665     455553  12    899997754 78899999999999  48888887


Q ss_pred             e
Q 032280          140 H  140 (144)
Q Consensus       140 ~  140 (144)
                      -
T Consensus        73 ~   73 (74)
T PF03880_consen   73 R   73 (74)
T ss_dssp             E
T ss_pred             E
Confidence            3

; PDB: 2G0C_A 3MOJ_B.

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.22  E-value=0.12  Score=44.95  Aligned_cols=79  Identities=20%  Similarity=0.266  Sum_probs=61.7

Q ss_pred             CCcceEEEcCCCCC-CCHHHHHHHhhcC----CCeEEEEEeecC-----------CCC----------------------
Q 032280           62 DEVRTLFVAGLPED-VKPREIYNLFREF----PGYESSHLRSST-----------QNS----------------------  103 (144)
Q Consensus        62 ~~~~tLfVgnLp~~-vte~~L~~~F~~~----G~v~~v~l~~~~-----------~~~----------------------  103 (144)
                      ..+++|-|-||.|+ +..++|.-+|+.|    |.|.+|.|-...           .+.                      
T Consensus       172 ~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~  251 (650)
T KOG2318|consen  172 EETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEE  251 (650)
T ss_pred             cccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhh
Confidence            45688999999997 8899999999977    578888873210           000                      


Q ss_pred             ---------------Cc-EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280          104 ---------------QP-FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus       104 ---------------~~-~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                                     +. ||.|+|.+...|.+..+..+|..|...+..|-+.|
T Consensus       252 ~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  252 DVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                           11 89999999999999999999999965666665554

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

Probab=95.17  E-value=0.011  Score=50.06  Aligned_cols=58  Identities=16%  Similarity=0.101  Sum_probs=47.6

Q ss_pred             CHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           77 KPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        77 te~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +.++|...|.+||+|..|.+.+...    -|.|+|.+..+|-+|. ...|..|+  ++.|+|-|-
T Consensus       386 t~a~ln~hfA~fG~i~n~qv~~~~~----~a~vTF~t~aeag~a~-~s~~avln--nr~iKl~wh  443 (526)
T KOG2135|consen  386 TIADLNPHFAQFGEIENIQVDYSSL----HAVVTFKTRAEAGEAY-ASHGAVLN--NRFIKLFWH  443 (526)
T ss_pred             hHhhhhhhhhhcCccccccccCchh----hheeeeeccccccchh-ccccceec--CceeEEEEe
Confidence            4567999999999999999865422    7999999999997775 57888885  788888884

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.13  E-value=0.016  Score=51.35  Aligned_cols=77  Identities=22%  Similarity=0.181  Sum_probs=56.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEE-EEEeec-CCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYES-SHLRSS-TQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~-v~l~~~-~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....|||-.||..+++.++-+.|...-.|++ |.|.+. +....+-|||+|...+++.+|...-.-..+  ..+.|+|+
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~--G~r~irv~  509 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYP--GHRIIRVD  509 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhccccccc--CceEEEee
Confidence            45678999999999999999999999888887 665443 233344899999998888888633222222  35667776


Q ss_pred             e
Q 032280          140 H  140 (144)
Q Consensus       140 ~  140 (144)
                      -
T Consensus       510 s  510 (944)
T KOG4307|consen  510 S  510 (944)
T ss_pred             c
Confidence            4

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=93.87  E-value=0.26  Score=39.82  Aligned_cols=58  Identities=14%  Similarity=0.200  Sum_probs=41.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCH-------HHHHHHHHHhc
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQ-------QSALGAMYALN  125 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~-------~~A~~A~~~ln  125 (144)
                      .-||++||++++.-.||+..+++-|.+- .++  ..++..+-||++|-|.       .+..++++.+|
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~p-m~i--swkg~~~k~flh~~~~~~~~~~~~~~~~~~~s~~  395 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTP-MSI--SWKGHFGKCFLHFGNRKGVPSTQDDMDKVLKSLN  395 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCc-eeE--eeecCCcceeEecCCccCCCCCchHHHHHhccCC
Confidence            4599999999999999999999887641 122  2344444799999875       44556655554

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=92.57  E-value=0.071  Score=42.81  Aligned_cols=64  Identities=19%  Similarity=0.107  Sum_probs=51.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ....++|+|++.+++.+.++..++..+|.+..+.+....  ...++++.+.|...+.+..|+....
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~  151 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESG  151 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhh
Confidence            346789999999999999999999999988777765532  3344499999999999999985443

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

Probab=91.81  E-value=0.042  Score=42.66  Aligned_cols=71  Identities=18%  Similarity=0.261  Sum_probs=59.5

Q ss_pred             CCCCCcceEEEcC----CCCCCCHHHHHHHhhcCCCeEEEEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           59 GSYDEVRTLFVAG----LPEDVKPREIYNLFREFPGYESSHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        59 ~~~~~~~tLfVgn----Lp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      ...+..++++.|+    |...++++.+++.|+..|.++.+++-.+.. .++.++|+++...++.-.++..++|...
T Consensus        75 ~~~e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~  150 (267)
T KOG4454|consen   75 EEDEEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLEL  150 (267)
T ss_pred             ccchhhcccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCc
Confidence            3455667899999    999999999999999999999998865533 3444999999999999999999988865

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

Probab=91.50  E-value=0.53  Score=40.84  Aligned_cols=65  Identities=12%  Similarity=0.176  Sum_probs=45.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhc----------------------------CCCeEEEEEeecCC--CCCcEEEEEeCCH
Q 032280           65 RTLFVAGLPEDVKPREIYNLFRE----------------------------FPGYESSHLRSSTQ--NSQPFAFAVFSDQ  114 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~----------------------------~G~v~~v~l~~~~~--~~~~~aFV~F~~~  114 (144)
                      .++-|+||+..-+..+|.++.+.                            .|...-+-|..|-+  .+-+||||.|.+.
T Consensus       362 tt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp  441 (549)
T KOG4660|consen  362 TTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSP  441 (549)
T ss_pred             hhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCH
Confidence            46778888887777777776642                            23333333333422  2333999999999


Q ss_pred             HHHHHHHHHhcCCcc
Q 032280          115 QSALGAMYALNNFAP  129 (144)
Q Consensus       115 ~~A~~A~~~lnG~~~  129 (144)
                      +++..+.++.||+.+
T Consensus       442 ~ai~~F~kAFnGk~W  456 (549)
T KOG4660|consen  442 EAIIRFYKAFNGKKW  456 (549)
T ss_pred             HHHHHHHHHHcCCch
Confidence            999999999999987

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=90.36  E-value=0.057  Score=45.07  Aligned_cols=63  Identities=17%  Similarity=0.040  Sum_probs=50.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      .+|++|++|...+...++-++|..+|+|.-.++.  .+....+|-|+|....+...|+ .++|..+
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a--sk~~s~~c~~sf~~qts~~hal-r~~gre~  213 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTA--SKSRSSSCSHSFRKQTSSKHAL-RSHGRER  213 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh--ccCCCcchhhhHhhhhhHHHHH-Hhcchhh
Confidence            3799999999999999999999999998766553  2333448889999999988887 4566665

>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]

Probab=87.14  E-value=0.52  Score=44.69  Aligned_cols=37  Identities=16%  Similarity=0.222  Sum_probs=29.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST  100 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~  100 (144)
                      .++++|--+-..+..+.|+.+-+.++..-++....|+
T Consensus        72 ak~~~v~t~ka~~PpeHLrki~~~~sdm~s~~~~~Dk  108 (2365)
T COG5178          72 AKTLHVLTLKAPIPPEHLRKIQSPCSDMPSVLTKVDK  108 (2365)
T ss_pred             hhheeeeccCCCCCHHHHHhhhCccccchhhhhhhhh
Confidence            4688888888999999999999999987766554443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=86.50  E-value=0.029  Score=47.31  Aligned_cols=75  Identities=16%  Similarity=0.166  Sum_probs=60.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+|.+-|.|++....++-|..|..+||.++.|..+. .......--|+|.+.+.+..||..|||..|.  ...+++.|
T Consensus        79 rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvn-t~~etavvnvty~~~~~~~~ai~kl~g~Q~e--n~~~k~~Y  153 (584)
T KOG2193|consen   79 RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVN-TDSETAVVNVTYSAQQQHRQAIHKLNGPQLE--NQHLKVGY  153 (584)
T ss_pred             HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhc-cchHHHHHHHHHHHHHHHHHHHHhhcchHhh--hhhhhccc
Confidence            357788999999999999999999999999997743 2322225668899999999999999999984  55566654

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=85.70  E-value=0.31  Score=39.33  Aligned_cols=65  Identities=20%  Similarity=0.324  Sum_probs=44.0

Q ss_pred             ceEEEcCCCCC------------CCHHHHHHHhhcCCCeEEEEEee-c-------CC-CC---CcE---------EEEEe
Q 032280           65 RTLFVAGLPED------------VKPREIYNLFREFPGYESSHLRS-S-------TQ-NS---QPF---------AFAVF  111 (144)
Q Consensus        65 ~tLfVgnLp~~------------vte~~L~~~F~~~G~v~~v~l~~-~-------~~-~~---~~~---------aFV~F  111 (144)
                      .|||+.+||-.            -+|+-|+..|+.||.|..|.+.. |       .+ ++   .+|         |||.|
T Consensus       150 dti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayvqf  229 (445)
T KOG2891|consen  150 DTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYVQF  229 (445)
T ss_pred             CceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHHHH
Confidence            46777776642            46788999999999998887622 1       11 00   002         45666


Q ss_pred             CCHHHHHHHHHHhcCCcc
Q 032280          112 SDQQSALGAMYALNNFAP  129 (144)
Q Consensus       112 ~~~~~A~~A~~~lnG~~~  129 (144)
                      ..-..-..|+.+|.|+.+
T Consensus       230 meykgfa~amdalr~~k~  247 (445)
T KOG2891|consen  230 MEYKGFAQAMDALRGMKL  247 (445)
T ss_pred             HHHHhHHHHHHHHhcchH
Confidence            666667788999999887

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]

Probab=84.15  E-value=0.2  Score=43.49  Aligned_cols=66  Identities=23%  Similarity=0.318  Sum_probs=53.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      .+||+.|+..+++-++|..+.+.+-.+..+-+....  +.-..++.|+|+-......|+.+|||..+.
T Consensus       232 ~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~  299 (648)
T KOG2295|consen  232 CSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLR  299 (648)
T ss_pred             HHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccc
Confidence            479999999999999999999999888777664321  111117999999999999999999999874

>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2

Probab=84.13  E-value=5.5  Score=25.01  Aligned_cols=44  Identities=20%  Similarity=0.192  Sum_probs=31.1

Q ss_pred             HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           79 REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        79 ~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      +++.+.++++| +....+.  ..+++++.|+.+++.+.++++.+.|.
T Consensus        37 ~~~~~~~~~~G-a~~~~~s--GsG~G~~v~~l~~~~~~~~~v~~~l~   80 (85)
T PF08544_consen   37 DELKEAAEENG-ALGAKMS--GSGGGPTVFALCKDEDDAERVAEALR   80 (85)
T ss_dssp             HHHHHHHHHTT-ESEEEEE--TTSSSSEEEEEESSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCC-CCceecC--CCCCCCeEEEEECCHHHHHHHHHHHH
Confidence            35677778898 4555552  23334489999999999998888774

7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....

>PHA01732 proline-rich protein

Probab=83.57  E-value=2.6  Score=28.01  Aligned_cols=15  Identities=13%  Similarity=0.087  Sum_probs=8.5

Q ss_pred             hhcCCCeEEEEEeec
Q 032280           85 FREFPGYESSHLRSS   99 (144)
Q Consensus        85 F~~~G~v~~v~l~~~   99 (144)
                      -...|+-.+++|-.+
T Consensus        58 qq~a~gTasLrIpkq   72 (94)
T PHA01732         58 QQKAGGTASLRIPKQ   72 (94)
T ss_pred             hhhccCcceeEeecc
Confidence            344556666676544

>PF09707 Cas_Cas2CT1978: CRISPR-associated protein (Cas_Cas2CT1978); InterPro: IPR010152 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []

Probab=83.08  E-value=2.7  Score=27.82  Aligned_cols=47  Identities=19%  Similarity=0.222  Sum_probs=33.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeC
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFS  112 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~  112 (144)
                      .-+||||++..+.|.-.+.+.+..+. -++.++......++|+|-+.-
T Consensus        26 ~GVyVg~~s~rVRe~lW~~v~~~~~~-G~a~m~~~~~neqG~~~~t~G   72 (86)
T PF09707_consen   26 PGVYVGNVSARVRERLWERVTEWIGD-GSAVMVWSDNNEQGFDFRTLG   72 (86)
T ss_pred             CCcEEcCCCHHHHHHHHHHHHhhCCC-ccEEEEEccCCCCCEEEEEeC
Confidence            35999999999999877777665554 445555554445569888773

CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799 from INTERPRO. Cas2 is one of four protein families (Cas1 to Cas4) that are associated with CRISPR elements and always occur near a repeat cluster, usually in the order cas3-cas4-cas1-cas2. The function of Cas2 (and Cas1) is unknown. Cas3 proteins appear to be helicases while Cas4 proteins resemble RecB-type exonucleases, suggesting that these genes are involved in DNA metabolism or gene expression [].

>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]

Probab=81.86  E-value=14  Score=32.11  Aligned_cols=32  Identities=6%  Similarity=0.045  Sum_probs=19.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEE
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSH   95 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~   95 (144)
                      .+.+-+..|+..-..++|.+--++=|.++.+.
T Consensus       481 l~~ve~t~~~~~dgR~~LmaqIRqG~~Lk~v~  512 (569)
T KOG3671|consen  481 LKKVETTALSSGDGRDALMAQIRQGGQLKKVD  512 (569)
T ss_pred             ccceeeccCcCcccHHHHHHHHHhcccccccc
Confidence            34566677876666666665555545555443

>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=80.01  E-value=5  Score=32.47  Aligned_cols=56  Identities=18%  Similarity=0.258  Sum_probs=44.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC---------CCCcEEEEEeCCHHHHH
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ---------NSQPFAFAVFSDQQSAL  118 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~---------~~~~~aFV~F~~~~~A~  118 (144)
                      ..|.|...|+..+++-.++-.-|.+||.|++|-++.+..         +......+.|-+++.+.
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CL   78 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICL   78 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHH
Confidence            457799999999999999999999999999999986541         11226788888877654

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	144
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-06
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-05
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-09
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-08
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-08
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-08
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-07
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	6e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	6e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	6e-08
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	7e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-07
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-06
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-07
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	4e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-07
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-06
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-06
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-06
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-05
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	9e-06
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-06
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-06
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-06
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-06
1x5o_A	114	RNA binding motif, single-stranded interacting pro	6e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-06
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	7e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-06
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-05
2div_A	99	TRNA selenocysteine associated protein; structural	1e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-05
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-05
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-05
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-05
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-05
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-05
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-05
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-05
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-05
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-05
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-05
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-05
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-05
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-05
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-05
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-05
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	8e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-05
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-05
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-04
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-04
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-04
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-04
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-04
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-04
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-04
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-04
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-04
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-04
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-04
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	5e-04
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	6e-04
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	7e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-04
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	8e-04
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	9e-04

>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 = 55.5 bits (134), Expect = 4e-11
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           R L++  LP  +   E+Y++F ++       +  +T  ++  A+ V+ D   A  A+  L
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG-NTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 125 NNF 127
           + F
Sbjct: 68  SGF 70

>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 = 56.8 bits (136), Expect = 1e-10
 Identities = 32/127 (25%), Positives = 44/127 (34%), Gaps = 3/127 (2%)

Query: 1   MAEYYPPPAGLHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGS 60
           M      P  +H+   Q P  PPP   P   +AP   P    P    +            
Sbjct: 144 MPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSE 203

Query: 61  YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
                 LF+  LPE+     +  LF +FPG++   L          AF  F ++  A  A
Sbjct: 204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV---PGRHDIAFVEFDNEVQAGAA 260

Query: 121 MYALNNF 127
             AL  F
Sbjct: 261 RDALQGF 267

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

 Score = 49.9 bits (118), Expect = 3e-08
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 65  RTLFVAGLPEDVKPRE----IYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
            T+++  L E +K  E    +Y +F +F G     L S +   +  AF +F +  SA  A
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQF-GQILDILVSRSLKMRGQAFVIFKEVSSATNA 68

Query: 121 MYALNNF 127
           + ++  F
Sbjct: 69  LRSMQGF 75

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 55.7 bits (134), Expect = 1e-10
 Identities = 19/117 (16%), Positives = 37/117 (31%), Gaps = 8/117 (6%)

Query: 11  LHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVA 70
           +    +Q    P       G+        + + + P   ++   FP         TL ++
Sbjct: 73  ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS------ATLHLS 126

Query: 71  GLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
            +P  V   ++  LF    G          Q  +  A       + A+ A+  L+N 
Sbjct: 127 NIPPSVSEEDLKVLFSSNGGVVKGFKF--FQKDRKMALIQMGSVEEAVQALIDLHNH 181

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 42.6 bits (100), Expect = 9e-06
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 4/64 (6%)

Query: 65  RTLFVAGL-PEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
             L V+ L PE V P+ ++ LF  +   +   +     N +  A    +D   A  AM  
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI---LFNKKENALVQMADGNQAQLAMSH 60

Query: 124 LNNF 127
           LN  
Sbjct: 61  LNGH 64

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

 Score = 53.3 bits (128), Expect = 2e-10
 Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 3/79 (3%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS     P          ++V  LP D +  ++    RE     S  LR + Q  +  AF
Sbjct: 4   GSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRE---LGSVPLRLTWQGPRRRAF 60

Query: 109 AVFSDQQSALGAMYALNNF 127
             + D  +A  A+  L   
Sbjct: 61  LHYPDSAAAQQAVSCLQGL 79

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

 Score = 53.9 bits (130), Expect = 7e-10
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 2/98 (2%)

Query: 32  VAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGY 91
           +  P               Y     +    D    LF+ GLP  +   ++  L   F   
Sbjct: 82  IRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPL 141

Query: 92  ESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
           ++ +L   S+T  S+ +AF  + D      A+  LN  
Sbjct: 142 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179

>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 = 41.6 bits (98), Expect = 2e-05
 Identities = 12/71 (16%), Positives = 19/71 (26%), Gaps = 8/71 (11%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-------TQNSQPFAFAVFSDQ 114
              R L+V  +P  +    + + F                         + FAF  F   
Sbjct: 2   AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 115 QSALGAMYALN 125
                AM A +
Sbjct: 62  DETTQAM-AFD 71

>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 = 3e-09
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 53  ASFPAYGSYDEV---RTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFA 107
              P + SY+     + L++  L   V  R++ +LF  F   +   +  R  T   +  A
Sbjct: 11  RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 70

Query: 108 FAVFSDQQSALGAMYALNNF 127
           F  F +++ A  A++ +N +
Sbjct: 71  FITFPNKEIAWQALHLVNGY 90

>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 = 50.3 bits (121), Expect = 9e-09
 Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 57  AYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQ 114
            Y        LF+ GLP  +   ++  L   F   ++ +L   S+T  S+ +AF  + D 
Sbjct: 87  DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146

Query: 115 QSALGAMYALNNF 127
                A+  LN  
Sbjct: 147 NVTDQAIAGLNGM 159

>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 = 42.6 bits (101), Expect = 6e-06
 Identities = 12/71 (16%), Positives = 19/71 (26%), Gaps = 8/71 (11%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-------TQNSQPFAFAVFSDQ 114
              R L+V  +P  +    + + F                         + FAF  F   
Sbjct: 2   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 115 QSALGAMYALN 125
                AM A +
Sbjct: 62  DETTQAM-AFD 71

>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 = 48.4 bits (116), Expect = 1e-08
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH-LRSSTQNSQPFA 107
           GS  +S        + R LFV  L +     ++  LF+ F   +    LR    +S+  A
Sbjct: 1   GSSGSSGSESRGGRD-RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCA 59

Query: 108 FAVFSDQQSALGAMYALNN 126
           F  FS    A  A++AL+ 
Sbjct: 60  FVKFSSHTEAQAAIHALHG 78

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS-STQNSQPFAFAVFSDQQSALGAM 121
           R++++ G P D    +I     +     +  +R    +  +   F VF   +SA   +
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 69

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 13/120 (10%), Positives = 29/120 (24%), Gaps = 4/120 (3%)

Query: 23  PPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVR--TLFVAGLPEDVKPRE 80
           P   P                       +S    A  +  +     L     P +V    
Sbjct: 80  PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEEN 139

Query: 81  IYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF 138
            + +  E      + ++  S            +  +  AL  +  LN++   +      +
Sbjct: 140 FFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199

>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 = 4e-08
 Identities = 12/79 (15%), Positives = 32/79 (40%), Gaps = 16/79 (20%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             + V  LP+D   +E+++L +++   +  ++  + +     AF    + + A  A+   
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKR----TAFVTLLNGEQAQNAIQMF 60

Query: 125 NN-----------FAPSDS 132
           +              P+D+
Sbjct: 61  HQYSFRGKDLIVQLQPTDA 79

>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 = 4e-08
 Identities = 14/64 (21%), Positives = 26/64 (40%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
           E+ T+ V  LP+     ++Y  F+         +  S + +  FA   F+    AL A+ 
Sbjct: 40  ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT 99

Query: 123 ALNN 126
             + 
Sbjct: 100 KTHK 103

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMY 122
            TL++   P     R I +L ++      S  L S   N S+ FA+   + ++ A   + 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 123 ALNNF 127
            LN  
Sbjct: 178 KLNGL 182

>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 = 42.7 bits (101), Expect = 9e-06
 Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 59  GSYDEVRTLFVAGLPEDV-KPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQ 114
            +  E R + +  L  ++     +   F  F   E  ++   +     +   AF VF ++
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264

Query: 115 QSALGAMYALNN 126
            SA  A+  +N 
Sbjct: 265 DSAERAL-QMNR 275

>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 = 48.8 bits (116), Expect = 5e-08
 Identities = 19/122 (15%), Positives = 39/122 (31%), Gaps = 8/122 (6%)

Query: 11  LHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVA 70
           +    +Q    P       G+        + + + P   ++   FP         TL ++
Sbjct: 104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS------ATLHLS 157

Query: 71  GLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS 130
            +P  V   ++  LF    G          Q  +  A       + A+ A+  L+N    
Sbjct: 158 NIPPSVSEEDLKVLFSSNGGVVKGFKF--FQKDRKMALIQMGSVEEAVQALIDLHNHDLG 215

Query: 131 DS 132
           ++
Sbjct: 216 EN 217

>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 = 46.5 bits (110), Expect = 4e-07
 Identities = 22/123 (17%), Positives = 34/123 (27%), Gaps = 17/123 (13%)

Query: 22  PPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGL-PEDVKPRE 80
                   G    P   +M +   P L                  L V+ L PE V P+ 
Sbjct: 5   HHHHHHSSG--LVPRGSHMGRIAIPGLAG-----------AGNSVLLVSNLNPERVTPQS 51

Query: 81  IYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH 140
           ++ LF  +   +   +     N +  A    +D   A  AM  LN          +    
Sbjct: 52  LFILFGVYGDVQRVKI---LFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 108

Query: 141 SMA 143
              
Sbjct: 109 HQN 111

>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 = 6e-08
 Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL----RSSTQNSQPFAFAVFSDQQSAL 118
           +   +FV  +P     +++  LF ++      ++      +   S+   F  F  +++AL
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 119 GAMYALNN 126
            A  AL+N
Sbjct: 62  EAQNALHN 69

>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 = 46.8 bits (112), Expect = 2e-07
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSH-LRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           LF+  + +     +I  +F  F   E    LR     S+  AF  F+ +  A  A+ A++
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157

Query: 126 N 126
            
Sbjct: 158 Q 158

>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 = 47.1 bits (112), Expect = 6e-08
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 4/66 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQN---SQPFAFAVFSDQQSALGA 120
             LF+ G+P+  K  EI     +   G     + +S  +   ++ FAF  +   ++A  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 121 MYALNN 126
              L  
Sbjct: 69  RRKLMP 74

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

 Score = 47.6 bits (113), Expect = 6e-08
 Identities = 15/99 (15%), Positives = 36/99 (36%), Gaps = 14/99 (14%)

Query: 33  APPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPRE----IYNLFREF 88
           A   + +M  P      +   + P+       + + +  +  +V   +    +Y L    
Sbjct: 7   AKFERQHMDSPDLGS--TPPHTEPS-------QVVLITNINPEVPKEKLQALLYALASSQ 57

Query: 89  PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
            G     +   + ++   A+ VF+ Q+SA   + A   +
Sbjct: 58  -GDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGY 95

>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 = 46.9 bits (112), Expect = 6e-08
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 3/65 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAM 121
             + V  +P     REI  LF  F   ++  L    + T   + F F  F  +Q A  A 
Sbjct: 16  SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75

Query: 122 YALNN 126
            AL +
Sbjct: 76  NALCH 80

>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 = 46.5 bits (111), Expect = 7e-08
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQP 105
           GS  +S P      +  T++V GL E V    ++ LF +     ++H+   R  T   Q 
Sbjct: 1   GSSGSSGPISERNQD-ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-TGQHQG 58

Query: 106 FAFAVFSDQQSALGAMYALNN 126
           + F  F  ++ A  A+  ++ 
Sbjct: 59  YGFVEFLSEEDADYAIKIMDM 79

>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 = 47.6 bits (113), Expect = 8e-08
 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 3/62 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             ++V  L  +    E+   F  +    S  +     N   FAF  F D + A  A+  L
Sbjct: 74  CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR---NPPGFAFVEFEDPRDAADAVREL 130

Query: 125 NN 126
           + 
Sbjct: 131 DG 132

>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 = 46.1 bits (110), Expect = 9e-08
 Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 4/82 (4%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQP 105
           GS  +S  + G      T++V+ LP  +   ++Y +F ++       +   +  T+ S+ 
Sbjct: 1   GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK-DTRKSKG 59

Query: 106 FAFAVFSDQQSALGAMYALNNF 127
            AF +F D+ SA     A+NN 
Sbjct: 60  VAFILFLDKDSAQNCTRAINNK 81

>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 = 46.1 bits (110), Expect = 1e-07
 Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 1/80 (1%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFA 107
           GS  +S       +  RT+FV  L   V+   +Y LF +        + +      + F 
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60

Query: 108 FAVFSDQQSALGAMYALNNF 127
           F  F   +S   A+  LN  
Sbjct: 61  FVCFKHPESVSYAIALLNGI 80

>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 = 47.1 bits (113), Expect = 1e-07
 Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYA 123
           R L+V  L + +    +   F+      +  +       +  +AF  +     A  A+  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 124 LN 125
           LN
Sbjct: 61  LN 62

>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 = 42.1 bits (100), Expect = 9e-06
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 53  ASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAV 110
           A      S D+   LFV  L  +V    + N F++FP Y S H+     T +S+ + F  
Sbjct: 76  AFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVS 135

Query: 111 FSDQQSALGAMYALNN 126
           F+ Q  A  AM ++  
Sbjct: 136 FTSQDDAQNAMDSMQG 151

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

 Score = 45.8 bits (109), Expect = 1e-07
 Identities = 11/69 (15%), Positives = 23/69 (33%), Gaps = 4/69 (5%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR----SSTQNSQPFAFAVFSDQQSA 117
             + T+ +  +        I      +     +++R      TQ ++ FAF   S    A
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 118 LGAMYALNN 126
              +  L +
Sbjct: 67  SQLLQILQS 75

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 47.2 bits (112), Expect = 1e-07
 Identities = 24/111 (21%), Positives = 34/111 (30%), Gaps = 2/111 (1%)

Query: 19  PPPPPPPPPPGGVVAP-PTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVK 77
           P    P    GG   P P     P P       + +        +    L V+ L   V 
Sbjct: 42  PRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVS 101

Query: 78  PREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
             +I  LF EF   + + +    +  S   A   F  +  AL AM      
Sbjct: 102 DADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGV 152

>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 = 46.8 bits (112), Expect = 2e-07
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSH-LR-SSTQNSQPFAFAVFSDQQSALGAMYAL 124
           L+V+GLP+ +  +E+  LF ++    +S  L    T  S+   F  F  +  A  A+  L
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 125 NN 126
           N 
Sbjct: 151 NG 152

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 42.6 bits (101), Expect = 7e-06
 Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHL-R-SSTQNSQPFAFAVFSDQQSALGAMYA 123
            L V  LP+++   E  +LF      ES  L R   T  S  + F  + D + A  A+  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 124 LNN 126
           LN 
Sbjct: 64  LNG 66

>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 = 45.8 bits (109), Expect = 2e-07
 Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             ++V  LP D++ ++I ++F ++       L+ + +   PFAF  F D + A  A+Y  
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-NRRGGPPFAFVEFEDPRDAEDAVYGR 81

Query: 125 NNF 127
           + +
Sbjct: 82  DGY 84

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

 Score = 46.3 bits (110), Expect = 2e-07
 Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQP 105
           G    S  + GS    R L+V GL E+V  + ++  F  F       +      T+  + 
Sbjct: 48  GGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRG 106

Query: 106 FAFAVFSDQQSALGAMYALNNF 127
           FAF  F   + A  A+  +N  
Sbjct: 107 FAFVEFELAEDAAAAIDNMNES 128

>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 = 46.8 bits (112), Expect = 2e-07
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSH-LR-SSTQNSQPFAFAVFSDQQSALGAMYAL 124
           L+V  LP  +   ++  +F ++      + LR   T   +  AF  ++ ++ A  A+ AL
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 125 NN 126
           NN
Sbjct: 152 NN 153

>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-06
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL-R-SSTQNSQPFAFAVFSDQQSALGAMY 122
             L V  LP+D+  RE+Y LFR      +  + R   T  S  +AF  F+ +  +  A+ 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 123 ALNN 126
            LN 
Sbjct: 64  VLNG 67

>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 = 2e-07
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 52  SASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVF 111
           S S  +      +R L +  +P  ++   + +L  ++ G   S  + +T +        +
Sbjct: 3   SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQY-GVVESCEQVNTDSETAVVNVTY 61

Query: 112 SDQQSALGAMYALNNF 127
           S +  A  A+  LN F
Sbjct: 62  SSKDQARQALDKLNGF 77

>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 = 45.5 bits (108), Expect = 4e-07
 Identities = 27/113 (23%), Positives = 38/113 (33%), Gaps = 10/113 (8%)

Query: 17  QTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDV 76
           Q P      P          Q    Q  PP   +           D +R L V  +P  V
Sbjct: 3   QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMN--------PEPDVLRNLMVNYIPTTV 54

Query: 77  KPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYALNNF 127
              ++  LF  +   ES  +     T+ S+ + F  F    SA  A+  LN F
Sbjct: 55  DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107

>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 = 44.1 bits (105), Expect = 4e-07
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAM 121
           R L+V GL E+V  + ++  F  F       +      T+  + FAF  F   + A  A+
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAI 66

Query: 122 YALNNF 127
             +N  
Sbjct: 67  DNMNES 72

>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 = 44.1 bits (105), Expect = 5e-07
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 65  RTLFVAGLPEDVKP----REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
            T+++  L E +K     + ++ +F  F G     L S +   +  AF +F +  SA  A
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRF-GQILDILVSRSLKMRGQAFVIFKEVSSATNA 67

Query: 121 MYALNNF 127
           + ++  F
Sbjct: 68  LRSMQGF 74

>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 = 43.8 bits (104), Expect = 6e-07
 Identities = 16/77 (20%), Positives = 25/77 (32%), Gaps = 2/77 (2%)

Query: 52  SASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFA 109
           S S  +         + V  +P  V   EI + F  +     S      +   P   A  
Sbjct: 3   SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62

Query: 110 VFSDQQSALGAMYALNN 126
            F  +  A  A+  LN+
Sbjct: 63  AFESRDEATAAVIDLND 79

>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 = 44.2 bits (105), Expect = 6e-07
 Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS S S     +   V+ L+V  L        I   F               +  + +AF
Sbjct: 1   GS-SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAV----ERVKKIRDYAF 55

Query: 109 AVFSDQQSALGAMYALNN 126
             FS+++ A+ AM ALN 
Sbjct: 56  VHFSNREDAVEAMKALNG 73

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

 Score = 45.8 bits (109), Expect = 7e-07
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 59  GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQS 116
           G+   +  ++V  +  ++    I   F  F   +S  +   S T   + FAF  +   ++
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 117 ALGAMYALN 125
           A  A+  +N
Sbjct: 83  AQLALEQMN 91

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 11/98 (11%)

Query: 32  VAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGY 91
           V  P+     QP    L   + +F           ++VA + +D+   +I ++F  F   
Sbjct: 102 VGRPSNIGQAQPIIDQLAEEARAF---------NRIYVASVHQDLSDDDIKSVFEAFGKI 152

Query: 92  ESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
           +S+ L    +T   + + F  +   QS+  A+ ++N F
Sbjct: 153 KSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 44.9 bits (106), Expect = 7e-07
 Identities = 18/122 (14%), Positives = 38/122 (31%), Gaps = 5/122 (4%)

Query: 11  LHYGYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRT-LFV 69
           +H+ ++ +                P  P   +P P P     A    Y      R  ++V
Sbjct: 1   MHHHHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYV 60

Query: 70  AGLPEDVKPREIYNLFREFPGYESSHLR----SSTQNSQPFAFAVFSDQQSALGAMYALN 125
                    +++  + R    Y+   L+     +   S+ +A  V + + S    +  L 
Sbjct: 61  GSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLP 120

Query: 126 NF 127
             
Sbjct: 121 GK 122

>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 = 44.8 bits (106), Expect = 7e-07
 Identities = 11/70 (15%), Positives = 28/70 (40%), Gaps = 7/70 (10%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLR-------SSTQNSQPFAFAVFSDQQSA 117
             ++V  L + V+ +++  +F  +  + S   R             +  AF    ++++A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 118 LGAMYALNNF 127
             A+   N +
Sbjct: 106 AKALKEANGY 115

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

 Score = 43.7 bits (104), Expect = 8e-07
 Identities = 12/64 (18%), Positives = 22/64 (34%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
              +FV  LP D   + + + F E      + ++     S+      F   + A  A   
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 67

Query: 124 LNNF 127
           +N  
Sbjct: 68  MNGM 71

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

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 56  PAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFS 112
           P      E   LFV  + E+ +  EI   F ++   ++ HL   R  T  S+ +A   + 
Sbjct: 64  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYE 122

Query: 113 DQQSALGAMYALNNF 127
             + AL A  ALN  
Sbjct: 123 THKQALAAKEALNGA 137

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

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPG--YESSHLR-SSTQNSQPFAFAVFSDQQSALGAMYA 123
           LF+  +P ++  +++  LF EF G  YE + L+   T   +  AF  + +++SAL A  A
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEF-GKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 124 LNN 126
           L+ 
Sbjct: 75  LHE 77

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

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 10/64 (15%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMY 122
           + +  A L ++V+   + ++ R++   E   +     T+     A  +F+  + A   + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 123 ALNN 126
            L+ 
Sbjct: 67  NLHL 70

>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 = 45.0 bits (107), Expect = 1e-06
 Identities = 14/66 (21%), Positives = 29/66 (43%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
            +F+  L + +  + +Y+ F  F    S  +      S+ + F  F  Q++A  A+  +N
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164

Query: 126 NFAPSD 131
               +D
Sbjct: 165 GMLLND 170

>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 = 42.3 bits (100), Expect = 1e-05
 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 47  PLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQ 104
           PLGS + S P+Y       +L+V  L  DV    +Y  F       S  +     T+ S 
Sbjct: 2   PLGSMNPSAPSYPM----ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSL 57

Query: 105 PFAFAVFSDQQSALGAMYALN 125
            +A+  F     A  A+  +N
Sbjct: 58  GYAYVNFQQPADAERALDTMN 78

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 5/62 (8%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           R + + GLP DV  +E+++L  ++   +           +  AF    + + A  A+ A 
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDY-ELKYCF----VDKYKGTAFVTLLNGEQAEAAINAF 77

Query: 125 NN 126
           + 
Sbjct: 78  HQ 79

>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 = 42.7 bits (101), Expect = 9e-06
 Identities = 10/67 (14%), Positives = 16/67 (23%), Gaps = 2/67 (2%)

Query: 63  EVRTLFVAGLPEDVKPRE-IYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGA 120
             R L V  LP      + +              L        + FA   +   + A  A
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242

Query: 121 MYALNNF 127
               +  
Sbjct: 243 QQQADGL 249

>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 = 41.5 bits (98), Expect = 3e-05
 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS--TQNSQPFAFAVFSDQQSALGAMYA 123
            L VA LP  +  ++   L R F   E   L  S  T  S+ + FA +  + SA  A   
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 124 LNNF 127
           L   
Sbjct: 157 LLGK 160

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

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS  +S  +       + L V+ +P   +  ++  +F +F       +  + + S+ F F
Sbjct: 1   GSSGSSGNSESK-STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGF 59

Query: 109 AVFSDQQSALGAMYALNNF 127
             F +   A  A   L+  
Sbjct: 60  VTFENSADADRAREKLHGT 78

>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 = 43.0 bits (102), Expect = 2e-06
 Identities = 12/64 (18%), Positives = 21/64 (32%), Gaps = 6/64 (9%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS-STQNSQPFAFAVFSDQQSALGAMYA 123
             L+V GL  +     +   F  F       +R+        FA+  +    +A  A   
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRF-----GSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72

Query: 124 LNNF 127
           +  F
Sbjct: 73  MRGF 76

>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 = 43.0 bits (102), Expect = 2e-06
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 3/79 (3%)

Query: 49  GSYSASFPAYGSYDEV-RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-TQNSQPF 106
           GS+    P  GS       LF+  L  +    E+     E        +    T  ++ F
Sbjct: 1   GSHMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKF 60

Query: 107 AFAVFSDQQSALGAMYALN 125
            +  F   +    A+  L 
Sbjct: 61  GYVDFESAEDLEKAL-ELT 78

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 10/66 (15%), Positives = 19/66 (28%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGA 120
                LF+  L  +    E+     E        +    T  ++ F +  F   +    A
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 121 MYALNN 126
           +  L  
Sbjct: 71  L-ELTG 75

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 43.0 bits (102), Expect = 4e-06
 Identities = 11/68 (16%), Positives = 23/68 (33%), Gaps = 7/68 (10%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALG 119
              RTL    L  ++   E+  +F +        +R  +Q+ +    A+  F  +  A  
Sbjct: 97  RAARTLLAKNLSFNITEDELKEVFEDA-L----EIRLVSQDGKSKGIAYIEFKSEADAEK 151

Query: 120 AMYALNNF 127
            +      
Sbjct: 152 NLEEKQGA 159

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

 Score = 42.6 bits (101), Expect = 2e-06
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 4/61 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             L++  L   V   ++  LF +      +           +AF  + DQ  A+ A+  L
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDR-KLPLA---GQVLLKSGYAFVDYPDQNWAIRAIETL 64

Query: 125 N 125
           +
Sbjct: 65  S 65

>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 = 42.3 bits (100), Expect = 3e-06
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 3/80 (3%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--F 106
           GS  +S  + G       + V  +P  V   EI + F  +     S      +   P   
Sbjct: 1   GSSGSSGASSGK-PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE 59

Query: 107 AFAVFSDQQSALGAMYALNN 126
           A   F  +  A  A+  LN+
Sbjct: 60  AMVAFESRDEATAAVIDLND 79

>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 = 42.3 bits (100), Expect = 4e-06
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALG 119
            E +T+F+  L  D +   +  + ++F   +   +     T++S+  AFA F  Q++A  
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 120 AMYALNNFAPSD 131
            + A +  A   
Sbjct: 73  CLAAASLEAEGG 84

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

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 20/115 (17%), Positives = 32/115 (27%), Gaps = 8/115 (6%)

Query: 14  GYYQTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLP 73
           G             P G                 +G  S       + D    L V GL 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMTG------GQQMGRGSRHVGNRANPDPNCCLGVFGLS 55

Query: 74  EDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYALNN 126
                R++  +F ++       +     ++ S+ FAF  F +   A  A    N 
Sbjct: 56  LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110

>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 = 41.8 bits (99), Expect = 4e-06
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMY 122
           R +++  +P D    +I +L        +  +     T  S+ +AF  F D +S+  A+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 123 ALNNF 127
            LN +
Sbjct: 63  NLNGY 67

>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 = 41.8 bits (99), Expect = 5e-06
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 4/65 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAM 121
           R L+V GL E+V  + ++  F  F       +      T+  + FAF  F   + A  A+
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAI 71

Query: 122 YALNN 126
             +N 
Sbjct: 72  DNMNE 76

>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 = 42.0 bits (99), Expect = 6e-06
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 61  YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSA 117
             E   LFV G+ E+    +I++ F E+   ++ HL   R  T   + +    +   + A
Sbjct: 19  SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEA 77

Query: 118 LGAMYALNN 126
             AM  LN 
Sbjct: 78  QAAMEGLNG 86

>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 = 41.9 bits (99), Expect = 6e-06
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 53  ASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH-LRSSTQNSQPFAFAVF 111
           A        D    L+++ LP  +  +E+ N+ + F    S+  LR S+  S+   FA  
Sbjct: 15  AQMAKQQEQDPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARM 73

Query: 112 SDQQSALGAMYALNNF 127
              +     +   N  
Sbjct: 74  ESTEKCEAVIGHFNGK 89

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 41.5 bits (98), Expect = 7e-06
 Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             LFV   P DV+  E+  +F  F   +   +         FAF  F + +SA  A+  +
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVKI------LNGFAFVEFEEAESAAKAIEEV 85

Query: 125 NNF 127
           +  
Sbjct: 86  HGK 88

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 41.1 bits (97), Expect = 7e-06
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 3/60 (5%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
           ++V  L       E+   F  +    +  +     N   FAF  F D + A  A+  L+ 
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIAR---NPPGFAFVEFEDPRDAEDAVRGLDG 59

>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 = 41.1 bits (97), Expect = 7e-06
 Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQP 105
           GS  +S P        +TLFV GL ED        L   F G   + +   R  T +S+ 
Sbjct: 1   GSSGSSGPN-ARSQPSKTLFVKGLSEDTTEET---LKESFDGSVRARIVTDR-ETGSSKG 55

Query: 106 FAFAVFSDQQSALGAMYALNN 126
           F F  F+ ++ A  A  A+ +
Sbjct: 56  FGFVDFNSEEDAKAAKEAMED 76

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 41.1 bits (97), Expect = 9e-06
 Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 4/77 (5%)

Query: 53  ASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFA 109
            S  + G   +   LFV GL  D   + +  +F ++       +   R  TQ S+ F F 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-TQRSRGFGFV 59

Query: 110 VFSDQQSALGAMYALNN 126
            F +   A  AM A+N 
Sbjct: 60  TFENIDDAKDAMMAMNG 76

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 23/104 (22%), Positives = 38/104 (36%), Gaps = 5/104 (4%)

Query: 26  PPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLF 85
           P  G   A  T P           + +         +    LF+  LP++    ++ + F
Sbjct: 5   PQFGSASALSTSPLASVALSAAAAAAAGK--QIEGPEGCN-LFIYHLPQEFTDTDLASTF 61

Query: 86  REFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
             F    S+ +     T  S+ F F  F +  SA  A+ A+N F
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF 105

>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 = 40.8 bits (96), Expect = 1e-05
 Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 5/71 (7%)

Query: 59  GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR----SSTQNSQPFAFAVFSDQ 114
           GS     +L++  L   +    I   F    G     ++      T     + F  F+D 
Sbjct: 4   GSSGMAASLWMGDLEPYMDENFISRAFATM-GETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 115 QSALGAMYALN 125
            +A   ++ +N
Sbjct: 63  ATAEKCLHKIN 73

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFA 107
            S S+    Y +  E   LF++GLP      E+  + +     +   L  +     +  A
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA 61

Query: 108 FAVFSDQQSALGAMYALNN 126
           +  + ++  A  A+  ++ 
Sbjct: 62  YVEYENESQASQAVMKMDG 80

>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 = 40.7 bits (96), Expect = 1e-05
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS  +S  +  S  E +TL ++ L        +  +F +         ++    S+ +AF
Sbjct: 1   GSSGSSGNSTWS-GESKTLVLSNLSYSATEETLQEVFEKA--TFIKVPQNQNGKSKGYAF 57

Query: 109 AVFSDQQSALGAMYALNNF 127
             F+  + A  A+ + N  
Sbjct: 58  IEFASFEDAKEALNSCNKR 76

>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 = 40.7 bits (96), Expect = 1e-05
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS  +S          RTL+V  L  DV    I  LF +    +S  + +   ++ P+ F
Sbjct: 1   GSSGSSGMMEDDGQP-RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF 59

Query: 109 AVFSDQQSALGAMYALN 125
             F + + A  A+ A+N
Sbjct: 60  VEFYEHRDAAAALAAMN 76

>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 = 40.2 bits (95), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAMYA 123
           LFV  L  +V    + N F++FP Y S H+      T +S+ + F  F+ Q  A  AM +
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ-TGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 124 LNN 126
           +  
Sbjct: 63  MQG 65

>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 = 40.7 bits (96), Expect = 1e-05
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQP 105
           GS  +S P   + D+  T+ V  L ED +  ++  LFR F      +L   + +T  S+ 
Sbjct: 1   GSSGSSGPNRRA-DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK-TTGQSKG 58

Query: 106 FAFAVFSDQQSALGAMYALNNF 127
           FAF  F  ++ A  A+  ++ F
Sbjct: 59  FAFISFHRREDAARAIAGVSGF 80

>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 = 42.0 bits (99), Expect = 2e-05
 Identities = 11/61 (18%), Positives = 20/61 (32%), Gaps = 1/61 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           L V  L   V    +   F +F   E + +       +    F  F+ +  A  A+    
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158

Query: 126 N 126
           +
Sbjct: 159 D 159

>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 = 40.5 bits (95), Expect = 2e-05
 Identities = 11/75 (14%), Positives = 23/75 (30%), Gaps = 3/75 (4%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESS-HL-RSSTQNSQPF 106
           GS S S              +  +P  +   ++       P  E++ H+   +       
Sbjct: 1   GS-SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ 59

Query: 107 AFAVFSDQQSALGAM 121
           A   F ++  A  + 
Sbjct: 60  ALVQFKNEDDARKSE 74

>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 = 40.6 bits (95), Expect = 2e-05
 Identities = 14/93 (15%), Positives = 24/93 (25%), Gaps = 5/93 (5%)

Query: 34  PPTQPYMPQPQ---PPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPG 90
             +   +P+         G                 + + GLP      EI   F     
Sbjct: 9   HHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEI 68

Query: 91  YESSHLRSSTQNSQP--FAFAVFSDQQSALGAM 121
             +          +    AF  F+ Q+ A  A+
Sbjct: 69  VPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101

>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 = 40.4 bits (95), Expect = 2e-05
 Identities = 18/93 (19%), Positives = 28/93 (30%), Gaps = 1/93 (1%)

Query: 36  TQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH 95
            Q     P       + +        +    L V+ L   V   +I  LF EF   + + 
Sbjct: 7   GQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 66

Query: 96  L-RSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
           +    +  S   A   F  +  AL AM      
Sbjct: 67  VDYDRSGRSLGTADVHFERRADALKAMKQYKGV 99

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 12/85 (14%)

Query: 53  ASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-----------TQ 101
                + S+ +  T+FV GL E+V    + + F++  G   ++ ++            T 
Sbjct: 2   GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQI-GIIKTNKKTGQPMINLYTDRETG 60

Query: 102 NSQPFAFAVFSDQQSALGAMYALNN 126
             +  A   F D  SA  A+   + 
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDG 85

>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 = 39.9 bits (94), Expect = 2e-05
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 5/82 (6%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQP 105
           GS S S     + D    L V GL      R++  +F ++       +   +  ++ S+ 
Sbjct: 1   GS-SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-QSRRSRG 58

Query: 106 FAFAVFSDQQSALGAMYALNNF 127
           FAF  F +   A  A    N  
Sbjct: 59  FAFVYFENVDDAKEAKERANGM 80

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

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 18/109 (16%), Positives = 36/109 (33%), Gaps = 2/109 (1%)

Query: 20  PPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPR 79
                     G+V   +                +        + + +L V  L     P 
Sbjct: 3   SSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPD 62

Query: 80  EIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYALNN 126
            +  +F ++      ++     T+ S+ FAF  F D++ A  AM A++ 
Sbjct: 63  TLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111

>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 = 41.0 bits (96), Expect = 2e-05
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 4/97 (4%)

Query: 33  APPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYE 92
                 Y    +   +   S     +   + + +L V  L     P  +  +F ++    
Sbjct: 39  VDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG 98

Query: 93  SSHL---RSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
             ++   R  T+ S+ FAF  F D++ A  AM A++ 
Sbjct: 99  DVYIPRDR-YTKESRGFAFVRFHDKRDAEDAMDAMDG 134

>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 = 40.9 bits (96), Expect = 3e-05
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMY 122
            TL+V  L       +IY LF +    +   +      + +  F F  +  +  A  AM 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 123 ALNN 126
            +N 
Sbjct: 100 YING 103

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

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 18/92 (19%), Positives = 30/92 (32%), Gaps = 9/92 (9%)

Query: 36  TQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH 95
           T    PQ  P  +     S P         T ++  +P      ++  LF+ F G+    
Sbjct: 4   TIGLPPQVNPQAVDHIIRSAPPRV-----TTAYIGNIPHFATEADLIPLFQNF-GFILD- 56

Query: 96  LRSSTQNSQPFAFAVFSDQQSALGAMYALNNF 127
                   +   F  +   + A   + AL NF
Sbjct: 57  --FKHYPEKGCCFIKYDTHEQAAVCIVALANF 86

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 11/73 (15%), Positives = 21/73 (28%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS  +S        +   + V G+P      ++ + F          L+     +     
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGL 60

Query: 109 AVFSDQQSALGAM 121
             F   Q    A+
Sbjct: 61  VKFLSPQDTFEAL 73

>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 = 40.6 bits (96), Expect = 3e-05
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSA 117
           D+   +FV G+  DV+P+E    F ++     + L     T  S+ F F  +    + 
Sbjct: 85  DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142

>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 = 39.0 bits (92), Expect = 3e-05
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 59  GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQS 116
           GS      L++ GL      +++  L + +    S+      +T   + + F  F    +
Sbjct: 1   GSSGSSG-LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSA 59

Query: 117 ALGAMYALNNF 127
           A  A+ AL   
Sbjct: 60  AQKAVTALKAS 70

>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 = 39.6 bits (93), Expect = 3e-05
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 61  YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSA 117
             E   LFV  + E+ +  EI   F ++   ++ HL   R  T  S+ +A   +   + A
Sbjct: 23  SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-TGFSKGYALVEYETHKQA 81

Query: 118 LGAMYALNNF 127
           L A  ALN  
Sbjct: 82  LAAKEALNGA 91

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 10/73 (13%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREF----PGYESSHLRSS------TQNSQPFAFAVFSDQ 114
            T+FV GL E+V    + + F++        ++     +      T   +  A   F D 
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 115 QSALGAMYALNNF 127
            SA  A+   +  
Sbjct: 68  PSAKAAIDWFDGK 80

>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 = 39.6 bits (93), Expect = 4e-05
 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGA 120
           D    LF+ GL  +   + +  +F +        L +  T  S+ FAF  F +   A  A
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64

Query: 121 MYALNN 126
              +N 
Sbjct: 65  AKDMNG 70

>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 = 39.1 bits (92), Expect = 4e-05
 Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAF 108
           GS  +S      Y  V  L+V  L + +    +   F  F    S+ +      S+ F F
Sbjct: 1   GSSGSSGDRITRYQVVN-LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGF 59

Query: 109 AVFSDQQSALGAMYALNN 126
             FS  + A  A+  +N 
Sbjct: 60  VCFSSPEEATKAVTEMNG 77

>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 = 39.1 bits (92), Expect = 4e-05
 Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 2/63 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYA 123
            LFV  L       ++  LF  +      H    S T+  + FAF  F   + A+ A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 124 LNN 126
           ++ 
Sbjct: 70  VDG 72

>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 = 39.1 bits (92), Expect = 4e-05
 Identities = 13/68 (19%), Positives = 22/68 (32%), Gaps = 6/68 (8%)

Query: 59  GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSAL 118
           GS      +FV  +      +E+ +LF          +         +AF     +  A 
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD------YAFVHMEKEADAK 57

Query: 119 GAMYALNN 126
            A+  LN 
Sbjct: 58  AAIAQLNG 65

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

 Score = 39.2 bits (92), Expect = 4e-05
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 52  SASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFA 109
               P      E   LFV G+ E+    +I++ F E+   ++ HL     T   + +   
Sbjct: 11  DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70

Query: 110 VFSDQQSALGAMYALNNF 127
            +   + A  AM  LN  
Sbjct: 71  EYETYKEAQAAMEGLNGQ 88

>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 = 38.7 bits (91), Expect = 5e-05
 Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 6/65 (9%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
            +  LF+  LP +   +EI +LF ++       +  +      + F    D+ +A  A+ 
Sbjct: 7   GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN------YGFVHIEDKTAAEDAIR 60

Query: 123 ALNNF 127
            L+++
Sbjct: 61  NLHHY 65

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 39.2 bits (92), Expect = 5e-05
 Identities = 12/66 (18%), Positives = 27/66 (40%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
            + + L V+ +P   +  ++  +F +F       +  + + S+ F F  F +   A  A 
Sbjct: 27  SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAR 86

Query: 122 YALNNF 127
             L+  
Sbjct: 87  EKLHGT 92

>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 = 39.0 bits (91), Expect = 5e-05
 Identities = 12/63 (19%), Positives = 14/63 (22%), Gaps = 4/63 (6%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             +    LP      EI   F  F        R         A   F +   A  A   L
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLG----RVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 125 NNF 127
              
Sbjct: 67  AYS 69

>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 = 38.8 bits (91), Expect = 6e-05
 Identities = 23/90 (25%), Positives = 32/90 (35%), Gaps = 11/90 (12%)

Query: 40  MPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS- 98
           M       L   SA             L+V  L  ++    +  +F  F   ES  L   
Sbjct: 11  MAAAMANNLQKGSAGP---------MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 99  -STQNSQPFAFAVFSDQQSALGAMYALNNF 127
             T  S+ + F  FSD + A  A+  LN F
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGF 91

>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 = 38.7 bits (91), Expect = 7e-05
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPF 106
           GS  +S P     D + TL V  L     P  +  +F ++      ++     T+  + F
Sbjct: 1   GSSGSSGPDV---DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGF 57

Query: 107 AFAVFSDQQSALGAMYALNN 126
           AF  F D++ A  A  A++ 
Sbjct: 58  AFVRFHDRRDAQDAEAAMDG 77

>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 = 38.9 bits (91), Expect = 7e-05
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 11/88 (12%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREF--------PGYESSHLRSST 100
           GS  +S       D    ++V GL + V   ++ + F++          G    H+    
Sbjct: 1   GSSGSSGDPDEDSDN-SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK 59

Query: 101 QNSQP--FAFAVFSDQQSALGAMYALNN 126
           +  +P   A   + D  +A  A+   + 
Sbjct: 60  ETGKPKGDATVSYEDPPTAKAAVEWFDG 87

>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 = 38.4 bits (90), Expect = 8e-05
 Identities = 11/62 (17%), Positives = 21/62 (33%), Gaps = 6/62 (9%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             L V  +      +E+   F E+       +         +AF      + A+ A+  L
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK------DYAFVHMERAEDAVEAIRGL 64

Query: 125 NN 126
           +N
Sbjct: 65  DN 66

>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 = 38.5 bits (90), Expect = 8e-05
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 7/62 (11%)

Query: 67  LFVAGLP-EDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           LF+  LP ++V   +++ +F  +      +++        F F  F + QS   A+   +
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEXES 78

Query: 126 NF 127
             
Sbjct: 79  QE 80

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 38.4 bits (90), Expect = 9e-05
 Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 51  YSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFA 109
           + + F      +    L V+ L   V   +I  LF EF   + + +    +  S   A  
Sbjct: 16  FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADV 75

Query: 110 VFSDQQSALGAMYALNNF 127
            F  +  AL AM   N  
Sbjct: 76  HFERKADALKAMKQYNGV 93

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

 Score = 38.3 bits (90), Expect = 9e-05
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 7/62 (11%)

Query: 66  TLFVAGLP-EDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
            LF+  LP ++V   +++ +F  +      +++        F F  F + QS   A+   
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIECE 65

Query: 125 NN 126
           + 
Sbjct: 66  SQ 67

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 59  GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQS 116
           G++  V+ +FV G+ ED +   + + F ++   E   + +   +   + FAF  F D  S
Sbjct: 99  GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS 158

Query: 117 A 117
            
Sbjct: 159 V 159

>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 = 38.4 bits (90), Expect = 1e-04
 Identities = 13/61 (21%), Positives = 27/61 (44%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
           +F+  L + +  + +Y+ F  F    S  +      S+ + F  F  Q++A  A+  +N 
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67

Query: 127 F 127
            
Sbjct: 68  M 68

>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 = 37.7 bits (88), Expect = 1e-04
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 59  GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSA 117
            S     T+ + G P +V  + +           +  + R++  N   + F  FS+++  
Sbjct: 5   SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEV 63

Query: 118 LGAM 121
             A+
Sbjct: 64  KQAL 67

>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 = 37.6 bits (88), Expect = 2e-04
 Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
            LFV  LP D+   E+  LF ++       +       + F F     +  A  A   L+
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI----HKDKGFGFIRLETRTLAEIAKVELD 72

Query: 126 NF 127
           N 
Sbjct: 73  NM 74

>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 = 37.6 bits (88), Expect = 2e-04
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 60  SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSA 117
               +R++FV  +P +    ++ ++F E     S  L     T   + + F  + DQ++A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 118 LGAMYALNNF 127
           L AM  LN  
Sbjct: 64  LSAMRNLNGR 73

>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 = 38.1 bits (89), Expect = 2e-04
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 3/79 (3%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPF 106
           GS  +S     + +    +FV  L  ++   +I   F  F     + +    +T  S+ +
Sbjct: 1   GSSGSSGQKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGY 59

Query: 107 AFAVFSDQQSALGAMYALN 125
            F  F ++  A  A+  + 
Sbjct: 60  GFVSFFNKWDAENAIQQMG 78

>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 = 38.3 bits (89), Expect = 2e-04
 Identities = 18/105 (17%), Positives = 26/105 (24%), Gaps = 7/105 (6%)

Query: 17  QTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDV 76
                     P G  +A  T           +G  S              + + GLP   
Sbjct: 6   HHHHHSSGLVPRGSHMASMTGG-------QQMGRGSGDSEFTVQSTTGHCVHMRGLPYKA 58

Query: 77  KPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
              +IYN F                     A   F+  + A+ AM
Sbjct: 59  TENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAM 103

>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 = 37.1 bits (87), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 4/65 (6%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAMY 122
            L+V  L  ++    +  +F  F   ++  L      T  S+ + F  FSD + A  A+ 
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD-TGRSKGYGFITFSDSECARRALE 65

Query: 123 ALNNF 127
            LN F
Sbjct: 66  QLNGF 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 = 37.3 bits (87), Expect = 2e-04
 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
            +V+ LFV  L   V    +   F +F   E           + +AF  F ++  A+ AM
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK------LKDYAFIHFDERDGAVKAM 62

Query: 122 YALNN 126
             +N 
Sbjct: 63  EEMNG 67

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 5/78 (6%)

Query: 49  GSYSASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREF---PGYESSHLRSSTQNSQP 105
           G  S     + S +    + + GLP      E+   F +     G +   L  +  + +P
Sbjct: 8   GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRP 67

Query: 106 --FAFAVFSDQQSALGAM 121
              AF +F+ ++ A  A+
Sbjct: 68  TGDAFVLFACEEYAQNAL 85

>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 = 36.9 bits (86), Expect = 3e-04
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS-STQNSQPFAFAVFSDQQSALGAM 121
            + TL+V GL + +   ++ N F +F       +R+ +    Q  AF  F+ +Q+A  A 
Sbjct: 11  TITTLYVGGLGDTITETDLRNHFYQF-----GEIRTITVVQRQQCAFIQFATRQAAEVAA 65

Query: 122 YALNN 126
               N
Sbjct: 66  EKSFN 70

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 3/56 (5%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSA 117
             +R++FV+G P  V   ++   F  F    S  +    ++   FA     D  + 
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMD---KDKGVFAIVEMGDVGAR 58

>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 = 3e-04
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 5/65 (7%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLR----SSTQNSQPFAFAVFSDQQSALGAM 121
            +F+  L  ++  + +Y+ F  F G      +      T NS+ +AF  F+   ++  A+
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAF-GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65

Query: 122 YALNN 126
            A+N 
Sbjct: 66  EAMNG 70

>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 = 36.5 bits (85), Expect = 3e-04
 Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 3/66 (4%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
              RTL    L  ++   E+  +F +    E   +      S+  A+  F  +  A   +
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDA-L-EIRLVS-QDGKSKGIAYIEFKSEADAEKNL 70

Query: 122 YALNNF 127
                 
Sbjct: 71  EEKQGA 76

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 36.9 bits (86), Expect = 3e-04
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 3/65 (4%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGA 120
           + RT+F   L   ++PR++ + F          + S  +++ S+  A+  F + QS   A
Sbjct: 24  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 83

Query: 121 MYALN 125
           +  L 
Sbjct: 84  I-GLT 87

>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 = 36.4 bits (85), Expect = 4e-04
 Identities = 10/65 (15%), Positives = 24/65 (36%), Gaps = 3/65 (4%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAMY 122
            + +  L  +V    I  +F  +   +   +   R     S+ +A+  F +   A  A+ 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 123 ALNNF 127
            ++  
Sbjct: 66  HMDGG 70

>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 = 36.3 bits (84), Expect = 5e-04
 Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 4/79 (5%)

Query: 52  SASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVF 111
           S S  ++        + V GL E V   ++     +F       +       +  A   F
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM----MPFKRQALVEF 58

Query: 112 SDQQSALGAMYALNNFAPS 130
            +  SA   +    +    
Sbjct: 59  ENIDSAKECVTFAADVPVY 77

>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 = 36.0 bits (84), Expect = 5e-04
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAMYAL 124
           +FV  L  ++    I   F  F     + +    +T  S+ + F  F ++  A  A+  +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 125 N 125
            
Sbjct: 69  G 69

>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 = 36.2 bits (84), Expect = 6e-04
 Identities = 11/63 (17%), Positives = 26/63 (41%), Gaps = 7/63 (11%)

Query: 65  RTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
             +F+  L    VK  ++  +F ++       +       + +AF  +S+++ A  A+  
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV------HKGYAFVQYSNERHARAAVLG 81

Query: 124 LNN 126
            N 
Sbjct: 82  ENG 84

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 36.3 bits (84), Expect = 6e-04
 Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
           + +  LPE    +++ +L RE    E++    +T++        F  ++  + A+  LNN
Sbjct: 31  ITMKNLPEGCSWQDLKDLAREN-SLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNN 89

Query: 127 F 127
            
Sbjct: 90  I 90

>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 = 35.7 bits (83), Expect = 7e-04
 Identities = 11/70 (15%), Positives = 22/70 (31%), Gaps = 5/70 (7%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHL-----RSSTQNSQPFAFAVFSDQQSA 117
               LF+  L        +  +F +    +S  +     ++    S  F F  +   + A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 118 LGAMYALNNF 127
             A+  L   
Sbjct: 64  QKALKQLQGH 73

>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 = 36.1 bits (84), Expect = 8e-04
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           LF+  LP++   +++  +F  F    S+ +     T  S+ F F  + +  SA  A+ ++
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 125 NNF 127
           N F
Sbjct: 88  NGF 90

>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 = 35.2 bits (82), Expect = 8e-04
 Identities = 8/64 (12%), Positives = 18/64 (28%), Gaps = 4/64 (6%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRSS----TQNSQPFAFAVFSDQQSALGAMY 122
           L++  L       ++          +   ++         S+ FA      + S+   M 
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 123 ALNN 126
            L  
Sbjct: 64  LLPK 67

>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 = 35.2 bits (82), Expect = 9e-04
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGA 120
           +R ++V  L       ++  LF +F    +  L   R  T+  + F F    + +S   A
Sbjct: 1   MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR-ETKKPKGFGFVEMQE-ESVSEA 58

Query: 121 MYALNN 126
           +  L+N
Sbjct: 59  IAKLDN 64

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 35.5 bits (82), Expect = 9e-04
 Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 6/67 (8%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYES-SHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
             + + GL + V   ++    +EF        +    Q     A   F D   A  A+  
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQ-----ALVEFEDVLGACNAVNY 76

Query: 124 LNNFAPS 130
             +    
Sbjct: 77  AADNQIY 83

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	144
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.9
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.88
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.88
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.87
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.87
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.87
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.87
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.87
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.86
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.86
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.86
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.86
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.86
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.86
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.85
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.85
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.85
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.85
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.85
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.85
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.85
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.85
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.85
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.85
2div_A	99	TRNA selenocysteine associated protein; structural	99.85
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.85
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.85
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.85
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.84
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.84
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.84
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.84
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.84
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.84
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.84
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.84
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.84
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.84
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.84
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.84
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.83
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.83
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.83
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.83
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.83
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.83
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.83
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.83
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.83
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.83
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.83
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.83
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.83
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.83
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.83
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.83
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.83
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.82
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.82
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.82
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.82
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.82
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.82
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.82
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.82
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.82
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.82
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.81
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.81
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.81
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.81
1x5p_A	97	Negative elongation factor E; structure genomics,	99.81
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.81
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.8
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.8
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.8
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.8
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.8
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.8
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.8
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.8
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.8
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.8
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.8
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.79
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.79
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.79
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.79
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.79
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.79
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.79
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.78
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.78
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.78
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.78
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.78
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.77
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.77
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.77
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.77
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.77
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.63
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.76
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.76
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.76
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.76
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.76
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.76
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.75
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.74
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.74
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.74
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.73
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.73
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.72
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.71
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.71
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.7
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.7
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.69
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.69
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.68
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.67
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.65
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.65
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.65
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.65
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.65
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.64
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.64
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.64
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.62
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.6
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.59
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.57
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.51
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.48
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.39
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.29
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.17
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.11
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.86
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.4
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.23
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.86
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.74
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.65
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.56
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.51
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.29
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	97.01
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.64
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.85
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.02
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	83.9

>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=99.90  E-value=2.9e-23  Score=140.02  Aligned_cols=80  Identities=19%  Similarity=0.259  Sum_probs=72.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+|||.++||++|+++|++||.|.+|++.+++.+++  +||||+|.+.++|++|++.|||..|+  |+.|+|+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~--gr~l~V~   94 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQ--SKTIKVS   94 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            3567899999999999999999999999999999998865544  39999999999999999999999995  8999999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      |+..
T Consensus        95 ~AkP   98 (99)
T 4fxv_A           95 YARP   98 (99)
T ss_dssp             ECCB
T ss_pred             EeeC
Confidence            9863

>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=99.88  E-value=5.6e-22  Score=133.44  Aligned_cols=81  Identities=22%  Similarity=0.334  Sum_probs=74.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++.++++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL--GKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEET--TEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcC--CCeEEEE
Confidence            44567899999999999999999999999999999999887666679999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        89 ~a~   91 (103)
T 2cqi_A           89 WAT   91 (103)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            975

>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=99.88  E-value=1.3e-22  Score=139.86  Aligned_cols=77  Identities=17%  Similarity=0.326  Sum_probs=71.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..+||||||+.+++|++|+++|++||.|++|+|+++++++++||||+|++.++|++|++.|||..|+  |+.|+|+|..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~--g~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN--DRKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEET--TEECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEECC
Confidence            4689999999999999999999999999999999987666679999999999999999999999994  8899999864

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

Probab=99.88  E-value=4.3e-22  Score=136.82  Aligned_cols=78  Identities=12%  Similarity=0.163  Sum_probs=71.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..++|||+||+++++|++|+++|++||.|++|+|.++..+++  +||||+|++.++|++|++.|||..|+  |+.|+|++
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~--gr~i~V~~   82 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVM--GNIIHAQL   82 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEEE
Confidence            458999999999999999999999999999999999876544  49999999999999999999999995  89999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        83 a~   84 (110)
T 3s8s_A           83 DI   84 (110)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.88  E-value=1.2e-21  Score=131.83  Aligned_cols=82  Identities=16%  Similarity=0.227  Sum_probs=74.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ......++|||+||+.++++++|+++|++||.|++|++..++.+.++||||+|++.++|++|++.|||..|.  |+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE--GRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEET--TEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEE
Confidence            344567899999999999999999999999999999999886666669999999999999999999999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        88 ~~a~   91 (103)
T 2cq3_A           88 NNAT   91 (103)
T ss_dssp             EECC
T ss_pred             EEcc
Confidence            9975

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

Probab=99.87  E-value=1.2e-21  Score=129.57  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=72.3

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++.++  ++||||+|++.++|++|++.|||..|.  |+.|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   89 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF--GRVIK   89 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEET--TEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeC--CcEEE
Confidence            34567899999999999999999999999999999998875433  449999999999999999999999995  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|++
T Consensus        90 v~~ak   94 (94)
T 2e5h_A           90 ASIAI   94 (94)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            99974

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=5.4e-22  Score=135.53  Aligned_cols=81  Identities=15%  Similarity=0.235  Sum_probs=74.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++++.++||||+|++.++|++|++.|||..|.  |+.|+|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE--GRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            34567899999999999999999999999999999999886666679999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       103 ~a~  105 (109)
T 2err_A          103 NAT  105 (109)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            975

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.87  E-value=1.9e-21  Score=130.87  Aligned_cols=83  Identities=19%  Similarity=0.247  Sum_probs=73.3

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           58 YGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        58 ~~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....+.++|||+||+.++++++|+++|++||.|++|++..+.+..++||||+|.+.++|++|++.|||..|.  |+.|+
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   86 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVA--TKPLY   86 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSS--SSBCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeC--CcEEE
Confidence            3344578899999999999999999999999999999999873333449999999999999999999999994  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        87 V~~a~   91 (103)
T 2d9p_A           87 VALAQ   91 (103)
T ss_dssp             EEECS
T ss_pred             EEEec
Confidence            99975

>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=99.87  E-value=1.1e-21  Score=127.27  Aligned_cols=79  Identities=20%  Similarity=0.280  Sum_probs=71.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..+..++  ++||||+|++.++|++|++.|||..++  |+.|+|+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~   82 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIRVN   82 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEEE
Confidence            457899999999999999999999999999999998874443  349999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            974

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

Probab=99.87  E-value=5.8e-21  Score=134.82  Aligned_cols=82  Identities=23%  Similarity=0.316  Sum_probs=73.6

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ......++|||+||+.++++++|+++|++||.|++|+++.++.++  ++||||+|++.++|++|++.|||..|.  |+.|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l  114 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL--NKRL  114 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS--SCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CeEE
Confidence            344667899999999999999999999999999999999886544  349999999999999999999999995  8899


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus       115 ~v~~a~  120 (139)
T 1u6f_A          115 KVALAA  120 (139)
T ss_dssp             EEEESS
T ss_pred             EEEECC
Confidence            999975

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.86  E-value=1.7e-21  Score=126.89  Aligned_cols=79  Identities=13%  Similarity=0.176  Sum_probs=70.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..++.++.  +||||+|.+.++|++|++.|||..++  |+.|+|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v~   81 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG--GRQIRTN   81 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEE
Confidence            4568999999999999999999999999999999998754443  49999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        82 ~a~   84 (87)
T 3bs9_A           82 WAT   84 (87)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            985

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

Probab=99.86  E-value=3.3e-21  Score=127.48  Aligned_cols=81  Identities=19%  Similarity=0.190  Sum_probs=73.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++.++.  +||||+|++.++|++|++.|||..|+  |+.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   88 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GRRIR   88 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CEEEE
Confidence            345678999999999999999999999999999999998865443  39999999999999999999999995  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        89 v~~a~   93 (95)
T 2cqc_A           89 VSGPS   93 (95)
T ss_dssp             EECCS
T ss_pred             EEecC
Confidence            99975

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

Probab=99.86  E-value=2.5e-21  Score=130.28  Aligned_cols=83  Identities=24%  Similarity=0.321  Sum_probs=73.8

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCe
Q 032280           58 YGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACS  135 (144)
Q Consensus        58 ~~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~  135 (144)
                      .....+.++|||+||+.++++++|+++|++||.|++|++..++.++.  +||||+|.+.++|++|++.|||..|.  |+.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~   86 (103)
T 2cq0_A            9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD--HLI   86 (103)
T ss_dssp             CCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET--TEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeC--CcE
Confidence            33456678999999999999999999999999999999998754443  39999999999999999999999995  899


Q ss_pred             EEEEeec
Q 032280          136 LLFPHSM  142 (144)
Q Consensus       136 l~v~~s~  142 (144)
                      |+|+|+.
T Consensus        87 l~v~~a~   93 (103)
T 2cq0_A           87 LNVEWAK   93 (103)
T ss_dssp             CEEEESS
T ss_pred             EEEEECC
Confidence            9999975

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

Probab=99.86  E-value=3.8e-21  Score=129.90  Aligned_cols=82  Identities=23%  Similarity=0.301  Sum_probs=72.4

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeec-C--CCCCcEEEEEeCCHHHHHHHHHHh-cCCccCCCCC
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-T--QNSQPFAFAVFSDQQSALGAMYAL-NNFAPSDSAC  134 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~-~--~~~~~~aFV~F~~~~~A~~A~~~l-nG~~~~~~g~  134 (144)
                      ......++|||+||+.++++++|+++|++||.|++|++..+ +  +..++||||+|.+.++|++|++.| ||..|.  |+
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~--g~   87 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--GR   87 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--SC
T ss_pred             ccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeEC--CC
Confidence            34456789999999999999999999999999999999877 2  333459999999999999999999 999995  88


Q ss_pred             eEEEEeec
Q 032280          135 SLLFPHSM  142 (144)
Q Consensus       135 ~l~v~~s~  142 (144)
                      .|+|+|+.
T Consensus        88 ~l~v~~a~   95 (107)
T 2cph_A           88 RLVLEWAD   95 (107)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEeCC
Confidence            99999975

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

Probab=99.86  E-value=6.1e-21  Score=127.69  Aligned_cols=81  Identities=15%  Similarity=0.244  Sum_probs=72.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...+.++|||+||+.++++++|+++|++||.|++|++..++.+ .++||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v   90 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIK--ENIIKV   90 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESS--SCEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEE
Confidence            3456789999999999999999999999999999999987622 2349999999999999999999999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        91 ~~a~   94 (100)
T 2do4_A           91 AISN   94 (100)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9975

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.86  E-value=5.7e-21  Score=127.76  Aligned_cols=78  Identities=21%  Similarity=0.258  Sum_probs=70.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEE--------EEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYES--------SHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~--------v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      ...++||||||+.++++++|+++|++||.|.+        |++..++.+++  +||||+|.+.++|++|++.|||..|. 
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~-   89 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS-   89 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC-
Confidence            34689999999999999999999999999999        99988865443  49999999999999999999999995 


Q ss_pred             CCCeEEEEee
Q 032280          132 SACSLLFPHS  141 (144)
Q Consensus       132 ~g~~l~v~~s  141 (144)
                       |+.|+|+|+
T Consensus        90 -g~~l~V~~A   98 (99)
T 2la6_A           90 -GNPIKVSFA   98 (99)
T ss_dssp             -SSBCEEEEC
T ss_pred             -CcEEEEEec
Confidence             889999986

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

Probab=99.86  E-value=4.6e-21  Score=126.91  Aligned_cols=79  Identities=22%  Similarity=0.340  Sum_probs=71.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|++.++|++|++.|||..|+  |+.|+|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~   80 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELA--GRPMRVG   80 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSS--SSCCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeC--CcEEEEE
Confidence            35689999999999999999999999999999999987543  3449999999999999999999999995  8889999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        81 ~a~   83 (95)
T 2dnz_A           81 HVT   83 (95)
T ss_dssp             ESS
T ss_pred             Ecc
Confidence            875

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.86  E-value=5.4e-21  Score=130.97  Aligned_cols=82  Identities=12%  Similarity=0.179  Sum_probs=73.1

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ....+.++|||+||+.++++++|+++|++||.|++|++..++.++.  +||||+|.+.++|++|++.|||..|.  |+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l   87 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG--GRQI   87 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEET--TEEC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            3445678999999999999999999999999999999998854443  49999999999999999999999995  8899


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        88 ~V~~a~   93 (115)
T 2dgo_A           88 RTNWAT   93 (115)
T ss_dssp             EEEESS
T ss_pred             EEEEcc
Confidence            999975

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.86  E-value=3.5e-21  Score=132.47  Aligned_cols=81  Identities=25%  Similarity=0.297  Sum_probs=71.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...+.++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|.+.++|++|++.|||..|+  |+.|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~  113 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG--TKRLK  113 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEET--TEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEEC--CEEEE
Confidence            3456789999999999999999999999999999999887543  3449999999999999999999999995  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|++
T Consensus       114 V~~ak  118 (118)
T 2khc_A          114 VQLKK  118 (118)
T ss_dssp             EEEC-
T ss_pred             EEecC
Confidence            99874

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.86  E-value=1.6e-21  Score=132.38  Aligned_cols=78  Identities=14%  Similarity=0.090  Sum_probs=69.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...+++|||+||++++++++|+++|++||.|.+|++++++    +||||+|++.++|.+|++.|||..+.-+|+.|+|+|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~k----g~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~   93 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK----RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY   93 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCC----CEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEe
Confidence            3457899999999999999999999999999999997543    399999999999999999999987422599999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      |.
T Consensus        94 S~   95 (100)
T 3r27_A           94 ST   95 (100)
T ss_dssp             CS
T ss_pred             cc
Confidence            85

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

Probab=99.86  E-value=2.2e-21  Score=127.72  Aligned_cols=79  Identities=16%  Similarity=0.147  Sum_probs=71.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++..+.+..++||||+|.+.++|++|++.|||..|+  |+.|+|+|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~--g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLS--GREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBT--TBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEEEEc
Confidence            456899999999999999999999999999999998865445559999999999999999999999995  888999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        84 ~   84 (92)
T 2dgv_A           84 R   84 (92)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.86  E-value=2.1e-21  Score=129.62  Aligned_cols=78  Identities=18%  Similarity=0.223  Sum_probs=71.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHH----HHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIY----NLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~----~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .+.++|||+||+.++++++|+    ++|++||.|.+|++..++.+ ++||||+|++.++|++|++.|||..|+  |+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~-rg~afV~f~~~~~A~~Ai~~l~g~~~~--gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY-QLKAVVQMENLQDAIGAVNSLHRYKIG--SKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST-TCCEEEEESSHHHHHHHHHHHTTEEET--TEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC-CeEEEEEECCHHHHHHHHHHhCCCEEC--CeEEE
Confidence            346799999999999999999    99999999999999988666 669999999999999999999999995  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        84 V~~a~   88 (96)
T 2dgx_A           84 VSLAT   88 (96)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99975

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

Probab=99.86  E-value=4.3e-21  Score=128.11  Aligned_cols=79  Identities=19%  Similarity=0.209  Sum_probs=71.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~   83 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ--GRMLHVL   83 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS--SCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEEE
Confidence            45789999999999999999999999999999999887533  3349999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        84 ~a~   86 (99)
T 1whw_A           84 PST   86 (99)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            975

>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=99.86  E-value=4.7e-21  Score=123.80  Aligned_cols=76  Identities=26%  Similarity=0.411  Sum_probs=69.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .+|||+||+.++++++|+++|++||.|.++++.++..++.  +||||+|.+.++|++|++.|||..++  |+.|+|+|+.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~--g~~l~v~~a~   79 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN--GRPLRINWAA   79 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET--TEECEEEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeC--CcEEEEEecC
Confidence            5899999999999999999999999999999998855443  39999999999999999999999995  8999999975

>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=99.86  E-value=5.5e-21  Score=130.30  Aligned_cols=78  Identities=15%  Similarity=0.100  Sum_probs=68.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+++++|++|+++|++||.|.+|+++.+    ++||||+|++.++|++|++.|||..+.-.|+.|+|+|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            345789999999999999999999999999999998754    3499999999999999999998765222589999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        88 a~   89 (104)
T 1wex_A           88 ST   89 (104)
T ss_dssp             CS
T ss_pred             cc
Confidence            85

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

Probab=99.86  E-value=6.7e-21  Score=128.40  Aligned_cols=80  Identities=18%  Similarity=0.252  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v   89 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY--GKPIRV   89 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS--SCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeEC--CeEEEE
Confidence            3567899999999999999999999999999999998875433  349999999999999999999999995  889999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        90 ~~a~   93 (105)
T 1x5u_A           90 NKAS   93 (105)
T ss_dssp             EETT
T ss_pred             EECC
Confidence            9875

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

Probab=99.85  E-value=7.8e-21  Score=128.27  Aligned_cols=79  Identities=20%  Similarity=0.282  Sum_probs=71.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+||+.++++++|+++|++||.|.+|++..++.++.  +||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~   98 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM--GQPISVD   98 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSS--SSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEEC--CcEEEEE
Confidence            4568999999999999999999999999999999998865443  49999999999999999999999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        99 ~a~  101 (106)
T 1p27_B           99 WCF  101 (106)
T ss_dssp             ESE
T ss_pred             eec
Confidence            975

>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=99.85  E-value=4e-21  Score=131.74  Aligned_cols=80  Identities=21%  Similarity=0.305  Sum_probs=72.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.++|||+||+.++++++|+++|++||.|++|+++.++.++.  +||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V   99 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG--MKRLKV   99 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEEC--CEEEEE
Confidence            34568999999999999999999999999999999998864443  39999999999999999999999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       100 ~~a~  103 (115)
T 2cpz_A          100 QLKR  103 (115)
T ss_dssp             ECCC
T ss_pred             EEcC
Confidence            9875

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

Probab=99.85  E-value=3.8e-21  Score=129.35  Aligned_cols=81  Identities=20%  Similarity=0.253  Sum_probs=72.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...+.++|||+||+.++++++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   86 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD--GRELR   86 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBT--TBCCE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEEC--CcEEE
Confidence            34567899999999999999999999999999999998875433  349999999999999999999999995  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        87 V~~a~   91 (103)
T 2dnm_A           87 VQVAR   91 (103)
T ss_dssp             EEECS
T ss_pred             EEECC
Confidence            99975

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=8.1e-21  Score=126.88  Aligned_cols=78  Identities=18%  Similarity=0.309  Sum_probs=70.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|+++.++.+  .++||||+|++.++|++|++ |||..|.  |+.|+|+
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~--g~~l~V~   84 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIM--GKKVEVK   84 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSS--SCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEEC--CeEEEEE
Confidence            45789999999999999999999999999999999887543  34599999999999999998 9999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        85 ~a~   87 (99)
T 2dgs_A           85 RAE   87 (99)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            875

>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=99.85  E-value=2e-21  Score=132.33  Aligned_cols=76  Identities=11%  Similarity=0.056  Sum_probs=68.6

Q ss_pred             CCCcceEEEcCCCC-CCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCc--cCCCCCeEE
Q 032280           61 YDEVRTLFVAGLPE-DVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFA--PSDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfVgnLp~-~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~--~~~~g~~l~  137 (144)
                      .+..++|||+||++ +++|+||+++|++||.|.+|++++++    +||||+|++.++|++|++.|||..  |  .|+.|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~k----g~aFVef~~~~~A~~Ai~~l~~~~~~~--~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI----NEAFIEMATTEDAQAAVDYYTTTPALV--FGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS----SCEEEEESSHHHHHHHHHHHHHSCCEE--TTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCC----CEEEEEECCHHHHHHHHHHHcCCCceE--CCcEEE
Confidence            45678999999999 99999999999999999999998654    399999999999999999999764  6  599999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        86 V~~a~   90 (102)
T 1x4d_A           86 VHLSQ   90 (102)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            99986

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

Probab=99.85  E-value=1.3e-21  Score=131.36  Aligned_cols=80  Identities=13%  Similarity=0.187  Sum_probs=70.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCC--eEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCc----cCCCC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPG--YESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFA----PSDSA  133 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~--v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~----~~~~g  133 (144)
                      ..-.||||+||+.++|+++|+++|++||.  +.+|++++|+.++  ++||||+|.+.++|++|++.|||..    ++  |
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~--G   84 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID--G   84 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET--T
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC--C
Confidence            45689999999999999999999999995  6789998886544  4499999999999999999999984    54  8


Q ss_pred             CeEEEEeecC
Q 032280          134 CSLLFPHSMA  143 (144)
Q Consensus       134 ~~l~v~~s~~  143 (144)
                      +.|+|+|+..
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999863

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=5.8e-21  Score=128.11  Aligned_cols=80  Identities=19%  Similarity=0.305  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.++|||+||+.++++++|+++|++||.|++|++..++.++  ++||||+|++.++|++|++.|||..|.  |+.|+|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v   86 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD--GRQIRV   86 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT--SCCCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEE
Confidence            3567899999999999999999999999999999998875433  449999999999999999999999995  888999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        87 ~~a~   90 (102)
T 1x5s_A           87 DQAG   90 (102)
T ss_dssp             EEEE
T ss_pred             EECC
Confidence            9875

>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=99.85  E-value=1.5e-20  Score=126.68  Aligned_cols=82  Identities=23%  Similarity=0.294  Sum_probs=71.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCC-CCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSD-SACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~-~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..+..+. ++||||+|.+.++|++|++.|||..+.+ .++.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            3567899999999999999999999999999999999875322 3499999999999999999999999841 1289999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        92 ~~a~   95 (105)
T 2dnh_A           92 KFAD   95 (105)
T ss_dssp             EESC
T ss_pred             EECc
Confidence            9875

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

Probab=99.85  E-value=2.4e-21  Score=129.14  Aligned_cols=79  Identities=16%  Similarity=0.206  Sum_probs=71.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-----CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-----NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-----~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      .+.++|||+||+.++++++|+++|++||.|++|++..+..     ..++||||+|.+.++|++|++.|||..|+  |+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l   80 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD--GHKL   80 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET--TEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeC--CeEE
Confidence            4568999999999999999999999999999999988754     22349999999999999999999999995  8899


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        81 ~V~~a~   86 (98)
T 2cpf_A           81 EVRISE   86 (98)
T ss_dssp             EEECSS
T ss_pred             EEEEcc
Confidence            999875

>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=99.85  E-value=5.4e-21  Score=127.21  Aligned_cols=77  Identities=21%  Similarity=0.279  Sum_probs=70.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+||+.++++++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|++.|||..++  |+.|+|+|+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~~a   79 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLG--SRFLKCGYS   79 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeEC--CeEEEEEEc
Confidence            4799999999999999999999999999999998875433  449999999999999999999999995  899999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        80 ~   80 (96)
T 2x1f_A           80 S   80 (96)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.8e-21  Score=133.22  Aligned_cols=77  Identities=17%  Similarity=0.112  Sum_probs=68.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcC--CccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN--FAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG--~~~~~~g~~l~  137 (144)
                      +....++|||+||+++++|++|+++|++||.|++|++++++    +||||+|++.++|++|++.|||  ..|  .|+.|+
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~k----GfaFVeF~~~~~A~~Ai~~l~~~~~~l--~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK----NQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHTTSCCEE--TTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCC----CEEEEEECCHHHHHHHHHHhccCCceE--CCEEEE
Confidence            34567899999999999999999999999999999998653    4999999999999999999875  677  489999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        86 V~~A~   90 (105)
T 1sjq_A           86 IQFSN   90 (105)
T ss_dssp             BCCCS
T ss_pred             EEEcC
Confidence            99875

>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=99.85  E-value=1.4e-20  Score=125.44  Aligned_cols=78  Identities=15%  Similarity=0.230  Sum_probs=69.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..+    ++||||+|++.++|++|++.|||..|.+.|+.|+|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            345689999999999999999999999999999998754    3499999999999999999999999953388999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        90 a~   91 (97)
T 1why_A           90 AK   91 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.85  E-value=4.5e-21  Score=126.95  Aligned_cols=80  Identities=20%  Similarity=0.279  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..++.+. ++||||+|++.++|++|++.|||..|.  |+.|+|+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~   90 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLY--GRPINVS   90 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEEC--CCEEEEE
Confidence            4567899999999999999999999999999999999875422 339999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            875

>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=99.85  E-value=1e-20  Score=128.56  Aligned_cols=80  Identities=21%  Similarity=0.440  Sum_probs=71.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++. .++||||+|++.++|++|++.|||..|+  |+.|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG-GPPFAFVEFEDPRDAEDAVYGRDGYDYD--GYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSS-SSCCEEEEESCHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-CCcEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEE
Confidence            345678999999999999999999999999999999976533 4459999999999999999999999994  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        95 ~a~   97 (109)
T 1x4a_A           95 FPR   97 (109)
T ss_dssp             CCC
T ss_pred             Ecc
Confidence            975

>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=99.85  E-value=1.1e-20  Score=129.06  Aligned_cols=81  Identities=22%  Similarity=0.329  Sum_probs=72.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....++|||+||+.++++++|+++|++||.|.+|++..++.+++  +||||+|.+.++|++|++.|||..|.  |+.|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~--g~~l~   99 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA--GRPMK   99 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS--SSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CEEEE
Confidence            345678999999999999999999999999999999998755443  49999999999999999999999995  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus       100 V~~a~  104 (108)
T 2jrs_A          100 VGHVT  104 (108)
T ss_dssp             EECSC
T ss_pred             EEEcc
Confidence            99875

>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=99.85  E-value=6.5e-21  Score=123.77  Aligned_cols=76  Identities=21%  Similarity=0.264  Sum_probs=69.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHh-cCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL-NNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~l-nG~~~~~~g~~l~v~  139 (144)
                      ....++|||+||+.++++++|+++|++||.|.+|++..++    +||||+|++.++|++|++.| ||..++  |+.|+|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~k----g~afV~f~~~~~A~~a~~~l~~~~~~~--g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ----QCAFIQFATRQAAEVAAEKSFNKLIVN--GRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGG----TEEEEEESSHHHHHHHHHTTTTTCEET--TEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCC----CEEEEEECCHHHHHHHHHHhcCCeeEC--CCEEEEE
Confidence            3567899999999999999999999999999999998653    39999999999999999999 999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>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=99.85  E-value=1.4e-20  Score=127.90  Aligned_cols=80  Identities=18%  Similarity=0.235  Sum_probs=72.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhc------CCccCCC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALN------NFAPSDS  132 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~ln------G~~~~~~  132 (144)
                      ....++|||+||+.++++++|+++|++||.|.+|++.+++.++  ++||||+|.+.++|++|++.||      |..|+  
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~--   89 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD--   89 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS--
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc--
Confidence            4567899999999999999999999999999999998875543  4499999999999999999999      99994  


Q ss_pred             CCeEEEEeec
Q 032280          133 ACSLLFPHSM  142 (144)
Q Consensus       133 g~~l~v~~s~  142 (144)
                      |+.|+|+|+.
T Consensus        90 g~~l~v~~a~   99 (111)
T 1x4h_A           90 GRQLKVDLAV   99 (111)
T ss_dssp             SCEEEEECCC
T ss_pred             CEEEEEEECC
Confidence            8999999975

>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=99.85  E-value=1.4e-21  Score=128.91  Aligned_cols=76  Identities=13%  Similarity=0.074  Sum_probs=66.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCC--CeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFP--GYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G--~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+||||||++++++++|+++|++||  .|.+|++..++.+++  +||||+|.+.++|++|++.|||..|+  |+.|+|++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~--gr~i~V~~   79 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTP   79 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSS--SCCCEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeC--CEEEEEEE
Confidence            4799999999999999999999999  999999998865444  49999999999999999999999995  88899988


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        80 ~~   81 (90)
T 3p5t_L           80 SN   81 (90)
T ss_dssp             C-
T ss_pred             CC
Confidence            64

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=9.2e-21  Score=130.12  Aligned_cols=82  Identities=18%  Similarity=0.229  Sum_probs=71.9

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCe
Q 032280           58 YGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACS  135 (144)
Q Consensus        58 ~~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~  135 (144)
                      .......++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|++.++|++|++.||| .|.  |+.
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~--g~~   87 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID--GRK   87 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET--TEE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCC--CEE
Confidence            334556789999999999999999999999999999999887543  344999999999999999999999 774  899


Q ss_pred             EEEEeec
Q 032280          136 LLFPHSM  142 (144)
Q Consensus       136 l~v~~s~  142 (144)
                      |+|+|+.
T Consensus        88 l~V~~a~   94 (116)
T 2cqd_A           88 ANVNLAY   94 (116)
T ss_dssp             CEEEEST
T ss_pred             EEEEEcc
Confidence            9999974

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=4.4e-21  Score=128.06  Aligned_cols=80  Identities=13%  Similarity=0.140  Sum_probs=71.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeE-EEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCe--
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYE-SSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACS--  135 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~-~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~--  135 (144)
                      ....++|||+||+.++++++|+++|++||.|+ +|++..++.++.  +||||+|.+.++|++|++.|||..++  |+.  
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~~~   83 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLP--GATPA   83 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEES--SCSSC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccC--CCCcc
Confidence            35678999999999999999999999999999 999998865443  49999999999999999999999995  666  


Q ss_pred             --EEEEeec
Q 032280          136 --LLFPHSM  142 (144)
Q Consensus       136 --l~v~~s~  142 (144)
                        |+|+|+.
T Consensus        84 ~~l~v~~a~   92 (99)
T 2div_A           84 KRFKLNYAT   92 (99)
T ss_dssp             EECCEEETT
T ss_pred             eeEEEeecC
Confidence              9999874

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

Probab=99.85  E-value=4.2e-21  Score=128.77  Aligned_cols=81  Identities=20%  Similarity=0.263  Sum_probs=72.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~V   86 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIRV   86 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET--TEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEE
Confidence            356789999999999999999999999999999999887443  3449999999999999999999999994  899999


Q ss_pred             EeecC
Q 032280          139 PHSMA  143 (144)
Q Consensus       139 ~~s~~  143 (144)
                      +|+..
T Consensus        87 ~~a~~   91 (102)
T 2cqb_A           87 NLAKP   91 (102)
T ss_dssp             EECCC
T ss_pred             EeCCC
Confidence            99753

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=6.5e-22  Score=131.29  Aligned_cols=77  Identities=19%  Similarity=0.169  Sum_probs=67.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCC-CeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhc-CCccCCCCCeEEEE
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFP-GYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALN-NFAPSDSACSLLFP  139 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G-~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~ln-G~~~~~~g~~l~v~  139 (144)
                      +++|||+|||.++||++|+++|++|| .|++|++++++.+  .++||||+|.+.++|++|++.|+ |..++  |+.|+|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~--gr~i~V~   78 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNIL--GQKVSMH   78 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEET--TEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEEC--CEEEEEE
Confidence            47899999999999999999999999 7999999887544  34599999999999999999885 55674  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        79 ~a~   81 (91)
T 2lxi_A           79 YSD   81 (91)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            985

>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=99.85  E-value=6.7e-21  Score=124.18  Aligned_cols=79  Identities=13%  Similarity=0.220  Sum_probs=70.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC---CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN---SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~---~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +.++|||+||+.++++++|+++|++||.|.+|++..+..+   .++||||+|++.++|++|++.|||..++  |+.|+|+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~   80 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQID--GQEITAT   80 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeEC--CeEEEEE
Confidence            4589999999999999999999999999999999887543   3449999999999999999999999995  8999999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      ++..
T Consensus        81 ~a~~   84 (88)
T 4a8x_A           81 AVLA   84 (88)
T ss_dssp             EECC
T ss_pred             ECCC
Confidence            8753

>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=99.85  E-value=7.9e-21  Score=128.26  Aligned_cols=82  Identities=18%  Similarity=0.281  Sum_probs=72.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~  137 (144)
                      ..+.++|||+||+.++++++|+++|++||.|.+|++..++.+  .++||||+|.+.++|++|++.|||..+ .+.++.|+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            356789999999999999999999999999999999887543  344999999999999999999999885 44589999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        90 v~~a~   94 (106)
T 2dgp_A           90 VKPAD   94 (106)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            99875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.85  E-value=6.4e-21  Score=138.47  Aligned_cols=79  Identities=10%  Similarity=0.093  Sum_probs=70.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCC--CeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFP--GYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G--~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .+.++||||||+++++|++|+++|++||  .|.+|+++.|+.+++  +||||+|.+.++|++||+.|||..|+  |+.|+
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~--Gr~l~  130 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN--GEKVD  130 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEET--TEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CeEeE
Confidence            4568999999999999999999999999  999999998865554  49999999999999999999999995  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+++.
T Consensus       131 V~~a~  135 (156)
T 3n9u_C          131 VRPAT  135 (156)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99863

>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=99.84  E-value=1.5e-20  Score=127.00  Aligned_cols=81  Identities=20%  Similarity=0.187  Sum_probs=71.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++.+. ++||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V  102 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD--GRPMNI  102 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeC--CcEEEE
Confidence            34567899999999999999999999999999999999886222 339999999999999999999999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9874

>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=99.84  E-value=1.7e-20  Score=127.28  Aligned_cols=78  Identities=15%  Similarity=0.119  Sum_probs=68.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc--CCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN--NFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln--G~~~~~~g~~l  136 (144)
                      ......++|||+||+++++|++|+++|++||.|.+|++..+    ++||||+|++.++|++|++.||  |..+  .|+.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~~--~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG----KNQAFLELATEEAAITMVNYYSAVTPHL--RNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCEE--TTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceE--CCcEE
Confidence            33456789999999999999999999999999999998764    3499999999999999999875  5667  48999


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        84 ~V~~a~   89 (101)
T 2cq1_A           84 YIQYSN   89 (101)
T ss_dssp             EEEECS
T ss_pred             EEEEcC
Confidence            999975

>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=99.84  E-value=8.8e-21  Score=133.52  Aligned_cols=82  Identities=21%  Similarity=0.224  Sum_probs=73.0

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ...+..++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|++.++|++|++.|||..|+  |+.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~--g~~l  118 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GRRI  118 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSS--SSCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--CEEE
Confidence            34456789999999999999999999999999999999887543  3449999999999999999999999995  8899


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus       119 ~V~~a~  124 (129)
T 2kxn_B          119 RVDFSI  124 (129)
T ss_dssp             EESCCS
T ss_pred             EEEEec
Confidence            999875

>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=99.84  E-value=1.1e-20  Score=130.51  Aligned_cols=79  Identities=19%  Similarity=0.280  Sum_probs=71.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +..++|||+||+.++++++|+++|++||.|++|++..++. ..++||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~--g~~l~V~~   82 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLH--GKAIKVEQ   82 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCS--SSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEE
Confidence            5568999999999999999999999999999999988752 23349999999999999999999999995  88999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        83 a~   84 (116)
T 2fy1_A           83 AK   84 (116)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6e-21  Score=126.58  Aligned_cols=79  Identities=14%  Similarity=0.272  Sum_probs=70.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEE-EEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESS-HLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v-~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...++|||+||+.++++++|+++|++||.|.+| ++..++.++  ++||||+|++.++|++|++.|||..|.  |+.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v   80 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC--NRPITV   80 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET--TEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEEC--CEEEEE
Confidence            356899999999999999999999999999999 998874433  349999999999999999999999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        81 ~~a~   84 (96)
T 1x5t_A           81 SYAF   84 (96)
T ss_dssp             EESC
T ss_pred             EEec
Confidence            9975

>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=99.84  E-value=7.4e-21  Score=130.14  Aligned_cols=80  Identities=20%  Similarity=0.289  Sum_probs=71.3

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH---HHhhcCCCeEEEEEeecCCC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIY---NLFREFPGYESSHLRSSTQN-----SQPFAFAVFSDQQSALGAMYALNNFAPSDS  132 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~---~~F~~~G~v~~v~l~~~~~~-----~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~  132 (144)
                      ....++|||+||+.++++++|+   ++|++||.|.+|++..++.+     .++||||+|++.++|++|++.|||..|+  
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~--   89 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD--   89 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET--
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC--
Confidence            3456799999999999999999   99999999999999877542     2349999999999999999999999995  


Q ss_pred             CCeEEEEeec
Q 032280          133 ACSLLFPHSM  142 (144)
Q Consensus       133 g~~l~v~~s~  142 (144)
                      |+.|+|+|+.
T Consensus        90 gr~l~V~~a~   99 (111)
T 2cpi_A           90 GRTLKASLGT   99 (111)
T ss_dssp             TEEEEEESCC
T ss_pred             CEEEEEEecc
Confidence            8999999875

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

Probab=99.84  E-value=4e-21  Score=129.33  Aligned_cols=79  Identities=13%  Similarity=0.133  Sum_probs=71.1

Q ss_pred             CCcceEEEcCCCC------CCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 032280           62 DEVRTLFVAGLPE------DVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSA  133 (144)
Q Consensus        62 ~~~~tLfVgnLp~------~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g  133 (144)
                      ...++|||+|||.      ++++++|+++|++||.|.+|++.+++.++  ++||||+|.+.++|++|++.|||..|+  |
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~--g   81 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD--L   81 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSS--S
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccC--C
Confidence            3468999999999      99999999999999999999999886543  449999999999999999999999995  6


Q ss_pred             -CeEEEEeec
Q 032280          134 -CSLLFPHSM  142 (144)
Q Consensus       134 -~~l~v~~s~  142 (144)
                       +.|+|+|+.
T Consensus        82 ~r~l~V~~a~   91 (100)
T 3ns6_A           82 KHRLFLYTMK   91 (100)
T ss_dssp             SCBCEEEESH
T ss_pred             CeEEEEEECc
Confidence             899999864

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

Probab=99.84  E-value=1.3e-20  Score=128.07  Aligned_cols=80  Identities=21%  Similarity=0.290  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.++|||+||+.++++++|+++|++||.|++|++..++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V  100 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQV  100 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEET--TEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC--CcEEEE
Confidence            3457899999999999999999999999999999998875443  349999999999999999999999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       101 ~~a~  104 (110)
T 1oo0_B          101 DWCF  104 (110)
T ss_dssp             EESE
T ss_pred             EEcc
Confidence            9975

>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=99.84  E-value=1.4e-20  Score=125.82  Aligned_cols=76  Identities=21%  Similarity=0.326  Sum_probs=69.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..++    +||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~k----g~afV~f~~~~~a~~a~~~l~g~~~~--g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK----GFGFIRLETRTLAEIAKVELDNMPLR--GKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTT----TEEEEECSSSHHHHHHHHHHTTCCBT--TBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCC----CEEEEEECCHHHHHHHHHHhCCCEeC--CceEEEEE
Confidence            3456899999999999999999999999999999997543    39999999999999999999999995  88999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        86 a~   87 (99)
T 2cpj_A           86 AC   87 (99)
T ss_dssp             SS
T ss_pred             cC
Confidence            74

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

Probab=99.84  E-value=3.1e-20  Score=126.84  Aligned_cols=80  Identities=14%  Similarity=0.067  Sum_probs=71.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++..++.+. ++||||+|++.++|++|++.|||..|.  |+.|+|+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~   89 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLF--DRPMHVK   89 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC--CCEEEEE
Confidence            3557899999999999999999999999999999999875422 339999999999999999999999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        90 ~a~   92 (114)
T 2do0_A           90 MDE   92 (114)
T ss_dssp             ECS
T ss_pred             Ecc
Confidence            874

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.84  E-value=2.9e-20  Score=129.10  Aligned_cols=81  Identities=20%  Similarity=0.178  Sum_probs=72.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++.+ .++||||+|++.++|++|++.|||..|.  |+.|+|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V  108 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD--GRPMDI  108 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESS--SCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEEC--CcEEEE
Confidence            4456789999999999999999999999999999999887522 3449999999999999999999999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       109 ~~a~  112 (124)
T 2kt5_A          109 QLVA  112 (124)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9985

>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=99.84  E-value=4.4e-21  Score=128.97  Aligned_cols=79  Identities=24%  Similarity=0.382  Sum_probs=71.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~   83 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS--GRALRVD   83 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS--SSCBEEE
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC--CcEEEEE
Confidence            356899999999999999999999999999999999875444  349999999999999999999999994  8889999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        84 ~a~   86 (104)
T 1p1t_A           84 NAA   86 (104)
T ss_dssp             ETT
T ss_pred             eCC
Confidence            875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=2.6e-20  Score=122.48  Aligned_cols=73  Identities=19%  Similarity=0.373  Sum_probs=67.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++.      ++||||+|++.++|++|++.|||..+.  |+.|+|+|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAAEDAIRNLHHYKLH--GVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE------TTEEEEEESSHHHHHHHHHHHTTCBCS--SCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE------CCEEEEEECCHHHHHHHHHHhcCCccC--CcEEEEEEC
Confidence            457899999999999999999999999999999986      239999999999999999999999994  889999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        78 ~   78 (90)
T 2dnq_A           78 K   78 (90)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.84  E-value=1.4e-20  Score=131.44  Aligned_cols=77  Identities=16%  Similarity=0.107  Sum_probs=68.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcC--CccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN--FAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG--~~~~~~g~~l~  137 (144)
                      .....++|||+||+++++|++|+++|++||.|++|+++.++    +||||+|++.++|++|++.|||  ..|  .|+.|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~k----G~AFVeF~~~e~A~~Ai~~l~~~~~~l--~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK----NQAFIEMNTEEAANTMVNYYTSVTPVL--RGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGG----TEEEEECSCHHHHHHHHHHHHHHCCCB--TTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCC----CEEEEEECCHHHHHHHHHHhccCCceE--CCeEEE
Confidence            34557899999999999999999999999999999998763    3999999999999999999985  567  489999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus       101 V~~a~  105 (119)
T 2ad9_A          101 IQFSN  105 (119)
T ss_dssp             EEECS
T ss_pred             EEEcc
Confidence            99985

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.8e-20  Score=128.00  Aligned_cols=81  Identities=14%  Similarity=0.184  Sum_probs=71.8

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeE--------EEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCcc
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYE--------SSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAP  129 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~--------~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~  129 (144)
                      .....++|||+||+.++++++|+++|++||.|.        .|++..++.++  ++||||+|.+.++|++|++.|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999998        69998875443  34999999999999999999999999


Q ss_pred             CCCCCeEEEEeec
Q 032280          130 SDSACSLLFPHSM  142 (144)
Q Consensus       130 ~~~g~~l~v~~s~  142 (144)
                      .  |+.|+|+|+.
T Consensus        91 ~--g~~l~V~~a~  101 (113)
T 2cpe_A           91 Q--GSKLKVSLAR  101 (113)
T ss_dssp             T--TEECEEECSS
T ss_pred             C--CCEEEEEECC
Confidence            4  8999999875

>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=99.84  E-value=9.7e-21  Score=126.14  Aligned_cols=80  Identities=16%  Similarity=0.142  Sum_probs=70.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++||.|.+++++.++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~V   89 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVKL   89 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET--TEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeC--CeEEEE
Confidence            3456899999999999999999999999999888777765544  349999999999999999999999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        90 ~~a~   93 (98)
T 2cqp_A           90 VLGS   93 (98)
T ss_dssp             EESS
T ss_pred             EEcC
Confidence            9874

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.2e-20  Score=127.30  Aligned_cols=81  Identities=16%  Similarity=0.229  Sum_probs=72.0

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ....+.++|||+||+.++++++|+++|++||.|++|++..++.++.  +||||+|++.++|++|++. ||..|+  |+.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~--g~~l   87 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD--GRNI   87 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEET--TEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeEC--CEEE
Confidence            3456779999999999999999999999999999999998855443  4999999999999999998 999995  8899


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        88 ~V~~a~   93 (105)
T 2dh8_A           88 DPKPCT   93 (105)
T ss_dssp             BCCCSC
T ss_pred             EEEEcc
Confidence            998875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=4.1e-20  Score=124.39  Aligned_cols=78  Identities=18%  Similarity=0.261  Sum_probs=70.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++|| |++|+++.++.+++  +||||+|++.++|++|+ .|||..|.  |+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~V   87 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLG--DRSLRV   87 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEET--TEECEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeEC--CeEEEE
Confidence            45678999999999999999999999996 99999998865443  39999999999999999 99999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        88 ~~a~   91 (103)
T 2dng_A           88 DIAE   91 (103)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9975

>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=99.84  E-value=3.1e-20  Score=127.18  Aligned_cols=78  Identities=21%  Similarity=0.349  Sum_probs=70.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +..++|||+||+.++++++|+++|++||.|.+|++..+..+ ++||||+|.+.++|.+|++.|||..++  |+.|+|+|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET-RGTAYVVYEDIFDAKNAVDHLSGFNVS--NRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTT-TTCEEEEESSHHHHHHHHHHHTTCBSS--SCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCC-CcEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEEEe
Confidence            45689999999999999999999999999999999876443 559999999999999999999999995  889999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        83 ~   83 (115)
T 3lqv_A           83 N   83 (115)
T ss_dssp             C
T ss_pred             c
Confidence            5

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

Probab=99.84  E-value=2.1e-20  Score=131.45  Aligned_cols=80  Identities=21%  Similarity=0.280  Sum_probs=70.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....++|||+||+.++++++|+++|++||.|+++++..++.+  .++||||+|++.++|++|++.|||..|.  |+.|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~  136 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIR  136 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEET--TEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEEC--CEEEE
Confidence            3456789999999999999999999999999999999887443  3449999999999999999999999995  89999


Q ss_pred             EEee
Q 032280          138 FPHS  141 (144)
Q Consensus       138 v~~s  141 (144)
                      |+|+
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9985

>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=99.83  E-value=2e-20  Score=137.23  Aligned_cols=79  Identities=20%  Similarity=0.176  Sum_probs=70.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..+.+|||+||++++++++|+++|++||.|++|++..++  .+.||||+|+|.++|++|++.|||..|.+.++.|+|+|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~--~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN--NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS--SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC--CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            456789999999999999999999999999999986432  344999999999999999999999999655699999998


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       122 k  122 (164)
T 1sjr_A          122 K  122 (164)
T ss_dssp             S
T ss_pred             c
Confidence            6

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

Probab=99.83  E-value=3.7e-21  Score=125.06  Aligned_cols=78  Identities=15%  Similarity=0.196  Sum_probs=69.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..++.++  ++||||+|++.++|++|++.|||..++  |+.|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~~~~~   80 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ--AQMAKQS   80 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC--EESCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEe--eEEEeec
Confidence            456899999999999999999999999999999998875433  449999999999999999999999994  7888887


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |+
T Consensus        81 ~~   82 (85)
T 1x4e_A           81 GP   82 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.6e-20  Score=127.53  Aligned_cols=78  Identities=17%  Similarity=0.193  Sum_probs=69.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++||||||+.++|+++|+++|++||.|.+|++.++.. ..++||||+|++.++|++|++ +||..|+  |+.|+|.|
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~--gr~l~V~~   85 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYK--ETDLLILF   85 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCT--TTTCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEEC--CEEEEEEE
Confidence            4568999999999999999999999999999999998754 234599999999999999998 9999995  88899988


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      ..
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            64

>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=99.83  E-value=3.6e-20  Score=120.83  Aligned_cols=78  Identities=15%  Similarity=0.289  Sum_probs=68.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++||.|.+|++..++.+++  +||||+|.+.++|++|++ ++|..|+  |+.|+|
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~--g~~i~v   84 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLD--GRVIDP   84 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEET--TEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEEC--CEEEEE
Confidence            45678999999999999999999999999999999998865443  499999999999999995 5888884  899999


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      +++
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            874

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.83  E-value=1.5e-20  Score=127.39  Aligned_cols=80  Identities=10%  Similarity=0.155  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCCC------CHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCC-
Q 032280           62 DEVRTLFVAGLPEDV------KPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSAC-  134 (144)
Q Consensus        62 ~~~~tLfVgnLp~~v------te~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~-  134 (144)
                      ...++||||||+.++      ++++|+++|++||.|.+|++....+..++||||+|.+.++|++|++.|||..|+  |+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~--g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD--KQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECS--TTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccC--CCc
Confidence            446899999999999      789999999999999999987544445569999999999999999999999995  77 


Q ss_pred             eEEEEeecC
Q 032280          135 SLLFPHSMA  143 (144)
Q Consensus       135 ~l~v~~s~~  143 (144)
                      .|+|+|+..
T Consensus        91 ~l~V~~a~~   99 (105)
T 2nlw_A           91 TFRVNLFTD   99 (105)
T ss_dssp             EEEEECSCC
T ss_pred             eEEEEEcch
Confidence            899998753

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.83  E-value=2.4e-20  Score=121.88  Aligned_cols=77  Identities=16%  Similarity=0.229  Sum_probs=69.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++|||+||+.++++++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|+ .|||..|.  |+.|+|++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~--g~~l~V~~   81 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFR--GRQIKVIP   81 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEET--TEECEEEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEEC--CcEEEEEE
Confidence            45899999999999999999999999999999999875433  449999999999999999 99999994  89999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        82 a~   83 (89)
T 3ucg_A           82 KR   83 (89)
T ss_dssp             TT
T ss_pred             cc
Confidence            75

>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=99.83  E-value=3e-20  Score=129.12  Aligned_cols=79  Identities=20%  Similarity=0.296  Sum_probs=71.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+||+.++++++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~   97 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM--GQPISVD   97 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSS--SSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeC--CeEEEEE
Confidence            456899999999999999999999999999999998875443  349999999999999999999999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        98 ~a~  100 (126)
T 3ex7_B           98 WCF  100 (126)
T ss_dssp             ESE
T ss_pred             Eec
Confidence            875

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=4.9e-20  Score=125.34  Aligned_cols=74  Identities=14%  Similarity=0.092  Sum_probs=68.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCC-----CeE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSA-----CSL  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g-----~~l  136 (144)
                      ...++|||+||++++++++|+++|++||.|++|++..+     +||||+|++.++|++||+.|||..|.  |     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFR--SHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-----TEEEEEESSHHHHHHHHHHSSSEEEE--CTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-----CEEEEEECCHHHHHHHHHHHCcCCcc--CCcCcceEE
Confidence            45689999999999999999999999999999999876     49999999999999999999999995  5     889


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+++.
T Consensus        86 ~V~~a~   91 (108)
T 1x4c_A           86 RVKVDG   91 (108)
T ss_dssp             EEEESS
T ss_pred             EEEeCC
Confidence            999864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=2.7e-20  Score=125.19  Aligned_cols=79  Identities=16%  Similarity=0.315  Sum_probs=70.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhc-CCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCc-cCCCCCeE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFRE-FPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFA-PSDSACSL  136 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~-~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~-~~~~g~~l  136 (144)
                      ....++|||+||+.++++++|+++|++ ||.|.+|++..++ ++  ++||||+|.+.++|++|++.|||.. |.  |+.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~--g~~l   82 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLG--SKPV   82 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSS--SSCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccC--CEeE
Confidence            355689999999999999999999999 9999999999886 33  3499999999999999999999999 85  8889


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        83 ~v~~a~   88 (104)
T 2dhg_A           83 RLSVAI   88 (104)
T ss_dssp             CCCBCC
T ss_pred             EEEEcc
Confidence            998874

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=3.5e-20  Score=122.36  Aligned_cols=74  Identities=16%  Similarity=0.208  Sum_probs=68.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+.++++++|+++|++||.|++|++.++      ||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~------~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD------YAFVHMERAEDAVEAIRGLDNTEFQ--GKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS------EEEEEESCHHHHHHHHHHHTTEEET--TEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC------EEEEEECCHHHHHHHHHHhCCCeeC--CcEEEEEE
Confidence            356789999999999999999999999999999998632      9999999999999999999999994  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        79 a~   80 (92)
T 2dgt_A           79 ST   80 (92)
T ss_dssp             SS
T ss_pred             cc
Confidence            75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.83  E-value=7.5e-21  Score=122.95  Aligned_cols=72  Identities=11%  Similarity=0.228  Sum_probs=63.8

Q ss_pred             ceEEEcCCCCCC------CHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCC-eEE
Q 032280           65 RTLFVAGLPEDV------KPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSAC-SLL  137 (144)
Q Consensus        65 ~tLfVgnLp~~v------te~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~-~l~  137 (144)
                      ++|||||||.++      ++++|+++|++||.|.+|++..+.+..++||||+|.+.++|++|++.|||..|+  |+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~--g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD--KQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCS--SSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccC--CceeEE
Confidence            789999999999      779999999999999999987544445569999999999999999999999995  66 676


Q ss_pred             E
Q 032280          138 F  138 (144)
Q Consensus       138 v  138 (144)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            5

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

Probab=99.83  E-value=1.4e-20  Score=126.13  Aligned_cols=75  Identities=17%  Similarity=0.222  Sum_probs=68.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++||||||+.++++++|+++|++||.|++|++..+    ++||||+|.+.++|++|++.|||..+.  |+.|+|+|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~----~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE----KGCCFIKYDTHEQAAVCIVALANFPFQ--GRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETT----TTEEEEECSSHHHHHHHHHHHTTCEET--TEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecC----CCEEEEEECCHHHHHHHHHHhCCCeEC--CeEEEEEec
Confidence            34689999999999999999999999999999998743    339999999999999999999999995  899999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        99 ~   99 (101)
T 2la4_A           99 K   99 (101)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.83  E-value=5.2e-20  Score=124.08  Aligned_cols=78  Identities=26%  Similarity=0.332  Sum_probs=69.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC---CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN---SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~---~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ....++|||+||+.++++++|+++|++|| |++|++..++.+   .++||||+|++.++|++|+ .|||..|.  |+.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~   87 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NKRIR   87 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET--TEECE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeC--CcEEE
Confidence            34568999999999999999999999999 999999887543   3449999999999999999 99999994  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        88 V~~a~   92 (104)
T 1wi8_A           88 VDVAD   92 (104)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            99875

>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=99.83  E-value=6.4e-21  Score=128.09  Aligned_cols=77  Identities=25%  Similarity=0.339  Sum_probs=67.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC---CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST---QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~---~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...++||||||+.++++++|+++|++|| |.+|++..++   +..++||||+|.+.++|++|+ .|||..|.  |+.|+|
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~--g~~l~V   92 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NRRIRV   92 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBT--TBCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEEC--CeEEEE
Confidence            4569999999999999999999999999 9999998875   223449999999999999999 99999994  888999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        93 ~~a~   96 (100)
T 2j76_E           93 DVAD   96 (100)
T ss_dssp             EECC
T ss_pred             Eecc
Confidence            9875

>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=99.83  E-value=5.8e-20  Score=132.23  Aligned_cols=79  Identities=18%  Similarity=0.192  Sum_probs=72.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|+|..++.++.  +||||+|++.++|++|++.|||..|+  |+.|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~  114 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DRIIRTD  114 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEE
Confidence            4568999999999999999999999999999999998865444  49999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       115 ~a~  117 (156)
T 1h2v_Z          115 WDA  117 (156)
T ss_dssp             EES
T ss_pred             ECC
Confidence            985

>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=99.83  E-value=1.5e-20  Score=128.62  Aligned_cols=78  Identities=21%  Similarity=0.337  Sum_probs=70.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+||+.++++++|+++|++||.|++|+++.++.+  .++||||+|.+.++|++|+ .|||..|.  |+.|+|+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~V~   99 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLL--GVPIIVQ   99 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEET--TEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeC--CeEEEEE
Confidence            45689999999999999999999999999999999887653  3449999999999999999 99999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       100 ~a~  102 (114)
T 2cq4_A          100 ASQ  102 (114)
T ss_dssp             EHH
T ss_pred             ecC
Confidence            874

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

Probab=99.83  E-value=6.4e-20  Score=122.29  Aligned_cols=77  Identities=18%  Similarity=0.240  Sum_probs=67.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+.++++++|+++|++||.|. ++++.+  ..++||||+|.+.++|++|++.|||..|.  |+.|+|+|
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ--GPRRRAFLHYPDSAAAQQAVSCLQGLRLG--TDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCCSS--SSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC--CCCcEEEEEECCHHHHHHHHHHhCCCEEC--CcEEEEEE
Confidence            34568999999999999999999999999996 666654  33449999999999999999999999995  88899998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        91 a~   92 (97)
T 2e5j_A           91 AR   92 (97)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.83  E-value=3.1e-20  Score=126.83  Aligned_cols=74  Identities=24%  Similarity=0.281  Sum_probs=68.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++||||||+.++++++|+++|++||.|++|++.      ++||||+|++.++|++|++.|||..|  .|+.|+|+|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~------kg~afV~f~~~~~A~~Ai~~l~g~~~--~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------NGFAFVEFEEAESAAKAIEEVHGKSF--ANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE------TTEEEEECSSHHHHHHHHHHHTTCEE--TTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE------CCEEEEEECCHHHHHHHHHHcCCCEE--CCeEEEEEE
Confidence            4567899999999999999999999999999999987      33999999999999999999999999  489999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       100 a~  101 (108)
T 2jvo_A          100 SK  101 (108)
T ss_dssp             CS
T ss_pred             ec
Confidence            75

>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=99.83  E-value=1.1e-20  Score=125.13  Aligned_cols=79  Identities=16%  Similarity=0.162  Sum_probs=69.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+++++.++.+++  +||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--gr~l~v~   90 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVKLS   90 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeEC--CcEEEEE
Confidence            3458999999999999999999999999998888877655443  49999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus        91 ~a~   93 (95)
T 2ek1_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             ecc
Confidence            874

>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=99.82  E-value=3e-20  Score=127.36  Aligned_cols=74  Identities=18%  Similarity=0.143  Sum_probs=67.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..++|||+||+.++++++|+++|++||.|.+|++..+    ++||||+|.+.++|++|++.|||..|+  |+.|+|+|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~----~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG----GITAIVEFLEPLEARKAFRHLAYSKFH--HVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS----SSCEEEEESCHHHHHHHHHHHTTCBSS--SSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC----CCEEEEEeCCHHHHHHHHHHhCCCEEC--CeEEEEEECC
Confidence            4579999999999999999999999999999998643    339999999999999999999999995  8899999974

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=2.4e-20  Score=123.77  Aligned_cols=72  Identities=17%  Similarity=0.168  Sum_probs=66.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +..||||||++.+||++|+++|.+||.|.++++..++    +||||+|.|.++|++|++.|||..+.  |+.|+|++.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~k----GfaFVey~~~~eA~~Ai~~Ln~~~l~--gr~I~V~~A   78 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ----GIALCKYTTREEANKAQMALNNCVLA--NTTIFAESP   78 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHTTEEET--TEEEEEECC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCC----cEEEEEECCHHHHHHHHHHhcCCEEC--CcEEEEEEC
Confidence            5679999999999999999999999999999997643    39999999999999999999999995  899999864

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=3.8e-20  Score=122.79  Aligned_cols=78  Identities=17%  Similarity=0.248  Sum_probs=69.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEE-EeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH-LRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~-l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ....++|||+||+.++++++|+++|++||.|.+|+ +..++.++  .|||+|.+.++|++|++.|||..|+  |+.|+|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~--~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA--VVNVTYSSKDQARQALDKLNGFQLE--NFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE--EEEEEESSHHHHHHHHHHHTTCBCS--SCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC--EEEEEECCHHHHHHHHHHhCCCEEC--CcEEEEE
Confidence            34568999999999999999999999999999995 76665444  4999999999999999999999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        88 ~a~   90 (96)
T 2e44_A           88 YIP   90 (96)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            875

>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=99.82  E-value=3.6e-20  Score=125.96  Aligned_cols=75  Identities=15%  Similarity=0.209  Sum_probs=69.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..+    ++||||+|++.++|++|++.|||..|.  |+.|+|+|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----KGYSFVRFSTHESAAHAIVSVNGTTIE--GHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTCEET--TEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHcCCCEEC--CcEEEEEec
Confidence            45689999999999999999999999999999999876    339999999999999999999999995  899999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        97 ~   97 (109)
T 1x4g_A           97 K   97 (109)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.82  E-value=4.9e-20  Score=130.51  Aligned_cols=78  Identities=21%  Similarity=0.222  Sum_probs=68.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcE-EEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPF-AFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~-aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...-+|||+||++.+|+++|+++|++||.|.+|++..+.   ++| |||+|++.++|++|++.|||..|.+..+.|+|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~---~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC---CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            345678999999999999999999999999999886532   346 9999999999999999999999964458999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      |.
T Consensus       103 ak  104 (130)
T 3zzy_A          103 SK  104 (130)
T ss_dssp             CS
T ss_pred             cC
Confidence            86

>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=99.82  E-value=2.9e-20  Score=128.54  Aligned_cols=76  Identities=12%  Similarity=0.076  Sum_probs=67.3

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCC--ccCCCCCeEE
Q 032280           61 YDEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF--APSDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~--~~~~~g~~l~  137 (144)
                      ....++|||+||+++ ++|++|+++|++||.|.+|++.+++    +||||+|++.++|++|++.|||.  .|  .|+.|+
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~k----g~aFVef~~~~~A~~Ai~~l~~~~~~l--~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK----SQAFIEMETREDAMAMVDHCLKKALWF--QGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTT----TEEEEECSSHHHHHHHHHHHHHSCCCS--SSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCC----CEEEEEECCHHHHHHHHHHhccCCceE--CCEEEE
Confidence            456789999999998 9999999999999999999997543    39999999999999999999764  46  489999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        96 V~~a~  100 (112)
T 1x4f_A           96 VDLSE  100 (112)
T ss_dssp             EEEEC
T ss_pred             EEECc
Confidence            99985

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=4.1e-20  Score=121.58  Aligned_cols=73  Identities=16%  Similarity=0.213  Sum_probs=67.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++.++      ||||+|.+.++|++|++.|||..|.  |+.|+|+|+
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~------~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD------YAFVHMEKEADAKAAIAQLNGKEVK--GKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS------CEEEEESCHHHHHHHHHHHTTCEET--TEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC------EEEEEECCHHHHHHHHHHhCCCEEC--CcEEEEEEC
Confidence            55789999999999999999999999999999998632      9999999999999999999999994  899999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        79 ~   79 (90)
T 2dnp_A           79 T   79 (90)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.82  E-value=6.2e-20  Score=129.27  Aligned_cols=78  Identities=15%  Similarity=0.203  Sum_probs=68.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHH----HHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIY----NLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~----~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...++||||||++++++++|+    ++|++||.|++|.+..+ +..++||||+|++.++|++|++.|||..|.  |+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~-~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~--gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS-DDNSGKAYIVFATQESAQAFVEAFQGYPFQ--GNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCC-CSSCCCEEEEESSHHHHHHHHHHSTTCCCT--TSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccC-CCcCCEEEEEECCHHHHHHHHHHHCCCEeC--CCEEE
Confidence            446899999999999999876    69999999999988643 334559999999999999999999999995  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus       104 V~~a~  108 (127)
T 2a3j_A          104 ITFSE  108 (127)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            99975

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.82  E-value=2.2e-20  Score=118.68  Aligned_cols=73  Identities=14%  Similarity=0.248  Sum_probs=65.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +|||+||+.++++++|+++|++||.|.+|++..++.+  .++||||+|++.++|++|++ |||..++  |+.|+|+|+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~--g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEIN--NKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSS--SCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEEC--CEEEEEEeC
Confidence            5999999999999999999999999999999887543  34499999999999999997 9999995  888999874

>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=99.82  E-value=1e-19  Score=121.85  Aligned_cols=73  Identities=19%  Similarity=0.333  Sum_probs=67.0

Q ss_pred             CCcceEEEcCCCC-CCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPE-DVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~-~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++||||||+. ++++++|+++|++||.|.+|++.      ++||||+|++.++|++|++.|||..+.  |+.|+|+|
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~~   91 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEXESQEMNF--GKKLILEV   91 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC------SSEEEEEESSHHHHHHHHHHHTTSEET--TEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEe
Confidence            4568999999998 99999999999999999999983      339999999999999999999999995  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        92 a~   93 (97)
T 2xnq_A           92 SS   93 (97)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

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

Probab=99.82  E-value=7e-20  Score=122.00  Aligned_cols=74  Identities=19%  Similarity=0.332  Sum_probs=66.5

Q ss_pred             CCCcceEEEcCCCC-CCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPE-DVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~-~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ....++|||+||+. ++++++|+++|++||.|.+|++.      ++||||+|++.++|++|++.|||..+.  |+.|+|+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~V~   78 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIECESQEMNF--GKKLILE   78 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE------TTEEEEEESCHHHHHHHHHHHTCSSCB--TTTBCEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCeeC--CcEEEEE
Confidence            35678999999998 99999999999999999999984      239999999999999999999999995  8889999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        79 ~a~   81 (96)
T 2kvi_A           79 VSS   81 (96)
T ss_dssp             EEE
T ss_pred             EcC
Confidence            875

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.82  E-value=1.7e-20  Score=131.83  Aligned_cols=79  Identities=14%  Similarity=0.150  Sum_probs=69.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEE--EEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCC----ccCCC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNF----APSDS  132 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~--v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~----~~~~~  132 (144)
                      ....++||||||+++++|++|+++|++||.|..  |+|++++.++  ++||||+|++. +|.+|++.|||.    .|+  
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~--   96 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID--   96 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC--
Confidence            355789999999999999999999999999976  9999886443  44999999999 999999999999    885  


Q ss_pred             CCeEEEEeec
Q 032280          133 ACSLLFPHSM  142 (144)
Q Consensus       133 g~~l~v~~s~  142 (144)
                      |+.|+|+|+.
T Consensus        97 gr~l~V~~a~  106 (131)
T 2m2b_A           97 GKTINVEFAK  106 (131)
T ss_dssp             GCCCCCEECC
T ss_pred             CEEEEEEECC
Confidence            8889998864

>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=99.82  E-value=2.8e-19  Score=122.16  Aligned_cols=82  Identities=17%  Similarity=0.245  Sum_probs=71.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCC------CC
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSD------SA  133 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~------~g  133 (144)
                      ..+.++|||+||+.++++++|+++|++||.|.+|++..++.+ .++||||+|.+.++|++|++.|||..|++      .+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            456689999999999999999999999999999999988622 23499999999999999999999999842      36


Q ss_pred             CeEEEEeec
Q 032280          134 CSLLFPHSM  142 (144)
Q Consensus       134 ~~l~v~~s~  142 (144)
                      +.|+|.|+.
T Consensus       102 ~~l~v~~a~  110 (114)
T 1x5o_A          102 EPLLCKFSG  110 (114)
T ss_dssp             SCBEEEECC
T ss_pred             CceeEEccC
Confidence            779998874

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.82  E-value=6.1e-20  Score=127.21  Aligned_cols=77  Identities=10%  Similarity=0.195  Sum_probs=69.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++|||+||+.++++++|+++|++||.|++|++..++.++  ++||||+|.+.++|++|+ .|||..|+  |+.|+|+|
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~V~~  111 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFR--GRTIKVLP  111 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEET--TEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeEC--CeEEEEEE
Confidence            46899999999999999999999999999999998875443  349999999999999999 89999995  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       112 a~  113 (124)
T 2jwn_A          112 KR  113 (124)
T ss_dssp             SS
T ss_pred             CC
Confidence            75

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.82  E-value=2.4e-19  Score=125.98  Aligned_cols=75  Identities=17%  Similarity=0.119  Sum_probs=66.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcE-EEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPF-AFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~-aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      +-.|||+||++.+++++|+++|++||.|++|++.. + .  +| |||+|+|.++|++|++.|||..|.++.+.|+|+|+.
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-~--Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-N--GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-S--SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-C--CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            34578999999999999999999999999999864 2 2  46 999999999999999999999997555799999975

>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=99.81  E-value=8.1e-21  Score=124.70  Aligned_cols=75  Identities=16%  Similarity=0.258  Sum_probs=67.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|++.+ |++|++.|||..+.  |+.|+|+|+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~--g~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFM--GRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCS--SSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEEC--CeEEEEEEcC
Confidence            68999999999999999999999999999999887543  3449999999999 99999999999995  8889999874

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=3.8e-20  Score=124.00  Aligned_cols=73  Identities=18%  Similarity=0.233  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ++|||+||+.++++++|+++|++||.|++|++..+   .++||||+|++.++|++|++.|||..++  |+.|+|+|+.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~V~~a~   73 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLDGKVIC--GSRVRVELST   73 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS---SSSEEEEECSSHHHHHHHHHHHHHSCSS--SCCCEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCEEEEEECCHHHHHHHHHHHCCCeEC--CcEEEEEEcc
Confidence            47999999999999999999999999999999876   4449999999999999999999999995  8889999875

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=4.5e-20  Score=127.26  Aligned_cols=76  Identities=16%  Similarity=0.152  Sum_probs=67.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCC-CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFP-GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G-~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...+|||+||++++++++|+++|++|| .|..+++..+  ..++||||+|++.++|++|++.|||..|+  |+.|+|+++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~--~~rGfaFV~F~~~e~A~~Ai~~lng~~l~--Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR--DFDGTGALEFPSEEILVEALERLNNIEFR--GSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC--SSSCCEEEEESSHHHHHHHHHHTTTEEET--TEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC--CCCCEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEEEC
Confidence            457999999999999999999999999 8999988532  24459999999999999999999999994  899999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       103 ~  103 (111)
T 2jvr_A          103 D  103 (111)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=3.2e-19  Score=119.16  Aligned_cols=75  Identities=23%  Similarity=0.274  Sum_probs=67.5

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcC--CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREF--PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~--G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....++|||+||+.++++++|+++|++|  |.|.+|++.+      +||||+|.+.++|++|++.|||..|.  |+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~------g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   82 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVHFSNREDAVEAMKALNGKVLD--GSPIE   82 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS------SEEEEEESSHHHHHHHHHHHSSEEET--TEEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeC------CeEEEEeCCHHHHHHHHHHhCCCEeC--CcEEE
Confidence            34567899999999999999999999999  9999988742      29999999999999999999999995  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        83 v~~a~   87 (99)
T 2cpd_A           83 VTLAK   87 (99)
T ss_dssp             EECCC
T ss_pred             EEECC
Confidence            99975

>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=99.81  E-value=1.6e-19  Score=129.76  Aligned_cols=79  Identities=20%  Similarity=0.276  Sum_probs=71.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~  145 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD--GRELRVQ  145 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESS--SSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEE
Confidence            44689999999999999999999999999999999887433  4459999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       146 ~a~  148 (158)
T 2kn4_A          146 MAR  148 (158)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            975

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=7.6e-20  Score=121.28  Aligned_cols=75  Identities=17%  Similarity=0.265  Sum_probs=66.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|  +.++.+++ ||||+|.+.++|++|++ |||..|+  |+.|+|+++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~-~afV~f~~~~~a~~ai~-l~g~~~~--g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV-FAIVEMGDVGAREAVLS-QSQHSLG--GHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC-EEEEEESSHHHHHHHHT-CSCCEET--TEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc-EEEEEECCHHHHHHHHh-cCCeEEC--CEEEEEEEC
Confidence            456899999999999999999999999999987  44555555 99999999999999999 9999995  888888875


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        80 ~   80 (94)
T 2e5g_A           80 E   80 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=3.4e-20  Score=118.14  Aligned_cols=75  Identities=15%  Similarity=0.211  Sum_probs=66.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ++|||+||+.++++++|+++|++||.|.+|++..++.+  .++||||+|.+.++|++|++.+| ..++  |+.|+|+|+.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~--g~~l~v~~a~   77 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELD--SKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCS--SCCCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccC--CEEEEEEecC
Confidence            47999999999999999999999999999999887543  34599999999999999999999 8884  8889998863

>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=99.81  E-value=1.4e-19  Score=129.37  Aligned_cols=77  Identities=19%  Similarity=0.246  Sum_probs=70.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++||||||+.++++++|+++|++||.|++|++..+   .++||||+|.+.++|++|++.|||..|.  |+.|+|+|
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAADAVRELDGRTLC--GCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS---SCSEEEEEESSHHHHHHHHHHHSSSCSS--SSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC---CCcEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEEE
Confidence            355789999999999999999999999999999999765   3449999999999999999999999994  88999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       145 a~  146 (150)
T 2i2y_A          145 SN  146 (150)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.81  E-value=1.5e-19  Score=136.00  Aligned_cols=79  Identities=18%  Similarity=0.174  Sum_probs=70.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...+|||||||+.++||++|+++|++||.|++|+|++++.+++.  ||||+|.+.++|++|++.|||..+.  |+.|++.
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~--g~~i~~~   90 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK--GKPVRIM   90 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcC--Ccccccc
Confidence            45689999999999999999999999999999999998665543  9999999999999999999999994  8889988


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus        91 ~~~   93 (213)
T 4f02_A           91 WSQ   93 (213)
T ss_dssp             ECC
T ss_pred             ccc
Confidence            874

>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=1.2e-19  Score=123.98  Aligned_cols=79  Identities=14%  Similarity=0.173  Sum_probs=67.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.++|||+||+.++++++|+++|++||.|++|++.+++.+  .++||||+|.+.++|++|++.+ |..|  +|+.|+|
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l--~g~~l~V   98 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHEL--DSKTIDP   98 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEE--TTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcC--CCEEEEE
Confidence            356789999999999999999999999999999999887543  3459999999999999999876 5777  4899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +++.
T Consensus        99 ~~a~  102 (109)
T 2rs2_A           99 KVAF  102 (109)
T ss_dssp             EECC
T ss_pred             EEcc
Confidence            9875

>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=99.81  E-value=1.2e-19  Score=122.27  Aligned_cols=73  Identities=22%  Similarity=0.319  Sum_probs=67.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++.+  +    ||||+|++.++|++|++.|||..|.  |+.|+|+|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--~----~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--D----YAFIHFDERDGAVKAMEEMNGKDLE--GENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--S----CEEEEESSHHHHHHHHHHHTTEEET--TEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--C----EEEEEeCCHHHHHHHHHHHCCCccC--CCEEEEEEc
Confidence            4568999999999999999999999999999999862  2    9999999999999999999999995  899999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        81 ~   81 (103)
T 2dgu_A           81 K   81 (103)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.81  E-value=4.4e-19  Score=119.17  Aligned_cols=79  Identities=14%  Similarity=0.220  Sum_probs=68.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++.++.  +||||+|++.++|++|++  +|..|  .|+.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~--~g~~l~   86 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMI--DGRWCD   86 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEE--TTEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCee--CCeEEE
Confidence            345678999999999999999999999999999999998865443  499999999999999998  57777  488999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        87 v~~a~   91 (103)
T 2cqg_A           87 CKLPN   91 (103)
T ss_dssp             EECCC
T ss_pred             EEecC
Confidence            99875

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

Probab=99.81  E-value=3.8e-19  Score=118.52  Aligned_cols=74  Identities=22%  Similarity=0.244  Sum_probs=66.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||  ++++++|+++|++||.|++|++..    .++||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~----~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVE--SVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHTTTEEET--TEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCeEC--CeEEEEEE
Confidence            346789999996  899999999999999999999853    2339999999999999999999999994  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        84 a~   85 (97)
T 1x5p_A           84 AR   85 (97)
T ss_dssp             CS
T ss_pred             CC
Confidence            75

>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=99.81  E-value=4.9e-20  Score=122.34  Aligned_cols=78  Identities=19%  Similarity=0.280  Sum_probs=69.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHH----HHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIY----NLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~----~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...++|||+||+.++++++|+    ++|++||.|.+|++..+ +..++||||+|.+.++|++|++.|||..+.  |+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS-LKMRGQAFVIFKEVSSATNALRSMQGFPFY--DKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH-HHHTTCEEEEESSHHHHHHHHHHHTTCEET--TEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcC-CCcCcEEEEEeCCHHHHHHHHHHhCCCEEC--CcEEE
Confidence            457899999999999999999    99999999999998642 223349999999999999999999999994  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        83 v~~a~   87 (97)
T 1nu4_A           83 IQYAK   87 (97)
T ss_dssp             EEECS
T ss_pred             EEEcc
Confidence            99975

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

Probab=99.81  E-value=3.7e-20  Score=131.14  Aligned_cols=81  Identities=20%  Similarity=0.267  Sum_probs=72.0

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...+.++|||+||+.++++++|+++|++||.|++|++..++.+  .++||||+|++.++|++|++.|||..|.  |+.|+
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~--g~~l~  120 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD--GRELR  120 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSS--SSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC--CEEEE
Confidence            3456789999999999999999999999999999999877433  3449999999999999999999999995  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus       121 V~~a~  125 (135)
T 2lea_A          121 VQMAR  125 (135)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            99975

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.81  E-value=1.3e-19  Score=125.52  Aligned_cols=80  Identities=13%  Similarity=0.063  Sum_probs=70.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCC---eEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCe
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPG---YESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACS  135 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~---v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~  135 (144)
                      ...+.++|||+||++++|+++|+++|++||.   |.+|+|++++.+. ++||||+|++.++|++|++ |||..|.  |+.
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~--gr~   89 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMG--HRY   89 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEET--TEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeEC--CeE
Confidence            3456789999999999999999999999999   8999998876532 3499999999999999998 9999994  889


Q ss_pred             EEEEeec
Q 032280          136 LLFPHSM  142 (144)
Q Consensus       136 l~v~~s~  142 (144)
                      |+|.++.
T Consensus        90 i~V~~a~   96 (118)
T 2db1_A           90 IEVFKSH   96 (118)
T ss_dssp             EEEEEEC
T ss_pred             EEEEECC
Confidence            9998863

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.9e-19  Score=117.54  Aligned_cols=77  Identities=12%  Similarity=0.156  Sum_probs=68.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++|||+||+.++++++|+++|++| .|.+|++.++..+ .++||||+|++.++|++|++ |||..|.  |+.|+|++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~--gr~i~v~~   83 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMG--GRYIEVFR   83 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEET--TEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeC--CcEEEEEE
Confidence            567899999999999999999999999 9999999987322 23499999999999999999 9999994  88999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        84 a~   85 (91)
T 2dgw_A           84 EK   85 (91)
T ss_dssp             ES
T ss_pred             CC
Confidence            75

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.4e-19  Score=122.71  Aligned_cols=79  Identities=18%  Similarity=0.208  Sum_probs=68.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCC-eEEEEEe-ecCC--CCCcEEEEEeCCHHHHHHHHHHhc--CCccCCCCCe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLR-SSTQ--NSQPFAFAVFSDQQSALGAMYALN--NFAPSDSACS  135 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~-v~~v~l~-~~~~--~~~~~aFV~F~~~~~A~~A~~~ln--G~~~~~~g~~  135 (144)
                      .+.++|||+||+.++++++|+++|++||. |.+|++. .++.  ..++||||+|.+.++|++|++.||  +..+.  |+.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~--g~~   83 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLW--GHQ   83 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBT--TBC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceec--CCe
Confidence            35689999999999999999999999998 9999987 5544  334599999999999999999996  47884  889


Q ss_pred             EEEEeec
Q 032280          136 LLFPHSM  142 (144)
Q Consensus       136 l~v~~s~  142 (144)
                      |+|+|+.
T Consensus        84 l~V~~a~   90 (109)
T 2dis_A           84 IAVDWAE   90 (109)
T ss_dssp             CEEEESC
T ss_pred             EEEEEcC
Confidence            9999975

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

Probab=99.80  E-value=3.4e-19  Score=119.40  Aligned_cols=79  Identities=19%  Similarity=0.280  Sum_probs=67.2

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ......++|||+||+.++++++|+++|+.|+   +|+++.++.++.  +||||+|++.++|++|++.|||..|.  |+.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l   84 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID--GNKV   84 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TEEC
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeEC--CeEE
Confidence            3446678999999999999999999999874   566666654433  49999999999999999999999995  8899


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        85 ~V~~a~   90 (102)
T 2fc8_A           85 TLDWAK   90 (102)
T ss_dssp             EEEECC
T ss_pred             EEEEec
Confidence            999975

>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=99.80  E-value=1.4e-19  Score=123.19  Aligned_cols=73  Identities=16%  Similarity=0.266  Sum_probs=66.5

Q ss_pred             CCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++|||+||+.+ +++++|+++|++||.|++|++  .    ++||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--~----~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--H----KGYAFVQYSNERHARAAVLGENGRVLA--GQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--E----TTEEEEECSSSHHHHHHHHHHTTCEET--TEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--e----CCEEEEEECCHHHHHHHHHHcCCCEEC--CeEEEEEE
Confidence            34589999999999 999999999999999999998  2    239999999999999999999999994  88999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        97 a~   98 (110)
T 1wf1_A           97 AG   98 (110)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

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

Probab=99.80  E-value=3.3e-19  Score=119.40  Aligned_cols=78  Identities=15%  Similarity=0.172  Sum_probs=66.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeec-CCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-TQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~-~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .....++|||+||+.++++++|+++|++||.|   ++..+ .+..++||||+|++.++|++|++.|||..|.  |+.|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v   85 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIE--GRAIRL   85 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEET--TEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeC--CeEEEE
Confidence            34567999999999999999999999999987   44444 2333459999999999999999999999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        86 ~~a~   89 (101)
T 2fc9_A           86 ELQG   89 (101)
T ss_dssp             EECS
T ss_pred             EEcC
Confidence            9975

>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=99.80  E-value=1.1e-19  Score=125.94  Aligned_cols=79  Identities=15%  Similarity=0.235  Sum_probs=68.3

Q ss_pred             CCCcceEEE--cCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc---CCCCCe
Q 032280           61 YDEVRTLFV--AGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP---SDSACS  135 (144)
Q Consensus        61 ~~~~~tLfV--gnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~---~~~g~~  135 (144)
                      ....++|||  |||+++++|++|+++|++||.|.+|.+..+    ++||||+|++.++|++|++.|||..+   .+.++.
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            345789999  889999999999999999999999987542    34999999999999999999999977   335888


Q ss_pred             EEEEeecC
Q 032280          136 LLFPHSMA  143 (144)
Q Consensus       136 l~v~~s~~  143 (144)
                      |.|+|...
T Consensus        98 l~v~~a~~  105 (114)
T 2cq2_A           98 LYLNFVEK  105 (114)
T ss_dssp             CEEEEESC
T ss_pred             EEEEeccc
Confidence            99988753

>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=99.80  E-value=1.3e-19  Score=138.92  Aligned_cols=78  Identities=12%  Similarity=0.055  Sum_probs=69.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCC--CeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFP--GYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G--~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..++|||+||++++||++|+++|++||  .|++|+|++++.+++  +||||+|++.++|++||+.|||..|.  |+.|+|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~--Gr~l~V  144 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQNPVV  144 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBT--TBCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeEC--CEEeEE
Confidence            567999999999999999999999999  999999999865544  49999999999999999999999995  888999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       145 ~~a~  148 (229)
T 3q2s_C          145 TPVN  148 (229)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9853

>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=99.80  E-value=1.6e-19  Score=124.00  Aligned_cols=79  Identities=8%  Similarity=0.096  Sum_probs=69.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCe-EEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGY-ESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v-~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.++|||+||++++++++|+++|++||.| .+|+|++++.+ .++||||+|++.++|++|++. ||..|.  |+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~--gr~i~v   88 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLN--GREAFV   88 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEET--TEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccC--CeEEEE
Confidence            4556899999999999999999999999999 88999887622 344999999999999999977 999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +++.
T Consensus        89 ~~a~   92 (114)
T 2cpy_A           89 HVVT   92 (114)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9864

>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=99.80  E-value=3.8e-19  Score=129.38  Aligned_cols=79  Identities=22%  Similarity=0.285  Sum_probs=70.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|+|..++.++.  +||||+|.+.++|++||+.|||..|.  |+.|+|+
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~  147 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQVD  147 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            4567999999999999999999999999999999998855543  49999999999999999999999994  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       148 ~a~  150 (165)
T 1rk8_A          148 WCF  150 (165)
T ss_dssp             ESE
T ss_pred             Eec
Confidence            974

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.7e-19  Score=123.75  Aligned_cols=78  Identities=17%  Similarity=0.287  Sum_probs=69.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++..++.++  ++||||+|.+.++|++|++. ||..|+  |+.|+|+
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~--g~~l~V~  101 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSID--GRVVEPK  101 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEET--TEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEEC--CEEEEEE
Confidence            345899999999999999999999999999999999875433  44999999999999999988 999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       102 ~a~  104 (116)
T 1x4b_A          102 RAV  104 (116)
T ss_dssp             CCS
T ss_pred             ECC
Confidence            875

>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=99.80  E-value=1e-19  Score=120.23  Aligned_cols=74  Identities=19%  Similarity=0.266  Sum_probs=65.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCC-eEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcC-CccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN-FAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~-v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG-~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||. |..+.+. .    ++||||+|++.++|++|++.||| ..|+  |+.|+|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-~----~g~afV~f~~~~~A~~A~~~l~g~~~~~--g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-K----SGYAFVDYPDQNWAIRAIETLSGKVELH--GKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-E----TTEEEECCSCHHHHHHHHHHHTTTCEET--TEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-C----CCEEEEEECCHHHHHHHHHHccCCeeEC--CEEEEEE
Confidence            45689999999999999999999999999 6666553 2    23999999999999999999999 8894  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        79 ~a~   81 (93)
T 2cqh_A           79 YSV   81 (93)
T ss_dssp             ECC
T ss_pred             Ecc
Confidence            975

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

Probab=99.80  E-value=2.8e-19  Score=122.19  Aligned_cols=77  Identities=19%  Similarity=0.299  Sum_probs=67.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCe----EEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGY----ESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v----~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...++|||+||+.++++++|+++|++||.|    ..+++.  .+..++||||+|.+.++|++|++.|||..|.  |+.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~--~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~   98 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM--TGRMRGQAFITFPNKEIAWQALHLVNGYKLY--GKILV   98 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE--CSSSCSEEEEECSSHHHHHHHHHHSTTCBCS--SCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC--CCccceEEEEEECCHHHHHHHHHHhCCCEeC--CcEEE
Confidence            456899999999999999999999999998    455554  3344559999999999999999999999994  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        99 v~~a~  103 (115)
T 2cpx_A           99 IEFGK  103 (115)
T ss_dssp             EEECC
T ss_pred             EEEcc
Confidence            99975

>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=99.79  E-value=7.3e-19  Score=118.84  Aligned_cols=79  Identities=20%  Similarity=0.112  Sum_probs=67.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEE-EEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYES-SHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~-v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||++++++++|+++|++||.|.+ |+|..+.. ..++||||+|++.++|++|++. ||..|.  |+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~--gr~i~v   88 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIG--HRYIEI   88 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSS--SSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhC--CcEEEE
Confidence            355689999999999999999999999999987 88877632 2344999999999999999987 999995  778888


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      .++.
T Consensus        89 ~~~~   92 (104)
T 1wg5_A           89 FKSS   92 (104)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            7764

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

Probab=99.79  E-value=1.8e-19  Score=119.56  Aligned_cols=77  Identities=16%  Similarity=0.144  Sum_probs=67.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+.++++++|+++|++||.|..+   ...+..++||||+|.+.++|++|++.|||..|.  |+.|+|+|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID--GRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---EETTEEEEEEEEEESSHHHHHHHHHHTTEEEET--TEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEEE
Confidence            4567899999999999999999999999988766   233334459999999999999999999999994  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        88 a~   89 (96)
T 1fjc_A           88 TG   89 (96)
T ss_dssp             CS
T ss_pred             cC
Confidence            74

>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=1.3e-19  Score=125.99  Aligned_cols=79  Identities=13%  Similarity=0.153  Sum_probs=67.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ..+.++|||+||++++++++|+++|++||.|.++.++.+..++  ++||||+|++.++|++||+ |||..|.  |+.|+|
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~--gr~i~V   98 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG--NRFIQV   98 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST--TSCBEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeEC--CcEEEE
Confidence            3456899999999999999999999999999885555544443  3499999999999999999 9999995  888999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +++.
T Consensus        99 ~~a~  102 (124)
T 1wel_A           99 HPIT  102 (124)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9864

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.79  E-value=2.5e-19  Score=127.62  Aligned_cols=80  Identities=13%  Similarity=0.062  Sum_probs=70.4

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCC---eEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCe
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPG---YESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACS  135 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~---v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~  135 (144)
                      ...+.++|||+||++++||++|+++|++||.   |.+|+|++++.+ .++||||+|++.++|++|++ |||..|.  |+.
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~--gr~  116 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMG--HRY  116 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESS--SSE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEEC--CEE
Confidence            3456789999999999999999999999999   889999988652 23499999999999999999 9999995  889


Q ss_pred             EEEEeec
Q 032280          136 LLFPHSM  142 (144)
Q Consensus       136 l~v~~s~  142 (144)
                      |+|.++.
T Consensus       117 i~V~~a~  123 (136)
T 2hgl_A          117 IEVFKSH  123 (136)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            9998863

>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=99.79  E-value=6e-19  Score=119.35  Aligned_cols=77  Identities=18%  Similarity=0.216  Sum_probs=66.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+++++|+||+++|++||. ++|+|++++ +++  +||||+|++.++|++|| .+||..|.  ++.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~--gr~i~V   86 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAM-AKDKANMQ--HRYVEL   86 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSS--SSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeEC--CcEEEE
Confidence            355689999999999999999999999994 599999886 333  39999999999999999 58999995  788888


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      .++.
T Consensus        87 ~~~~   90 (102)
T 1wez_A           87 FLNS   90 (102)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            8764

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.79  E-value=7.9e-19  Score=129.72  Aligned_cols=81  Identities=20%  Similarity=0.177  Sum_probs=71.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .....++|||+||+.++++++|+++|++||.|++|.+..+.. ..++||||+|++.++|++|++.|||..|+  |+.|+|
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~--Gr~l~V  161 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLD--GRPMDI  161 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCS--SSBCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEEC--CEEEEE
Confidence            345568999999999999999999999999999999988752 23449999999999999999999999995  889999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       162 ~~a~  165 (177)
T 2f3j_A          162 QLVA  165 (177)
T ss_dssp             EEES
T ss_pred             EEec
Confidence            9975

>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=3.5e-19  Score=133.91  Aligned_cols=78  Identities=18%  Similarity=0.337  Sum_probs=71.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..++|||+||+.++++++|+++|++||.|++|+|.+++.++++||||+|.+.++|++|++.|||..|+  |+.|+|+|..
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~--g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN--DRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEEC--CEEEEEEEcC
Confidence            35689999999999999999999999999999999887666679999999999999999999999994  8999999864

>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=99.79  E-value=2.7e-19  Score=123.19  Aligned_cols=73  Identities=14%  Similarity=0.111  Sum_probs=63.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCe-----E
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACS-----L  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~-----l  136 (144)
                      ....+|||+||++++++++|+++|++||.|++|.+..+     +||||+|++.++|++||+.|||..|+  |+.     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~--gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFR--SHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCC--CTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-----CEEEEEECCHHHHHHHHHHhCCCEEC--CcEeeeEEE
Confidence            45678999999999999999999999999999999765     49999999999999999999999995  555     5


Q ss_pred             EEEee
Q 032280          137 LFPHS  141 (144)
Q Consensus       137 ~v~~s  141 (144)
                      +|+.+
T Consensus        87 ~v~~~   91 (115)
T 3beg_B           87 RVKVD   91 (115)
T ss_dssp             EEEEC
T ss_pred             EeccC
Confidence            66543

>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=99.79  E-value=3.5e-19  Score=116.83  Aligned_cols=74  Identities=15%  Similarity=0.301  Sum_probs=66.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++| .|.+|++.    ..++||||+|.+.++|++|++.|||..+.  |+.|+|+|+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFR--GKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEET--TEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe----CCCcEEEEEECCHHHHHHHHHHhCCCeEC--CcEEEEEEc
Confidence            346899999999999999999999999 99999884    23349999999999999999999999994  899999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        76 ~   76 (88)
T 1wg1_A           76 P   76 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.78  E-value=6.8e-20  Score=122.77  Aligned_cols=77  Identities=12%  Similarity=0.131  Sum_probs=65.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+ .++.+.  +..++||||+|++.++|++|++ |||..|.  |+.|+|+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~--g~~l~V~   90 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF--GNEIKLE   90 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBT--TBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEEC--CcEEEEE
Confidence            45689999999999999999999999999877 444442  2344599999999999999998 9999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        91 ~a~   93 (101)
T 1fj7_A           91 KPK   93 (101)
T ss_dssp             CCS
T ss_pred             EcC
Confidence            875

>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=99.78  E-value=6e-18  Score=131.22  Aligned_cols=79  Identities=24%  Similarity=0.399  Sum_probs=70.6

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....++|||+||+.++++++|+++|++||.|++|++..++   ++||||+|.+.++|.+|++.|||..|+ .|+.|+|+
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-~g~~l~v~  278 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR---HDIAFVEFDNEVQAGAARDALQGFKIT-QNNAMKIS  278 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC---CcEEEEEeCCHHHHHHHHHHcCCcEeC-CCCEEEEE
Confidence            34467899999999999999999999999999999998544   249999999999999999999999994 38899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            975

>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=99.78  E-value=5.3e-19  Score=114.97  Aligned_cols=72  Identities=19%  Similarity=0.323  Sum_probs=64.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcC----C-------CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREF----P-------GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~----G-------~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ...++|||+||+.++++++|+++|++|    |       .|.++++..+    ++||||+|++.++|++|+ .|||..|.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~----kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS----SSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC----CcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            457899999999999999999999999    8       8999998754    349999999999999999 99999994


Q ss_pred             CCCCeEEEEe
Q 032280          131 DSACSLLFPH  140 (144)
Q Consensus       131 ~~g~~l~v~~  140 (144)
                        |+.|+|+.
T Consensus        79 --g~~l~V~r   86 (87)
T 2hzc_A           79 --GQSLKIRR   86 (87)
T ss_dssp             --TEECEEEC
T ss_pred             --CeEEEEeC
Confidence              88898874

>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=8.2e-19  Score=115.87  Aligned_cols=74  Identities=19%  Similarity=0.268  Sum_probs=63.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ....+||||||++++||++|+++|++||.|.+|++.++   .++||||+|++.++|+    .|+|..+..+|+.|+|.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~---srGfaFV~F~~~~~A~----~~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP---FRAFAFVTFADDKVAQ----SLCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS---CCSEEEEEESCHHHHH----HHTTCEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC---CCCEEEEEECCHHHHH----HHcCCCcccCCEEEEEEEc
Confidence            44689999999999999999999999999999999764   3459999999999988    4788877657888888876


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        82 ~   82 (89)
T 3d2w_A           82 E   82 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=8.7e-19  Score=132.01  Aligned_cols=75  Identities=20%  Similarity=0.172  Sum_probs=68.4

Q ss_pred             CcceEEEcCCC-CCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           63 EVRTLFVAGLP-EDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        63 ~~~tLfVgnLp-~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +.++|||+||+ +++++++|+++|++||.|.+|+++.++   ++||||+|++.++|++|++.|||..|.  |+.|+|+|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~---~g~afV~f~~~~~A~~Ai~~lng~~~~--g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK---PGAAMVEMADGYAVDRAITHLNNNFMF--GQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS---TTCEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC---CCEEEEEECCHHHHHHHHHHhCCCEEC--CceEEEEEc
Confidence            46799999999 899999999999999999999997642   349999999999999999999999995  899999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        78 ~   78 (205)
T 3tyt_A           78 K   78 (205)
T ss_dssp             S
T ss_pred             c
Confidence            4

>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=99.78  E-value=1.6e-19  Score=114.50  Aligned_cols=73  Identities=21%  Similarity=0.305  Sum_probs=64.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ||||+||+.++++++|+++|++||.|.+|++..++.+  .++||||+|++.++|++|++. +|..+.  |+.|+|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~--g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVG--LSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBT--TBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeEC--CEEEEEEEC
Confidence            6999999999999999999999999999999877543  344999999999999999974 888885  788888764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=119.44  Aligned_cols=76  Identities=13%  Similarity=0.175  Sum_probs=66.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+.++|||+||++++++++|+++|++| .|.+|+|++++.+ .++||||+|++.++|++|+ .|||..|.  |+.|+|..
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~--gr~i~V~~   89 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMI--QRYVEVSP   89 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEET--TEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeEC--CeEEEEEE
Confidence            456799999999999999999999999 8999999887543 3449999999999999999 79999995  78888865


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      +
T Consensus        90 a   90 (109)
T 2dnn_A           90 A   90 (109)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=2.6e-18  Score=122.43  Aligned_cols=77  Identities=22%  Similarity=0.300  Sum_probs=70.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+|||.++++++|+++|++||.|.++++..++.++.  +||||+|.+.++|++|++.|||..+.  |+.|+|+|+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~~   79 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ--TKTIKVSYA   79 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccC--CceEEEEec
Confidence            47999999999999999999999999999999998864443  49999999999999999999999994  888999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        80 ~   80 (167)
T 1fxl_A           80 R   80 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=3.3e-19  Score=121.16  Aligned_cols=79  Identities=14%  Similarity=0.101  Sum_probs=68.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCC---eEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPG---YESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~---v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ..+.++|||+||++++++++|+++|++||.   |.+|+|++++.+ .++||||+|.+.++|++|++ |||..|.  |+.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~--gr~i   84 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMG--QRYV   84 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSS--SSCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeC--CeEE
Confidence            356789999999999999999999999988   899999887552 34499999999999999998 9999994  7888


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|.++.
T Consensus        85 ~V~~a~   90 (107)
T 2lmi_A           85 EVYEIN   90 (107)
T ss_dssp             CCEECC
T ss_pred             EEEECC
Confidence            888763

>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=99.77  E-value=5.4e-18  Score=121.26  Aligned_cols=80  Identities=19%  Similarity=0.331  Sum_probs=71.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.++++..++.++.  +||||+|.+.++|.+|++.|||..+.++++.|+|+
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            4568999999999999999999999999999999988764443  49999999999999999999999997666999999


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |+
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

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

Probab=99.77  E-value=5e-18  Score=120.84  Aligned_cols=80  Identities=26%  Similarity=0.414  Sum_probs=71.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|++||.|.++++..+..++.  +||||+|.+.++|.+|++.|||..++  |+.|+|
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~i~v  161 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN--GRPLRI  161 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEET--TEECEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC--CcEEEE
Confidence            34567999999999999999999999999999999998755443  39999999999999999999999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       162 ~~a~  165 (166)
T 3md3_A          162 NWAA  165 (166)
T ss_dssp             EESC
T ss_pred             EecC
Confidence            9974

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.77  E-value=5.3e-19  Score=118.56  Aligned_cols=76  Identities=13%  Similarity=0.236  Sum_probs=67.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..++ ++  ++||||+|++.++|++|++  ||..++  |+.|+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~--g~~l~v~   81 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFH--GKKLKLG   81 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeEC--CEEEEEE
Confidence            456899999999999999999999999999999999886 33  3499999999999999998  888884  8888888


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      +++
T Consensus        82 ~a~   84 (102)
T 2xs2_A           82 PAI   84 (102)
T ss_dssp             EEE
T ss_pred             ECC
Confidence            765

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

Probab=99.63  E-value=2.7e-20  Score=127.92  Aligned_cols=79  Identities=20%  Similarity=0.242  Sum_probs=70.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEE--------EEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYES--------SHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~--------v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      .+.++|||+||+.++++++|+++|++||.|.+        |++..++.+  .++||||+|.+.++|++|++.|||..|. 
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-   83 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS-   83 (116)
Confidence            45689999999999999999999999999998        888877443  3449999999999999999999999995 


Q ss_pred             CCCeEEEEeec
Q 032280          132 SACSLLFPHSM  142 (144)
Q Consensus       132 ~g~~l~v~~s~  142 (144)
                       |+.|+|+|+.
T Consensus        84 -g~~l~V~~a~   93 (116)
T 2lcw_A           84 -GNPIKVSFAT   93 (116)
Confidence             8889999874

>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=99.76  E-value=5.8e-19  Score=125.28  Aligned_cols=78  Identities=14%  Similarity=0.278  Sum_probs=66.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEE--------EEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESS--------HLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSA  133 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v--------~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g  133 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|        ++.. .+..++||||+|.+.++|.+|++.|||..|.  |
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~-~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~--g  119 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK-EGRMKGQAFIGLPNEKAAAKALKEANGYVLF--G  119 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEE-ETTTEEEEEEECSSHHHHHHHHHHHTTBEET--T
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEecc-CCCcccEEEEEeCCHHHHHHHHHHhCCCEeC--C
Confidence            456899999999999999999999999998763        3332 2334559999999999999999999999995  8


Q ss_pred             CeEEEEeec
Q 032280          134 CSLLFPHSM  142 (144)
Q Consensus       134 ~~l~v~~s~  142 (144)
                      +.|+|+|+.
T Consensus       120 ~~l~V~~a~  128 (143)
T 3egn_A          120 KPMVVQFAR  128 (143)
T ss_dssp             EECEEEECC
T ss_pred             cEEEEEECC
Confidence            999999975

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

Probab=99.76  E-value=4.7e-18  Score=126.29  Aligned_cols=80  Identities=19%  Similarity=0.339  Sum_probs=71.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++..+..+++  +||||+|.+.++|.+|++.|||..|+  |+.|+|+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~--g~~i~V~  200 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLG--GQYLRVG  200 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCS--SSBCEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeC--CcEEEEE
Confidence            3457999999999999999999999999999999998854443  39999999999999999999999995  8999999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      |+..
T Consensus       201 ~a~~  204 (216)
T 2qfj_A          201 KAVT  204 (216)
T ss_dssp             ECSS
T ss_pred             EecC
Confidence            9753

>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=99.76  E-value=2.3e-18  Score=123.25  Aligned_cols=77  Identities=23%  Similarity=0.355  Sum_probs=69.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+|||.++++++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|++.|||..+.  |+.|+|+|+
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~--g~~l~v~~~   80 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR--NKRLKVSYA   80 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeC--CcEEEEEec
Confidence            5899999999999999999999999999999998875443  349999999999999999999999994  889999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        81 ~   81 (168)
T 1b7f_A           81 R   81 (168)
T ss_dssp             C
T ss_pred             C
Confidence            5

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

Probab=99.76  E-value=1.9e-18  Score=123.08  Aligned_cols=76  Identities=16%  Similarity=0.190  Sum_probs=68.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      |+|||+|||.++++++|+++|++||.|.+|++..++.+ .++||||+|.+.++|++|++.|||..+.  |+.|+|+|+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~i~v~~~~   77 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIE--NNIVKINWAF   77 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEECC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccC--CCeeEEEEcC
Confidence            68999999999999999999999999999999887543 3349999999999999999999999994  8889998874

>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=99.76  E-value=5.2e-18  Score=121.90  Aligned_cols=80  Identities=16%  Similarity=0.296  Sum_probs=70.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC----CcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS----QPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLL  137 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~----~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~  137 (144)
                      +.++|||+|||.++++++|+++|++||.|.+|++++++.++    ++||||+|.+.++|++|++.|||..+ .+.++.++
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46899999999999999999999999999999999886553    34999999999999999999999887 44577788


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      +.++.
T Consensus        82 ~~~~~   86 (175)
T 3nmr_A           82 MKPAD   86 (175)
T ss_dssp             EEECG
T ss_pred             Ecccc
Confidence            77653

>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=99.76  E-value=8.1e-18  Score=119.87  Aligned_cols=80  Identities=21%  Similarity=0.341  Sum_probs=70.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.++++..+..++  ++||||+|.+.++|.+|++.|||..+.++...|+|+
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            345789999999999999999999999999999998875444  349999999999999999999999997555668888


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |+
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>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=99.76  E-value=5.7e-18  Score=121.77  Aligned_cols=78  Identities=21%  Similarity=0.358  Sum_probs=70.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.++++..+..++  ++||||+|.+.++|.+|++.|||..++  |+.|+|+
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~V~  169 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG--DKKLLVQ  169 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEEC--CeEEEEE
Confidence            346899999999999999999999999999999999885444  349999999999999999999999995  8999999


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      |+
T Consensus       170 ~A  171 (172)
T 2g4b_A          170 RA  171 (172)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.76  E-value=4.4e-18  Score=141.31  Aligned_cols=80  Identities=18%  Similarity=0.224  Sum_probs=71.8

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++|+++|+++|++||.|+.|.|+.++.++  ++||||+|.+.++|.+||+.|||..|.  |+.|+|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~--gr~i~V  176 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKID--GRRVLV  176 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEEC--CEEEEE
Confidence            3456899999999999999999999999999999998875433  449999999999999999999999994  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       177 ~~a~  180 (437)
T 3pgw_S          177 DVER  180 (437)
T ss_pred             EEeC
Confidence            9975

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=4.9e-18  Score=113.85  Aligned_cols=70  Identities=20%  Similarity=0.146  Sum_probs=61.4

Q ss_pred             Ccce-EEEcCCCCCCCHHH----HHHHhhcCC-CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           63 EVRT-LFVAGLPEDVKPRE----IYNLFREFP-GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        63 ~~~t-LfVgnLp~~vte~~----L~~~F~~~G-~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      .+.| |||+||++++++++    |+++|++|| .|.+|.       + ++|||+|.+.++|.+|++.|||..+.  |+.|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt-------g-G~AfV~F~~~esA~~A~~~l~G~~l~--gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT-------G-CSAILRFINQDSAERAQKRMENEDVF--GNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC-------T-TCEEEEESSHHHHHHHHHHHTTCCSS--SSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe-------c-CEEEEEECCHHHHHHHHHHhcCCccC--CceE
Confidence            3566 99999999999988    558999995 999872       1 49999999999999999999999995  8889


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        77 ~v~~A~   82 (96)
T 2diu_A           77 IVSFTP   82 (96)
T ss_dssp             EEESSC
T ss_pred             EEEecC
Confidence            999875

>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=6.7e-18  Score=121.33  Aligned_cols=79  Identities=18%  Similarity=0.312  Sum_probs=70.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~v~~  140 (144)
                      ..++|||+||+.++++++|+++|++||.|+++++..+..+. ++||||+|.+.++|.+|++.|||..+ .+.++.|+|+|
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEe
Confidence            56899999999999999999999999999999998875432 34999999999999999999999988 43468999998


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      +
T Consensus       174 a  174 (175)
T 3nmr_A          174 A  174 (175)
T ss_dssp             C
T ss_pred             c
Confidence            5

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

Probab=99.74  E-value=1.5e-17  Score=122.10  Aligned_cols=79  Identities=22%  Similarity=0.374  Sum_probs=71.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..+..++  ++||||+|.+.++|++|++.|||..|+  |+.|+|+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l~v~  189 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG--DKKLLVQ  189 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            567899999999999999999999999999999999885444  349999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       190 ~a~  192 (198)
T 2yh0_A          190 RAS  192 (198)
T ss_dssp             ESC
T ss_pred             ECC
Confidence            975

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

Probab=99.74  E-value=9.2e-18  Score=124.71  Aligned_cols=78  Identities=14%  Similarity=0.186  Sum_probs=68.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..++|||+||+.++++++|+++|++||.|++|+++++..+  .++||||+|.+.++|++|++.|||..|.  |+.|+|++
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~--g~~l~v~~  104 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLG--GRNIKVGR  104 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC---CCCEEEC
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeC--CeeEEEec
Confidence            4579999999999999999999999999999999887533  3459999999999999999999999994  88899887


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       105 ~~  106 (216)
T 2qfj_A          105 PS  106 (216)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>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=99.74  E-value=1.5e-17  Score=129.02  Aligned_cols=79  Identities=19%  Similarity=0.274  Sum_probs=70.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHH----HHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIY----NLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~----~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ....++|||+||+.++++++|+    ++|++||.|++|++.++ +..++||||+|.+.++|++|++.|||..|.  |+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~--g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS-LKMRGQAFVIFKEVSSATNALRSMQGFPFY--DKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCC-CCcceEEEEEECCHHHHHHHHHHhcCCeeC--CcEE
Confidence            3567899999999999999977    89999999999998763 334559999999999999999999999995  8999


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        83 ~v~~a~   88 (282)
T 3pgw_A           83 RIQYAK   88 (282)
T ss_pred             EEEEec
Confidence            999874

>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=99.74  E-value=1.2e-17  Score=122.31  Aligned_cols=78  Identities=14%  Similarity=0.275  Sum_probs=69.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+||+.++++++|+++|++||.|.+|+++.++.++  ++||||+|.+.++|++|++. +|..+.  |+.|+|.
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~--g~~l~v~   87 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVD--GRVVEPK   87 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEEC--CEEeeee
Confidence            567899999999999999999999999999999999886544  34999999999999999976 898884  8889998


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus        88 ~~~   90 (196)
T 1l3k_A           88 RAV   90 (196)
T ss_dssp             ECC
T ss_pred             ccc
Confidence            864

>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=3.7e-18  Score=111.67  Aligned_cols=74  Identities=19%  Similarity=0.254  Sum_probs=62.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|.+|++..+   .++||||+|++.++|++    ++|..+..+++.|+|+|+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~----~~~~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP---FRAFAFVTFADDQIAQS----LCGEDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS---CCSCCEEECSCHHHHHH----TTTCEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC---CCCEEEEEECCHHHHHH----HhcCCceeCCEEEEEEec
Confidence            45689999999999999999999999999999998754   34499999999999974    566666446888998886


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        76 ~   76 (88)
T 1wf0_A           76 E   76 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.74  E-value=1.2e-18  Score=124.58  Aligned_cols=78  Identities=17%  Similarity=0.190  Sum_probs=66.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ....++|||+||++++||++|+++|++|| +++|+|++++.+ .++||||+|++.++|++|| .+||..|.  ++.|+|.
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~--gR~i~V~  118 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQ--HRYIELF  118 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSS--SCCCCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEEC--CEEEEEE
Confidence            34568999999999999999999999999 779999887542 2349999999999999999 89999995  7778887


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus       119 ~a~  121 (139)
T 2hgn_A          119 LNS  121 (139)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=6.7e-18  Score=115.81  Aligned_cols=67  Identities=25%  Similarity=0.402  Sum_probs=57.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-----CCCcEEEEEeCCHHHHHHHHHHh---cCCcc
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-----NSQPFAFAVFSDQQSALGAMYAL---NNFAP  129 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-----~~~~~aFV~F~~~~~A~~A~~~l---nG~~~  129 (144)
                      ...++||||||++++++++|+++|++||.|. +.++.+..     ..++||||+|++.++|++|++.|   ||..+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~   80 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLY   80 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEE
Confidence            4568999999999999999999999999999 77776643     33459999999999999999999   66533

>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=99.73  E-value=6.2e-18  Score=118.99  Aligned_cols=76  Identities=18%  Similarity=0.108  Sum_probs=64.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeE--EEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYE--SSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~--~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...++|||+||++++||++|+++|++| .|+  +|+|++++.+ .++||||+|++.++|++|++ ++|..|.  |+.|+|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~--gR~I~V  115 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERIG--HRYIEV  115 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHT-TTTCCBT--TBCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHH-HCCCEEC--CEEEEE
Confidence            456789999999999999999999999 677  8999887552 34499999999999999997 4778884  778888


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      ..+
T Consensus       116 ~~a  118 (126)
T 2hgm_A          116 FKS  118 (126)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            765

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.73  E-value=7.6e-18  Score=130.23  Aligned_cols=78  Identities=21%  Similarity=0.208  Sum_probs=69.2

Q ss_pred             CCCcceEEEcCCCCCC---------CHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC-
Q 032280           61 YDEVRTLFVAGLPEDV---------KPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS-  130 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~v---------te~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~-  130 (144)
                      ....+|||||||+.++         +|++|+++|++||.|++|+++.+++    ||||+|.+.++|+.|+++|||..|. 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~kG----~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKN----CGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGT----EEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCC----EEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            3467899999999998         7999999999999999999986543    9999999999999999999999991 


Q ss_pred             ---------CCCCeEEEEeec
Q 032280          131 ---------DSACSLLFPHSM  142 (144)
Q Consensus       131 ---------~~g~~l~v~~s~  142 (144)
                               +.|+.|+|.|+.
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~  227 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWAN  227 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC
T ss_pred             cccccccccCCCCEEEEEEcc
Confidence                     148889999974

>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=99.73  E-value=1e-17  Score=127.18  Aligned_cols=76  Identities=20%  Similarity=0.224  Sum_probs=69.7

Q ss_pred             CCcceEEEcCCCC-CCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPE-DVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~-~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++|||+||+. ++++++|+++|++||.|.+|++.+++   ++||||+|.+.++|++|++.|||..|.  |+.|+|+|
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~---~g~afV~F~~~~~A~~Ai~~l~g~~~~--g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT---SCCEEEEESCHHHHHHHHHHHTTCBCS--SSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC---CCEEEEEECCHHHHHHHHHHhCCCeEC--CeEEEEEE
Confidence            4578999999999 99999999999999999999998765   349999999999999999999999994  88999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       107 a~  108 (229)
T 2adc_A          107 SK  108 (229)
T ss_dssp             CS
T ss_pred             ec
Confidence            75

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1e-17  Score=117.36  Aligned_cols=77  Identities=16%  Similarity=0.141  Sum_probs=65.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCe----EEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGY----ESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v----~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      .+.++|||+||++++|+++|+++|++||.|    .+|+|+.+..+ .++||||+|++.++|++|++. ||..|.  ++.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~--gR~i   97 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLG--KRYI   97 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESS--SCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeC--CeEE
Confidence            456899999999999999999999999975    68999887432 234999999999999999986 998884  7778


Q ss_pred             EEEee
Q 032280          137 LFPHS  141 (144)
Q Consensus       137 ~v~~s  141 (144)
                      +|..+
T Consensus        98 ~V~~a  102 (123)
T 2dha_A           98 ELFRS  102 (123)
T ss_dssp             CCEEE
T ss_pred             EEEEC
Confidence            77654

>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=99.71  E-value=1.5e-17  Score=118.96  Aligned_cols=76  Identities=16%  Similarity=0.281  Sum_probs=68.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+||+.++++++|+++|++||.|.++++..++.+  .++||||+|.+.++|.+|++ +||..+.  |+.|+|+|+
T Consensus        87 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~--g~~i~V~~a  163 (167)
T 2cjk_A           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFK--DRKIEIKRA  163 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSS--SSCEEEEEC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeC--CeEEEEeec
Confidence            568999999999999999999999999999999887533  34499999999999999997 8999995  889999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       164 ~  164 (167)
T 2cjk_A          164 E  164 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.71  E-value=6.1e-17  Score=118.57  Aligned_cols=78  Identities=18%  Similarity=0.340  Sum_probs=68.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++++++|+++|++||.|++|++..+..++  ++||||+|.+.++|.+|++. +|..|+  |+.|+|.
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~--G~~i~v~  178 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVN--GHNCEVR  178 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEET--TEECEEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEEC--CEEEEEE
Confidence            345899999999999999999999999999999999885443  34999999999999999976 899995  8889998


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       179 ~a~  181 (196)
T 1l3k_A          179 KAL  181 (196)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.71  E-value=1.4e-17  Score=122.77  Aligned_cols=74  Identities=20%  Similarity=0.235  Sum_probs=67.9

Q ss_pred             cceEEEcCCCC-CCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPE-DVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~-~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++|||+||+. ++++++|+++|++||.|.+|++..++   ++||||+|.+.++|++|++.|||..+.  |+.|+|+|+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~---~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC---SSCCEEECTTTHHHHHHHHHHTTCCCS--SCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCeec--CeEEEEEEec
Confidence            58999999999 99999999999999999999997654   349999999999999999999999995  8889999875

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.70  E-value=1.1e-16  Score=109.11  Aligned_cols=79  Identities=10%  Similarity=-0.004  Sum_probs=67.4

Q ss_pred             CCcceEEEcCCCC-----CCCHHHHHHHhhcCCCeEEEEEeecCC---CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 032280           62 DEVRTLFVAGLPE-----DVKPREIYNLFREFPGYESSHLRSSTQ---NSQPFAFAVFSDQQSALGAMYALNNFAPSDSA  133 (144)
Q Consensus        62 ~~~~tLfVgnLp~-----~vte~~L~~~F~~~G~v~~v~l~~~~~---~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g  133 (144)
                      ..+++|+|+||-.     +-++++|+++|++||.|++|++..+..   ..++||||+|++.++|.+|++.|||..|+  |
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~--G   83 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG--G   83 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEET--T
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEEC--C
Confidence            3568999999963     347899999999999999999988743   33559999999999999999999999995  8


Q ss_pred             CeEEEEeec
Q 032280          134 CSLLFPHSM  142 (144)
Q Consensus       134 ~~l~v~~s~  142 (144)
                      +.|+|+|+.
T Consensus        84 r~i~v~~a~   92 (105)
T 2pe8_A           84 RVVKACFYN   92 (105)
T ss_dssp             EECEEEECC
T ss_pred             cEEEEEEcC
Confidence            999999863

>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=99.70  E-value=6.7e-17  Score=116.73  Aligned_cols=76  Identities=16%  Similarity=0.151  Sum_probs=67.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.|..+   ...+..++||||+|.+.++|.+|++.|||..|+  |+.|+|+|+
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID--GRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE---CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEET--TEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe---cCCCCCceEEEEEECCHHHHHHHHHHhCCCEEC--CeEEEEEec
Confidence            456899999999999999999999999988776   334445559999999999999999999999995  899999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       172 ~  172 (175)
T 1fje_B          172 G  172 (175)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.69  E-value=3.2e-17  Score=123.41  Aligned_cols=71  Identities=14%  Similarity=0.205  Sum_probs=62.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCe--EEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGY--ESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSA  133 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v--~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g  133 (144)
                      ..++|||+||+++++|++|+++|++||.|  .++++..++++.++||||+|++.++|.+|++.|||..|.+.+
T Consensus       122 p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            46799999999999999999999999999  899987765444469999999999999999999999995443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.69  E-value=4.2e-17  Score=115.22  Aligned_cols=75  Identities=9%  Similarity=0.104  Sum_probs=66.0

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCC----HHH----HHHHHH--HhcCCc
Q 032280           65 RTLFVAGL----PEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSD----QQS----ALGAMY--ALNNFA  128 (144)
Q Consensus        65 ~tLfVgnL----p~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~----~~~----A~~A~~--~lnG~~  128 (144)
                      ..||||||    ++.++|.+|+++|++||.|.+|+++.|..++++  ||||+|.|    .++    |.+|++  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    999999999999999999999999999887766  99999996    323    889988  799999


Q ss_pred             cCCCCCeEEEEee
Q 032280          129 PSDSACSLLFPHS  141 (144)
Q Consensus       129 ~~~~g~~l~v~~s  141 (144)
                      |+  |+.|+|++.
T Consensus        83 I~--Gr~irV~ln   93 (136)
T 2j8a_A           83 IM--GFKFEVILN   93 (136)
T ss_dssp             ET--TEEEEEEEC
T ss_pred             ec--CcEEEEEEC
Confidence            95  899999864

>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=99.69  E-value=7e-17  Score=125.72  Aligned_cols=78  Identities=19%  Similarity=0.300  Sum_probs=68.5

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+||+.++++++|+++|++||.|.+|++..+..++++||||+|.+.++|++|+ .|||..+.  |+.|+|++
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~-~~~~~~~~--g~~i~v~~  114 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVG--QNEIIVSH  114 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEET--TEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHH-HhCCcEeC--CcEEEEEE
Confidence            3457899999999999999999999999999999999887666679999999999999999 59999994  88898887


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      +
T Consensus       115 ~  115 (292)
T 2ghp_A          115 L  115 (292)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=6.3e-17  Score=115.73  Aligned_cols=76  Identities=14%  Similarity=0.215  Sum_probs=64.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++|||+|||.++++++|+++|++||.|.+|++++++.+  .++||||+|.+.++|++|++.  +..++  |+.|++.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~--g~~i~v~~   77 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILD--GKVIDPKR   77 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEET--TEECCCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccC--CeEccccc
Confidence            4689999999999999999999999999999999887533  345999999999999999985  55663  66777766


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        78 ~~   79 (167)
T 2cjk_A           78 AI   79 (167)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>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=99.68  E-value=1.2e-16  Score=123.48  Aligned_cols=75  Identities=19%  Similarity=0.254  Sum_probs=68.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++|+++|+++|++||.|.+|++.+++    +||||+|.+.++|.+|++.|||..+.  |+.|+|+|+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~k----g~afV~f~~~~~A~~A~~~l~g~~i~--g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR----GFGFIRLESRTLAEIAKAELDGTILK--SRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTT----TEEEEECSSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCC----cEEEEEECCHHHHHHHHHHcCCcEEC--CceeEeeec
Confidence            456799999999999999999999999999999996543    39999999999999999999999994  889999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        94 ~   94 (261)
T 3sde_A           94 T   94 (261)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.68  E-value=1.8e-16  Score=118.46  Aligned_cols=76  Identities=17%  Similarity=0.213  Sum_probs=66.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++|||+||+.++++++|+++|++||.|.+|++.++..+ .++||||+|++.++|++|++.++ ..|  .|+.|+|.|..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~--~Gr~l~V~~~~  185 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKY--KETDLLILFKD  185 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEE--TTEECEEEETT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeE--CCEEEEEEEhH
Confidence            589999999999999999999999999999999887542 23499999999999999997665 477  48899998864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.67  E-value=3.5e-16  Score=115.29  Aligned_cols=77  Identities=17%  Similarity=0.198  Sum_probs=68.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCC-CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFP-GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G-~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++|||+||+.++++++|+++|++|| .|.+|++..+.   ++||||+|.+.++|.+|++.|||..+. .|+.|+|+|
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-~g~~l~v~~  193 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLG-ENHHLRVSF  193 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT---SSCEEEECSSHHHHHHHHHHHTSSCCS-SCCSCCEEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhcCCccC-CCCeEEEEe
Confidence            3468999999999999999999999999 99999986532   349999999999999999999999993 378899999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       194 a~  195 (198)
T 1qm9_A          194 SK  195 (198)
T ss_dssp             EC
T ss_pred             ec
Confidence            85

>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=99.65  E-value=3e-16  Score=112.64  Aligned_cols=73  Identities=19%  Similarity=0.314  Sum_probs=64.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcC----C-------CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREF----P-------GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~----G-------~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      +.++|||+|||.++++++|+++|++|    |       .|.++++..+    ++||||+|.+.++|++|+ .|||..+. 
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~----~g~afV~f~~~~~A~~A~-~~~~~~~~-   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVDETTQAM-AFDGIIFQ-   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT----TTEEEEEESSHHHHHHHG-GGTTCEET-
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC----CCEEEEEeCCHHHHHHHH-HhCCcEec-
Confidence            46899999999999999999999999    6       7788877544    339999999999999999 99999994 


Q ss_pred             CCCeEEEEeec
Q 032280          132 SACSLLFPHSM  142 (144)
Q Consensus       132 ~g~~l~v~~s~  142 (144)
                       |+.|+|+++.
T Consensus        77 -g~~i~v~~~~   86 (172)
T 2g4b_A           77 -GQSLKIRRPH   86 (172)
T ss_dssp             -TEECEEECCS
T ss_pred             -CceeeecCCc
Confidence             8889998764

>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=99.65  E-value=5.5e-16  Score=117.56  Aligned_cols=76  Identities=17%  Similarity=0.206  Sum_probs=68.0

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCC-CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFP-GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G-~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..++|||+||+.++++++|+++|++|| .|.+|+++.+   +++||||+|++.++|.+|++.|||..+. .|+.|+|+|+
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~-~g~~l~v~~a  225 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---DRKMALIQMGSVEEAVQALIDLHNHDLG-ENHHLRVSFS  225 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS---STTCEEEEESSHHHHHHHHHHHTTCBSS-SSCBCEEEEC
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC---CCcEEEEEECCHHHHHHHHHHHCCCccC-CCCeEEEEEe
Confidence            468999999999999999999999999 9999998642   2349999999999999999999999993 3889999997


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus       226 ~  226 (229)
T 2adc_A          226 K  226 (229)
T ss_dssp             S
T ss_pred             c
Confidence            5

>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=99.65  E-value=1.2e-15  Score=104.30  Aligned_cols=77  Identities=10%  Similarity=0.027  Sum_probs=65.1

Q ss_pred             CCcceEEEcCCCCCCC-----------HHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           62 DEVRTLFVAGLPEDVK-----------PREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vt-----------e~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ...++|+|.||-....           +++|+++|++||.|.+|.+ .++. .++||||+|.+.++|++|++.|||..|+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~-~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRH-PDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTC-TTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCC-CCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            4578999999944332           5899999999999999966 4543 4559999999999999999999999995


Q ss_pred             CCCCeEEEEeec
Q 032280          131 DSACSLLFPHSM  142 (144)
Q Consensus       131 ~~g~~l~v~~s~  142 (144)
                        |+.|+|+|..
T Consensus        91 --gr~l~v~~a~  100 (112)
T 2dit_A           91 --GRQITAQAWD  100 (112)
T ss_dssp             --TEECEEEECC
T ss_pred             --CcEEEEEEeC
Confidence              8999999864

>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=99.65  E-value=5.6e-16  Score=125.31  Aligned_cols=78  Identities=17%  Similarity=0.245  Sum_probs=65.6

Q ss_pred             CCCCcceEEEcC--CCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCC--
Q 032280           60 SYDEVRTLFVAG--LPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP-SDSAC--  134 (144)
Q Consensus        60 ~~~~~~tLfVgn--Lp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~--  134 (144)
                      ....+++|||||  |+.++||++|+++|++||.|++|.+..    +++||||+|++.++|++|++.|||+.+ +..|+  
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            356678999999  688999999999999999999987743    345999999999999999999999988 33344  


Q ss_pred             eEEEEee
Q 032280          135 SLLFPHS  141 (144)
Q Consensus       135 ~l~v~~s  141 (144)
                      .|.++|.
T Consensus        90 ~ly~~~~   96 (345)
T 3tht_A           90 TLYLNFV   96 (345)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEe
Confidence            5777765

>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=99.65  E-value=1e-15  Score=118.69  Aligned_cols=78  Identities=24%  Similarity=0.263  Sum_probs=70.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..++|||+||+.++++++|+++|++||.|.+++++.+..++.  +||||+|.+.++|.+|++.|||..+.  |+.|+|+|
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~--g~~i~v~~  171 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG--PRTLYVHW  171 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeC--CcEEEEEE
Confidence            357899999999999999999999999999999988754443  49999999999999999999999994  88999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus       172 a~  173 (284)
T 3smz_A          172 TD  173 (284)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.65  E-value=6.4e-17  Score=116.84  Aligned_cols=80  Identities=13%  Similarity=0.149  Sum_probs=65.2

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeec-CCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS-TQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~-~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .....++|||+||+.++++++|+++|++||.+..+.+... .+..++||||+|.+.++|++|+ .|||..+.  |+.|+|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~--g~~l~v   85 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVF--GNEIKL   85 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEET--TEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeC--CeEEEE
Confidence            3456789999999999999999999999997755222211 2234459999999999999999 59999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        86 ~~~~   89 (175)
T 1fje_B           86 EKPK   89 (175)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            9875

>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=99.64  E-value=5.9e-16  Score=120.03  Aligned_cols=79  Identities=14%  Similarity=0.139  Sum_probs=70.5

Q ss_pred             CCcceEEEcCCCCCC-CHHHHHHHhhcCCCeEEEEEeecCCCC-CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDV-KPREIYNLFREFPGYESSHLRSSTQNS-QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~v-te~~L~~~F~~~G~v~~v~l~~~~~~~-~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||+.++ ++++|+++|+.||.|.+|++..+..+. ++||||+|.+.++|.+|++.|||..|.  |+.|+|+
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~--g~~l~v~  259 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLG--GSHLRVS  259 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccC--CeEEEEE
Confidence            456899999999995 999999999999999999998875332 449999999999999999999999994  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus       260 ~a~  262 (284)
T 3smz_A          260 FCA  262 (284)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            975

>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=4e-16  Score=121.44  Aligned_cols=78  Identities=18%  Similarity=0.234  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCC---CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQ---NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~---~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      ...++|||+||+.+ +++++|+++|++||.|.+|++..+..   ..++||||+|.+.++|.+|+ .|||..|.  |+.|+
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~--g~~i~  284 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLG--NREIS  284 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEET--TEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEEC--CcEEE
Confidence            45689999999999 99999999999999999999987643   33459999999999999999 99999994  89999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus       285 V~~a~  289 (292)
T 2ghp_A          285 VSLAD  289 (292)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            99975

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

Probab=99.64  E-value=4.2e-16  Score=114.25  Aligned_cols=73  Identities=19%  Similarity=0.304  Sum_probs=63.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcC----C-------CeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREF----P-------GYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~----G-------~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      ..++|||+||+.++++++|+++|++|    |       .|.++++..+    ++||||+|.+.++|++|+ .|||..|. 
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~----~g~afV~F~~~~~A~~Al-~l~g~~~~-   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVDETTQAM-AFDGIIFQ-   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETT----TTEEEEEESCSHHHHHHG-GGTTEEET-
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCC----CCEEEEEeCCHHHHHHHH-HhcCCEEc-
Confidence            46899999999999999999999999    5       6777776433    349999999999999999 89999994 


Q ss_pred             CCCeEEEEeec
Q 032280          132 SACSLLFPHSM  142 (144)
Q Consensus       132 ~g~~l~v~~s~  142 (144)
                       |+.|+|+++.
T Consensus        77 -g~~i~v~~~~   86 (198)
T 2yh0_A           77 -GQSLKIRRPH   86 (198)
T ss_dssp             -TEEEEEECCC
T ss_pred             -CceEEEeCCC
Confidence             8899999864

>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=99.62  E-value=1.8e-15  Score=102.96  Aligned_cols=77  Identities=12%  Similarity=0.117  Sum_probs=65.3

Q ss_pred             CcceEEEcCC--CCCCC--------HHHHHHHhhcCCCeEEEEEeecCCC----CCcEEEEEeCCHHHHHHHHHHhcCCc
Q 032280           63 EVRTLFVAGL--PEDVK--------PREIYNLFREFPGYESSHLRSSTQN----SQPFAFAVFSDQQSALGAMYALNNFA  128 (144)
Q Consensus        63 ~~~tLfVgnL--p~~vt--------e~~L~~~F~~~G~v~~v~l~~~~~~----~~~~aFV~F~~~~~A~~A~~~lnG~~  128 (144)
                      .++.|.+.|+  +.++.        +++|+++|++||.|++|++.++..+    +++||||+|++.++|.+|++.|||+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4688999998  33443        3689999999999999999877532    34599999999999999999999999


Q ss_pred             cCCCCCeEEEEee
Q 032280          129 PSDSACSLLFPHS  141 (144)
Q Consensus       129 ~~~~g~~l~v~~s  141 (144)
                      |+  |+.|+++|+
T Consensus        84 f~--GR~i~v~~~   94 (105)
T 3v4m_A           84 FA--NRVVVTKYC   94 (105)
T ss_dssp             ET--TEECEEEEE
T ss_pred             eC--CCEEEEEEe
Confidence            95  899999986

>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=99.60  E-value=3.2e-15  Score=115.42  Aligned_cols=80  Identities=15%  Similarity=0.112  Sum_probs=67.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCcc--CCCCCeEEEE
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAP--SDSACSLLFP  139 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~--~~~g~~l~v~  139 (144)
                      ..++|||+||+.++++++|+++|++||.|.+|++..+..+ .++||||+|.+.++|.+|++.|||..+  .+.++.|+|+
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            3578999999999999999999999999999999988432 234999999999999999999965444  3458889998


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus       175 ~~~  177 (261)
T 3sde_A          175 PME  177 (261)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            864

>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=99.59  E-value=4.1e-16  Score=105.92  Aligned_cols=71  Identities=17%  Similarity=0.154  Sum_probs=61.0

Q ss_pred             EcCCCCCCCHHHHHHHh------------hcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCe
Q 032280           69 VAGLPEDVKPREIYNLF------------REFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACS  135 (144)
Q Consensus        69 VgnLp~~vte~~L~~~F------------~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~  135 (144)
                      ++||++++++++|++.|            ++||.|++|++.++..+ .++||||+|++.++|.+|++.|||..|+  |+.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~--Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN--GQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET--TEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEEC--CEE
Confidence            67788888888887776            99999999999877543 2449999999999999999999999995  899


Q ss_pred             EEEEee
Q 032280          136 LLFPHS  141 (144)
Q Consensus       136 l~v~~s  141 (144)
                      |+|+||
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999987

>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=99.57  E-value=7.8e-15  Score=101.91  Aligned_cols=77  Identities=16%  Similarity=0.073  Sum_probs=65.2

Q ss_pred             CcceEEEcCCCC-----CCCHHHHHHHhhcCCCeEEEEEeecCCC------CCcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           63 EVRTLFVAGLPE-----DVKPREIYNLFREFPGYESSHLRSSTQN------SQPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        63 ~~~tLfVgnLp~-----~vte~~L~~~F~~~G~v~~v~l~~~~~~------~~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      .+++|++.|+=.     +--++||++.|++||.|.+|+|..+..+      +++|+||+|++.++|.+|++.|||+.|+ 
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~-   97 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA-   97 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET-
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC-
Confidence            468999999842     1236899999999999999999887432      2249999999999999999999999995 


Q ss_pred             CCCeEEEEee
Q 032280          132 SACSLLFPHS  141 (144)
Q Consensus       132 ~g~~l~v~~s  141 (144)
                       |+.|+++|+
T Consensus        98 -GR~i~v~~~  106 (118)
T 3ue2_A           98 -GRKVVAEVY  106 (118)
T ss_dssp             -TEECEEEEE
T ss_pred             -CcEEEEEEc
Confidence             899999986

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=1.3e-13  Score=93.11  Aligned_cols=72  Identities=13%  Similarity=-0.006  Sum_probs=58.3

Q ss_pred             cceEEEcCCC-------CCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           64 VRTLFVAGLP-------EDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        64 ~~tLfVgnLp-------~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      .++|-|.-..       .++++++|+++|++||.|++|++..   ..++||||+|++.++|++|++.++|.    .++.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~---~~rGfaFVeF~~~~~A~~Ai~~~~~~----~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS---KKPGTAVVEFATVKAAELAVQNEVGL----VDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES---SSSSEEEEEESCHHHHHHHHHTCCBC----SSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc---CCCCEEEEEECCHHHHHHHHHhcCCC----CCCeE
Confidence            4566665433       5689999999999999999999872   34459999999999999999987663    37889


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|..
T Consensus        83 ~V~~a~   88 (100)
T 2d9o_A           83 KISWLE   88 (100)
T ss_dssp             EEECSS
T ss_pred             EEEEcc
Confidence            999864

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.48  E-value=1.8e-13  Score=94.44  Aligned_cols=74  Identities=8%  Similarity=0.029  Sum_probs=61.4

Q ss_pred             cceEEEcCCCCCCC----------HHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCC
Q 032280           64 VRTLFVAGLPEDVK----------PREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSA  133 (144)
Q Consensus        64 ~~tLfVgnLp~~vt----------e~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g  133 (144)
                      +++|.+.|+=..-.          ++||++.|++||.|++|.+.++  ..++||||+|++.++|.+|++.|||..|+  |
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~--~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~--G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN--SAQGNVYVKCPSIAAAIAAVNALHGRWFA--G   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT--CTTCCEEEECSSHHHHHHHHHHHTTCEET--T
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC--CCcEEEEEEECCHHHHHHHHHHhCCCEEC--C
Confidence            57788888643221          3578999999999999998554  34559999999999999999999999995  8


Q ss_pred             CeEEEEee
Q 032280          134 CSLLFPHS  141 (144)
Q Consensus       134 ~~l~v~~s  141 (144)
                      +.|+++|+
T Consensus        83 R~i~v~~~   90 (114)
T 3s6e_A           83 KMITAAYV   90 (114)
T ss_dssp             EECEEEEE
T ss_pred             EEEEEEEE
Confidence            99999986

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.39  E-value=3.4e-12  Score=89.06  Aligned_cols=73  Identities=15%  Similarity=0.134  Sum_probs=62.4

Q ss_pred             CCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCC-HHHHHHHHHHhc--CCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSD-QQSALGAMYALN--NFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~-~~~A~~A~~~ln--G~~~~~~g~~l~  137 (144)
                      .....|||+||+.+ +++++|+++|++||.|..|.+..+..    .|||+|.+ ..+|..|++.||  |..|  ++..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~----tgfVrf~~~~~~A~~av~~ln~~~~~i--~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK----EGIILFKEKAKEALGKAKDANNGNLQL--RNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS----EEEEEESSCHHHHHHHHHHTTTSCBCT--TSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC----EEEEEECCChHHHHHHHHHhhcCCcEE--eCcEEE
Confidence            45678999999999 99999999999999999999976544    79999999 899999999996  5566  466677


Q ss_pred             EEe
Q 032280          138 FPH  140 (144)
Q Consensus       138 v~~  140 (144)
                      ++.
T Consensus        90 ~ev   92 (121)
T 1owx_A           90 WEV   92 (121)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.29  E-value=6.9e-12  Score=83.19  Aligned_cols=68  Identities=16%  Similarity=0.165  Sum_probs=56.6

Q ss_pred             ceEEEcCCC----CCCCH----HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           65 RTLFVAGLP----EDVKP----REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        65 ~tLfVgnLp----~~vte----~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      .||+|.-++    .+.-+    .+|.+.|++||.|..++++.++      +||+|++.++|.+|++ |||..+.  |+.|
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~------~fVtF~d~~sAlaAi~-mnG~~v~--Gr~L   78 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK------MWVTFLEGSSALNVLS-LNGKELL--NRTI   78 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS------EEEEESSHHHHHHGGG-GTTCEET--TEEE
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC------EEEEECChHHHHHHHh-cCCeEeC--CeEE
Confidence            578887665    22333    5799999999999999998653      8999999999999998 9999994  9999


Q ss_pred             EEEee
Q 032280          137 LFPHS  141 (144)
Q Consensus       137 ~v~~s  141 (144)
                      +|+..
T Consensus        79 kV~lk   83 (91)
T 2dnr_A           79 TIALK   83 (91)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99875

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.17  E-value=1.3e-11  Score=82.28  Aligned_cols=68  Identities=12%  Similarity=0.160  Sum_probs=57.3

Q ss_pred             cceEEEcCCCCC------CCH---HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 032280           64 VRTLFVAGLPED------VKP---REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSAC  134 (144)
Q Consensus        64 ~~tLfVgnLp~~------vte---~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~  134 (144)
                      ..||+|.-++.+      ..+   .+|.+.|++||.|..++++.++      +||+|.|.++|.+||+ |||.++.  |+
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~------~fVtF~d~~sAl~AI~-ldG~~v~--Gr   85 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ------MLVTFADSHSALSVLD-VDGMKVK--GR   85 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE------EEEECSCSHHHHHHHH-GGGSEET--TE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc------EEEEEcChHHHHHHHh-cCCeeeC--Ce
Confidence            368999888632      221   4689999999999999998654      9999999999999998 9999994  99


Q ss_pred             eEEEEe
Q 032280          135 SLLFPH  140 (144)
Q Consensus       135 ~l~v~~  140 (144)
                      .|+|.+
T Consensus        86 ~L~V~~   91 (95)
T 1ufw_A           86 AVKISG   91 (95)
T ss_dssp             EEEEEC
T ss_pred             EEEEec
Confidence            999976

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.11  E-value=2.5e-10  Score=85.79  Aligned_cols=64  Identities=16%  Similarity=0.008  Sum_probs=55.3

Q ss_pred             CCHHHHHHHhhcCCCeEEEEEeecCCC------CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           76 VKPREIYNLFREFPGYESSHLRSSTQN------SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        76 vte~~L~~~F~~~G~v~~v~l~~~~~~------~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      -.+++|++.|++||.|.++.+.++..+      .++++||+|.+.++|.+|++.|||+.|.  |+.|+++|+
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~--gr~i~~~~~  210 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA--GRKVVAEVY  210 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSS--SSBCEEEEC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceEC--CeEEEEEEc
Confidence            456789999999999999999865332      2349999999999999999999999995  899999885

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.86  E-value=1.1e-08  Score=69.85  Aligned_cols=72  Identities=18%  Similarity=0.127  Sum_probs=65.5

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcC-----CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREF-----PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~-----G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      +..|+|-+-|||..+++..|+.+.+.+     |.++.+.|+.|-+    =|+|+|.|..+|.+|.-+|||.+|+  |++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~----GAivef~d~~~AgKasLaL~G~ef~--gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN----GAIIIFRDSKFAAKMLMILNGSQFQ--GKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT----EEEEECSCHHHHHHHHHHHSSEEET--TEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC----ceEEEEccchhhHHHHhhcCCeeec--CeEE
Confidence            456899999999999999999999999     9999999987644    6999999999999999999999995  8999


Q ss_pred             EEE
Q 032280          137 LFP  139 (144)
Q Consensus       137 ~v~  139 (144)
                      ++.
T Consensus        93 r~g   95 (117)
T 2l9w_A           93 RSG   95 (117)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            874

>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=98.40  E-value=4.7e-06  Score=55.06  Aligned_cols=77  Identities=9%  Similarity=0.157  Sum_probs=60.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC----cEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEE--
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ----PFAFAVFSDQQSALGAMYALNNFAP-SDSACSLL--  137 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~----~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~--  137 (144)
                      .+|-|++||.++||+++.+.++....+.-...+..+.+.+    +-|||.|.+.+++..-.+.++|..| |++|..-.  
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            4688999999999999999999998876666654432222    2899999999999999999999999 66665443  


Q ss_pred             EEee
Q 032280          138 FPHS  141 (144)
Q Consensus       138 v~~s  141 (144)
                      ||++
T Consensus        82 VE~A   85 (91)
T 1uw4_A           82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            4543

>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=98.23  E-value=2.5e-06  Score=57.62  Aligned_cols=73  Identities=18%  Similarity=0.101  Sum_probs=60.9

Q ss_pred             cceEEEcCCCCCC-CH----HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           64 VRTLFVAGLPEDV-KP----REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        64 ~~tLfVgnLp~~v-te----~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      -.+|+|.||+.++ +.    +.++++|++|+.+.+.....+-+    -..|.|.+.++|.+|...|+|..|.  |+.+|+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR----Rirv~F~~~~~A~~AR~~Lh~~~f~--g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK----RVRINFSNPLSAADARLRLHKTEFL--GKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT----EEEEECSSTTHHHHHHHTSTTSEET--TEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce----EEEEEeCChHHHHHHHHHhccceec--CceeEE
Confidence            4689999998876 22    46799999999999888765533    5799999999999999999999994  778988


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      -|..
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            7753

>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=97.86  E-value=0.0001  Score=49.12  Aligned_cols=55  Identities=24%  Similarity=0.333  Sum_probs=45.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      .+.++| +.|..+.-.||.++|+.||.| .|+-+.|.     -|||.|.+.+.|..|++.++
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-----sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-----eEEEEecCHHHHHHHHHhcc
Confidence            355667 999999999999999999964 45555433     69999999999999998774

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.74  E-value=9.1e-05  Score=49.33  Aligned_cols=73  Identities=10%  Similarity=0.158  Sum_probs=52.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC----cEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeE
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ----PFAFAVFSDQQSALGAMYALNNFAP-SDSACSL  136 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~----~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l  136 (144)
                      +-+|-|++||..+||+++.+.++..-++.-...+..+.+.+    +.|||.|.+.++...-.+.++|..| |.+|..-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~   86 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEY   86 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEe
Confidence            45688999999999999888777665532222211111111    2799999999999999999999999 6666644

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.65  E-value=0.00033  Score=47.07  Aligned_cols=56  Identities=16%  Similarity=0.030  Sum_probs=46.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcC-----CCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHH
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREF-----PGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA  123 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~-----G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~  123 (144)
                      .-.++|.|.|||.+++++.|+-+|++-     |.|++++...      .-|+|+|.|.+.|++.++.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~------~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG------CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET------TEEEEEESSHHHHHHHHTC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC------CcEEEEEcChHHHHHHhcC
Confidence            345789999999999999999999872     4577776632      2699999999999998865

>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=97.56  E-value=0.00049  Score=47.41  Aligned_cols=62  Identities=13%  Similarity=0.149  Sum_probs=50.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ..+.|-|-+.+... -+.+.+.|++||.|++...    ..+..+-.|.|++..+|++|+ ..||+.|.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~----~~~~NWihI~Y~s~~~A~rAL-~kNG~ii~   84 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVM----SNTGNWMHIRYQSKLQARKAL-SKDGRIFG   84 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEE----CSSSSEEEEEESSHHHHHHHH-TTTTCEET
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEecc----CCCCCeEEEEeCCHHHHHHHH-HhCCeEec
Confidence            45678888988875 4567789999999998776    223349999999999999999 56999994

>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=97.51  E-value=0.00019  Score=47.94  Aligned_cols=54  Identities=24%  Similarity=0.342  Sum_probs=44.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      +.++| ++|..+.-.||.++|+.||+ ..|+-+.|.     -|||.|.+.+.|..|++.++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-----EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-----eEEEEecCHHHHHHHHHhcc
Confidence            34666 99999999999999999994 445555433     69999999999999998774

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.29  E-value=0.00011  Score=61.37  Aligned_cols=54  Identities=15%  Similarity=0.263  Sum_probs=40.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHH
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM  121 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~  121 (144)
                      .|+|||. .+.++++.+|.+.|++||.|.++..  ++. ++.|+.|||.+.+++.+++
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~--~~~-~g~~~~vef~~~~~~~~~~  106 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFF--YES-FGLYAVVEFCQKESIGSLQ  106 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEE--ECS-SSEEEEEECC---CCHHHH
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEE--Ecc-CCeEEEEEeCCHHHHHHHH
Confidence            4899998 7999999999999999999999876  332 2349999999999988664

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=97.01  E-value=0.00049  Score=48.30  Aligned_cols=35  Identities=11%  Similarity=-0.087  Sum_probs=29.9

Q ss_pred             EEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCC
Q 032280           93 SSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF  127 (144)
Q Consensus        93 ~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~  127 (144)
                      +++|++++...++||||+|.+.++|++|++.++|.
T Consensus         2 ~~kl~ln~~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNGKTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECSSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecCccccchhHHHHHHHHhHHHHHHhhccc
Confidence            56777787767779999999999999999998864

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=96.64  E-value=0.0012  Score=45.98  Aligned_cols=45  Identities=9%  Similarity=-0.011  Sum_probs=36.1

Q ss_pred             EEEeecCCCCCcEEEEEeCCHHHHHHHHHHh-cCCccCCCCCeEEEEee
Q 032280           94 SHLRSSTQNSQPFAFAVFSDQQSALGAMYAL-NNFAPSDSACSLLFPHS  141 (144)
Q Consensus        94 v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~l-nG~~~~~~g~~l~v~~s  141 (144)
                      ..|..+...-+++++|+|.+.++|++|++.| ||..++  | .++++++
T Consensus         3 ~al~l~g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~--G-~~~~~~a   48 (150)
T 2i2y_A            3 YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVD--G-EWTYDDA   48 (150)
T ss_dssp             EEEEECCSSSCEEEEEECSSHHHHTTTHHHHHHHHTCC--C-EEEEETT
T ss_pred             eEeeeccccccccceeeecCHHHHHHHHHHHhcCCCCC--C-ceecccc
Confidence            3455555555559999999999999999999 999996  5 7888765

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.85  E-value=0.0067  Score=42.36  Aligned_cols=70  Identities=17%  Similarity=0.232  Sum_probs=47.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEE-EEEee-----------cCC----CCCcEEEEEeCCHHHHHHHHHHhcCCc
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYES-SHLRS-----------STQ----NSQPFAFAVFSDQQSALGAMYALNNFA  128 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~-v~l~~-----------~~~----~~~~~aFV~F~~~~~A~~A~~~lnG~~  128 (144)
                      ..|-|=+.+.+... .+-+.|++||.|++ .....           .++    ++..+-.|+|++..+|.+|| ..||+.
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL-~~NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDAL-LENGAV   85 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHH-TTTTCE
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHH-HhCCeE
Confidence            34566677776655 46689999999866 21110           000    12338899999999999999 679999


Q ss_pred             cCCCCCeEEE
Q 032280          129 PSDSACSLLF  138 (144)
Q Consensus       129 ~~~~g~~l~v  138 (144)
                      |.  |..|-|
T Consensus        86 i~--G~mIGV   93 (132)
T 3p3d_A           86 FN--GVLLGV   93 (132)
T ss_dssp             ET--TEECEE
T ss_pred             eC--cEEEEE
Confidence            95  544444

>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=95.02  E-value=0.09  Score=44.13  Aligned_cols=55  Identities=22%  Similarity=0.326  Sum_probs=44.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ...++|+ ++..+...+|+++|+.||.+ +|+.+ |..    .|||.|.+.+.|..++++++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~wi-ddt----~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWI-DDT----SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEEC-SSS----EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEE-cCC----eEEEEECCHHHHHHHHHHHH
Confidence            3567777 88889999999999999964 44433 222    79999999999999999985

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=83.90  E-value=0.64  Score=28.39  Aligned_cols=67  Identities=7%  Similarity=0.150  Sum_probs=40.8

Q ss_pred             eEEEc-CCCCCCCHHHHHHHhhcCCCe-----EEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           66 TLFVA-GLPEDVKPREIYNLFREFPGY-----ESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        66 tLfVg-nLp~~vte~~L~~~F~~~G~v-----~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ||||+ +--..++..+|..++.+-+.+     -.+++.  ..    |.||+-.. +.+..+++.|++..+.  |+.++++
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~--d~----~s~v~v~~-~~~~~~~~~l~~~~i~--g~~~~v~   72 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIM--DN----ASYVEILN-GKGPHVLKVMKNTTVK--GKQLKVN   72 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEEC--SS----CEEEEECT-TCHHHHHHHHTTCCC-----CCCEE
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEe--CC----cEEEEECH-HHHHHHHHHhccccCc--CceEEEE
Confidence            57773 334457777888887766654     444542  12    88999775 4678899999999884  7777776


Q ss_pred             ee
Q 032280          140 HS  141 (144)
Q Consensus       140 ~s  141 (144)
                      ..
T Consensus        73 ~~   74 (76)
T 2g0c_A           73 KA   74 (76)
T ss_dssp             EC
T ss_pred             EC
Confidence            43

---

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	144
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-10
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-09
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-07
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	6e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	9e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-04
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-04
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	4e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	5e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	6e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.001
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.001
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.002
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.003
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	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 = 55.3 bits (133), Expect = 1e-11
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 3/65 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAM 121
             + V  +P     REI  LF  F   ++  L    + T   + F F  F  +Q A  A 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 122 YALNN 126
            AL +
Sbjct: 69  NALCH 73

>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 = 53.8 bits (129), Expect = 4e-11
 Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPG--YESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             L+V  LP  +   ++  +F ++     ++      T   +  AF  ++ ++ A  A+ 
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 123 ALNNF 127
           ALNN 
Sbjct: 67  ALNNV 71

>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 = 51.1 bits (122), Expect = 3e-10
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALG 119
            +   L V GLP     +++   F  F       ++    T +S+ F F  F++ ++ + 
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 120 AMYALNNF 127
            M   +  
Sbjct: 66  VMSQRHMI 73

>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 = 50.3 bits (120), Expect = 6e-10
 Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL-RSSTQNSQPFAFAVFSDQQSALGAMYALN 125
           L V+ L   V   +I  LF EF   + + +    +  S   A   F  +  AL AM   N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 126 NF 127
             
Sbjct: 63  GV 64

>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 = 49.5 bits (118), Expect = 1e-09
 Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMYA 123
           +L+V  L  DV    +Y  F       S  +     T+ S  +A+  F     A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 124 LNNF 127
           +N  
Sbjct: 62  MNFD 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 = 49.6 bits (118), Expect = 1e-09
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALG 119
           +++R LF+ GL  +     + + F ++       +    +T+ S+ F F  ++  +    
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 120 AMYALN 125
           AM A  
Sbjct: 64  AMNARP 69

>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 = 49.6 bits (118), Expect = 2e-09
 Identities = 14/68 (20%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALG 119
           ++  T++V GL E V    ++ LF +     +        T   Q + F  F  ++ A  
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 120 AMYALNNF 127
           A+  ++  
Sbjct: 67  AIKIMDMI 74

>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 = 49.3 bits (117), Expect = 2e-09
 Identities = 18/63 (28%), Positives = 30/63 (47%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           RTL+V  L  DV    I  LF +    +S  + +   ++ P+ F  F + + A  A+ A+
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 125 NNF 127
           N  
Sbjct: 69  NGR 71

>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 = 48.9 bits (116), Expect = 3e-09
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             L+V+GLP+ +  +E+  LF ++    +    +   T  S+   F  F  +  A  A+ 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 123 ALNNF 127
            LN  
Sbjct: 67  GLNGQ 71

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-09
 Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 4/66 (6%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             V+ L+V  L        I   F               +  + +AF  FS+++ A+ AM
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGA----VERVKKIRDYAFVHFSNREDAVEAM 61

Query: 122 YALNNF 127
            ALN  
Sbjct: 62  KALNGK 67

>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 = 48.9 bits (116), Expect = 3e-09
 Identities = 12/63 (19%), Positives = 26/63 (41%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           + L V+ +P   +  ++  +F +F       +  + + S+ F F  F +   A  A   L
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 71

Query: 125 NNF 127
           +  
Sbjct: 72  HGT 74

>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 = 48.9 bits (116), Expect = 5e-09
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           R L++  LP  +   E+Y++F ++          +T  ++  A+ V+ D   A  A   L
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIR-VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 125 NNF 127
           + F
Sbjct: 67  SGF 69

>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 = 48.0 bits (114), Expect = 6e-09
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALG 119
            +  TL+V  L       +IY LF +    +   +      + +  F F  +  +  A  
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 120 AMYALNNF 127
           AM  +N  
Sbjct: 65  AMRYINGT 72

>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 = 47.7 bits (113), Expect = 8e-09
 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALG 119
           D+  T+ V  L ED +  ++  LFR F            +T  S+ FAF  F  ++ A  
Sbjct: 6   DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 65

Query: 120 AMYALNNF 127
           A+  ++ F
Sbjct: 66  AIAGVSGF 73

>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 = 46.6 bits (110), Expect = 2e-08
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALG 119
           D    L V GL      R++  +F ++       +     ++ S+ FAF  F +   A  
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 120 AMYALNNF 127
           A    N  
Sbjct: 67  AKERANGM 74

>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 = 46.1 bits (109), Expect = 3e-08
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 12/76 (15%)

Query: 60  SYDEV--------RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVF 111
            +++V         T++  G+   +  + +   F  F       +       + ++F  F
Sbjct: 6   RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV----FPEKGYSFVRF 61

Query: 112 SDQQSALGAMYALNNF 127
           S  +SA  A+ ++N  
Sbjct: 62  STHESAAHAIVSVNGT 77

>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 = 45.7 bits (108), Expect = 3e-08
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAM 121
           +F+ GL  D   +++ + F +F       L+    T  S+ F F +F + +S    M
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58

>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 = 45.8 bits (108), Expect = 4e-08
 Identities = 14/64 (21%), Positives = 28/64 (43%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           V  +F+  L + +  + +Y+ F  F    S  +      S+ + F  F  Q++A  A+  
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 67

Query: 124 LNNF 127
           +N  
Sbjct: 68  MNGM 71

>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 = 45.3 bits (107), Expect = 5e-08
 Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 15/87 (17%)

Query: 60  SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALG 119
           ++ +   LFV  LP D+   E+  LF ++               + F F     +  A  
Sbjct: 4   TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF----IHKDKGFGFIRLETRTLAEI 59

Query: 120 AMYALNN-----------FAPSDSACS 135
           A   L+N           FA   ++ +
Sbjct: 60  AKVELDNMPLRGKQLRVRFACHSASLT 86

>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 = 45.3 bits (107), Expect = 5e-08
 Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 2/57 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFP--GYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +FV GL  D    +I   F  F         + + T   + F F  F +++     M
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 1e-07
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAMY 122
           R L+V GL E+V  + ++  F  F       +     T+  + FAF  F   + A  A+ 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 123 ALNNF 127
            +N  
Sbjct: 66  NMNES 70

>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 = 44.6 bits (105), Expect = 1e-07
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYE--SSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             LF+ GLP  +   ++  L   F   +  +    S+T  S+ +AF  + D      A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 123 ALNNF 127
            LN  
Sbjct: 62  GLNGM 66

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 45.0 bits (106), Expect = 1e-07
 Identities = 10/65 (15%), Positives = 19/65 (29%), Gaps = 3/65 (4%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             RTL    L  ++   E+  +F +               S+  A+  F  +  A   + 
Sbjct: 15  AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ---DGKSKGIAYIEFKSEADAEKNLE 71

Query: 123 ALNNF 127
                
Sbjct: 72  EKQGA 76

>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 = 44.7 bits (105), Expect = 1e-07
 Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 65  RTLFVAGLPEDVKPREI----YNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
            T+++  L E +K  E+    + +F  F       +   +   +  AF +F +  SA  A
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS-RSLKMRGQAFVIFKEVSSATNA 62

Query: 121 MYALNNF 127
           + ++  F
Sbjct: 63  LRSMQGF 69

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 5e-07
 Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 3/65 (4%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLR--SSTQNSQPFAFAVFSDQQSALGAM 121
           V+ +FV G+ ED +   + + F ++   E   +     +   + FAF  F D  S    +
Sbjct: 2   VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 61

Query: 122 YALNN 126
                
Sbjct: 62  -IQKY 65

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 6e-07
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL---RSSTQNSQPFAFAVFSDQQSALGAMYA 123
           +F+  L  ++  + +Y+ F  F     +        T NS+ +AF  F+   ++  A+ A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 124 LNNF 127
           +N  
Sbjct: 61  MNGQ 64

>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 = 42.4 bits (99), Expect = 6e-07
 Identities = 15/65 (23%), Positives = 23/65 (35%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGY--ESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             L V  LP+++   E  +LF                T  S  + F  + D + A  A+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 123 ALNNF 127
            LN  
Sbjct: 63  TLNGL 67

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 42.3 bits (99), Expect = 7e-07
 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFSDQQSALGAMYA 123
            L V  LP+D+  RE+Y LFR      +        T  S  +AF  F+ +  +  A+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 124 LNNF 127
           LN  
Sbjct: 64  LNGI 67

>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 = 42.3 bits (99), Expect = 8e-07
 Identities = 11/66 (16%), Positives = 22/66 (33%), Gaps = 5/66 (7%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHL-----RSSTQNSQPFAFAVFSDQQSALGAM 121
           LF+  L        +  +F +    +S  +     ++    S  F F  +   + A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 122 YALNNF 127
             L   
Sbjct: 61  KQLQGH 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 = 41.9 bits (98), Expect = 9e-07
 Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRS--STQNSQPFAFAVFSDQQSALGAMYAL 124
           +F+ GL        +   F +F   +   +     T+ S+ F F  F DQ      + A 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61

Query: 125 NNF 127
           +  
Sbjct: 62  SRH 64

>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 = 42.7 bits (100), Expect = 9e-07
 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 2/66 (3%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFRE--FPGYESSHLRSSTQNSQPFAFAVFSDQQSALG 119
           ++ R LF+ GL  +     + N + +             +++ S+ F F  FS       
Sbjct: 18  EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 120 AMYALN 125
           AM A  
Sbjct: 78  AMAARP 83

>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 = 41.9 bits (98), Expect = 2e-06
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 3/66 (4%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALGA 120
           + RT+F   L   ++PR++ + F               +++ S+  A+  F + QS    
Sbjct: 17  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-L 75

Query: 121 MYALNN 126
              L  
Sbjct: 76  AIGLTG 81

>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 = 41.2 bits (96), Expect = 2e-06
 Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 6/66 (9%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLR-----SSTQNSQPFAFAVFSDQQSALGA 120
            LF+ G+P+  K  EI     +        +      +    ++ FAF  +   ++A  A
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKV-TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 121 MYALNN 126
              L  
Sbjct: 62  RRKLMP 67

>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 = 40.5 bits (94), Expect = 3e-06
 Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 3/63 (4%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           +FV GL  +    ++ + F +F   +        +T   + F F  F  +         +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 125 NNF 127
           +  
Sbjct: 61  HFH 63

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 3e-06
 Identities = 12/71 (16%), Positives = 20/71 (28%), Gaps = 6/71 (8%)

Query: 59  GSYDE---VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQ 115
           GS +E       F   L +     +++ LF      +        +             +
Sbjct: 3   GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGI---ILFKEKAK 59

Query: 116 SALGAMYALNN 126
            ALG     NN
Sbjct: 60  EALGKAKDANN 70

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 5e-06
 Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMY 122
             LF+  LP++   +++  +F  F    S+ +    Q   S+ F F  + +  SA  A+ 
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 123 ALNNF 127
           ++N F
Sbjct: 79  SMNGF 83

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.4 bits (94), Expect = 6e-06
 Identities = 14/76 (18%), Positives = 24/76 (31%), Gaps = 4/76 (5%)

Query: 52  SASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVF 111
           S+    YG  +    L+V GL  +     +   F  F    +            FA+  +
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID----HVKGDSFAYIQY 60

Query: 112 SDQQSALGAMYALNNF 127
               +A  A   +  F
Sbjct: 61  ESLDAAQAACAKMRGF 76

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.8 bits (92), Expect = 6e-06
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           L++ GL      +++  L + +    S  + L  +T   + + F  F    +A  A+ AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 125 NNF 127
              
Sbjct: 61  KAS 63

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 6e-06
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 2/63 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYA 123
           R++++ G P D    +I     +     +  +R +     +   F VF   +SA   +  
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 124 LNN 126
              
Sbjct: 66  TPG 68

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 7e-06
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALG 119
            E +T+F+  L  D +   +  + ++F   +     L   T++S+  AFA F  Q++A  
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 120 AMYALNNFAPSD 131
            + A +  A   
Sbjct: 66  CLAAASLEAEGG 77

>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 = 41.5 bits (96), Expect = 7e-06
 Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESS--HLRSSTQNSQPFAFAVFSDQQSALG 119
           +++R LF+ GL  +     + + F ++            +T+ S+ F F  ++  +    
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 120 AMYALNNF 127
           AM A  + 
Sbjct: 64  AMNARPHK 71

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.7 bits (92), Expect = 9e-06
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGY--ESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
           E   LFV  + E+ +  EI   F ++        +L   T  S+ +A   +   + AL A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 121 MYALNNF 127
             ALN  
Sbjct: 66  KEALNGA 72

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 2e-05
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 4/61 (6%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN 125
            L++  L   V   ++  LF +     +            +AF  + DQ  A+ A+  L+
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ----VLLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 126 N 126
            
Sbjct: 59  G 59

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 3e-05
 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 64  VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
           V  + V  L   V    ++ +F +F           T+N+Q  A   ++D  SA  A  +
Sbjct: 7   VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF--TKNNQFQALLQYADPVSAQHAKLS 64

Query: 124 LNNF 127
           L+  
Sbjct: 65  LDGQ 68

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 26/113 (23%), Positives = 36/113 (31%), Gaps = 10/113 (8%)

Query: 17  QTPPPPPPPPPPGGVVAPPTQPYMPQPQPPPLGSYSASFPAYGSYDEVRTLFVAGLPEDV 76
           Q P      P          Q    Q  PP               D +R L V  +P  V
Sbjct: 3   QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPT--------QMNPEPDVLRNLMVNYIPTTV 54

Query: 77  KPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNF 127
              ++  LF  +   ES  +    +   S+ + F  F    SA  A+  LN F
Sbjct: 55  DEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 3e-05
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 6/65 (9%)

Query: 65  RTLFVA--GLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
           ++L VA  GL   V   ++  +  +    ++         ++P++FA +   + +  A  
Sbjct: 19  QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL----MPPNKPYSFARYRTTEESKRAYV 74

Query: 123 ALNNF 127
            LN  
Sbjct: 75  TLNGK 79

>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 = 37.4 bits (86), Expect = 6e-05
 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
           +    ++V  LP D++ ++I ++F ++ G        + +   PFAF  F D + A  A+
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKY-GAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAV 70

Query: 122 YALNNF 127
           Y  + +
Sbjct: 71  YGRDGY 76

>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 = 37.5 bits (87), Expect = 7e-05
 Identities = 10/64 (15%), Positives = 26/64 (40%), Gaps = 7/64 (10%)

Query: 65  RTLFVAGL-PEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYA 123
             +F+  L    VK  ++  +F ++       +       + FAF  + ++++A  A+  
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH------KGFAFVQYVNERNARAAVAG 69

Query: 124 LNNF 127
            +  
Sbjct: 70  EDGR 73

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 1e-04
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYES--SHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             LFV GL  D   + +  +F ++             TQ S+ F F  F +   A  AM 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 123 ALNNF 127
           A+N  
Sbjct: 66  AMNGK 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 = 36.3 bits (83), Expect = 1e-04
 Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMY 122
            TL++   P     R I +L ++      S    S +   S+ FA+   + ++ A   + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 123 ALNNF 127
            LN  
Sbjct: 62  KLNGL 66

>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 = 36.2 bits (83), Expect = 2e-04
 Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 2/65 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYE--SSHLRSSTQNSQPFAFAVFSDQQSALGAMY 122
             LFV  L       ++  LF  +         + S T+  + FAF  F   + A+ A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 123 ALNNF 127
            ++  
Sbjct: 69  EVDGQ 73

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 2e-04
 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 2/63 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMY 122
             +FV GLP       +   F  F   E + + +  Q   S+ + F   +D+ +A  A  
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 123 ALN 125
             N
Sbjct: 71  DPN 73

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 2e-04
 Identities = 12/75 (16%), Positives = 23/75 (30%), Gaps = 4/75 (5%)

Query: 52  SASFPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVF 111
           S S  ++        + V GL E V   ++     +F       +       +  A   F
Sbjct: 3   SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM----MPFKRQALVEF 58

Query: 112 SDQQSALGAMYALNN 126
            +  SA   +    +
Sbjct: 59  ENIDSAKECVTFAAD 73

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 3e-04
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPF--AFAVFSDQQSALGA 120
            +R++FV  +P +    ++ ++F E     S  L    +  +P    F  + DQ++AL A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 121 MYALNNF 127
           M  LN  
Sbjct: 67  MRNLNGR 73

>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 = 35.4 bits (81), Expect = 4e-04
 Identities = 13/64 (20%), Positives = 21/64 (32%), Gaps = 2/64 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHL--RSSTQNSQPFAFAVFSDQQSALGAMY 122
             + V  +P  V   EI + F  +     S     +        A   F  +  A  A+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 123 ALNN 126
            LN+
Sbjct: 70  DLND 73

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.1 bits (80), Expect = 4e-04
 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 5/69 (7%)

Query: 63  EVRTLFVAGLPEDVKPRE-IYNLFREFPGY---ESSHLRSSTQNSQPFAFAVFSDQQSAL 118
           E R + +  L  ++     +   F  F           +     +   AF VF ++ SA 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 119 GAMYALNNF 127
            A+  +N  
Sbjct: 63  RAL-QMNRS 70

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 4e-04
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 55  FPAYGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSH--LRSSTQNSQPFAFAVFS 112
           F +Y   +  + L++  L   V  R++ +LF  F   +      R  T   +  AF  F 
Sbjct: 9   FSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP 68

Query: 113 DQQSALGAMYALNNF 127
           +++ A  A++ +N +
Sbjct: 69  NKEIAWQALHLVNGY 83

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.9 bits (79), Expect = 5e-04
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 16/77 (20%)

Query: 67  LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNN 126
           + + GLP DV  +E+++L  ++               +  AF    + + A  A+   + 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYE-----LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQ 55

Query: 127 -----------FAPSDS 132
                        P+D+
Sbjct: 56  SRLRERELSVQLQPTDA 72

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 34.8 bits (79), Expect = 5e-04
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 3/63 (4%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
           + LF+  LPE+     +  LF +FPG++         N    AF  F+ +  +  A  AL
Sbjct: 9   QILFLTNLPEETNEMMLSMLFNQFPGFKEVR---LVPNRHDIAFVEFTTELQSNAAKEAL 65

Query: 125 NNF 127
             F
Sbjct: 66  QGF 68

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.7 bits (79), Expect = 6e-04
 Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 2/63 (3%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
            TL ++ +P  V   ++  LF    G          Q  +  A       + A+ A+  L
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVV--KGFKFFQKDRKMALIQMGSVEEAVQALIDL 68

Query: 125 NNF 127
           +N 
Sbjct: 69  HNH 71

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.001
 Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 10/75 (13%)

Query: 63  EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSS----------TQNSQPFAFAVFS 112
           +   ++V GL + V   ++ + F++    + +               T   +  A   + 
Sbjct: 7   DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 66

Query: 113 DQQSALGAMYALNNF 127
           D  +A  A+   +  
Sbjct: 67  DPPTAKAAVEWFDGK 81

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.9 bits (77), Expect = 0.001
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 5/63 (7%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL 124
             + V  LP+D   +E+++L +++              ++  AF    + + A  A+   
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDY-----DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 125 NNF 127
           + +
Sbjct: 61  HQY 63

>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 = 33.7 bits (76), Expect = 0.001
 Identities = 10/51 (19%), Positives = 19/51 (37%)

Query: 66  TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQS 116
           T+ V  LP+     ++Y  F+         +  S + +  FA   F+    
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDG 52

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.1 bits (75), Expect = 0.002
 Identities = 9/69 (13%), Positives = 18/69 (26%), Gaps = 5/69 (7%)

Query: 59  GSYDEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSA 117
           G  +  R + +           ++  L   F    +        N    AF   +  + A
Sbjct: 3   GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHL----ILNKINEAFIEMATTEDA 58

Query: 118 LGAMYALNN 126
             A+     
Sbjct: 59  QAAVDYYTT 67

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (74), Expect = 0.003
 Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 1/67 (1%)

Query: 62  DEVRTLFVAGLPEDVKPREIYNLFREF-PGYESSHLRSSTQNSQPFAFAVFSDQQSALGA 120
            +   L+++ LP  +  +E+ N+ + F     +  LR S+  S+   FA     +     
Sbjct: 16  QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAV 75

Query: 121 MYALNNF 127
           +   N  
Sbjct: 76  IGHFNGK 82

>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 = 32.7 bits (74), Expect = 0.004
 Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 3/57 (5%)

Query: 65  RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAM 121
             +FV     D+   E+   F ++            +  + FAF  F+D Q A    
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVF---IPKPFRAFAFVTFADDQIAQSLC 59

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	144
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.9
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.9
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.89
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.88
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.88
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.88
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.88
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.87
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.87
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.87
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.87
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.87
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.87
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.87
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.87
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.86
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.86
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.86
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.85
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.85
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.85
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.85
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.84
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.84
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.84
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.83
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.83
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.83
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.82
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.82
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.81
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.81
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.81
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.77
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.75
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.75
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.7
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.7
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	99.66
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.56
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.53
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.33
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.63
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.39
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.72
d1oj4a2	120	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol k	89.83
d1ueka2	120	4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol k	87.82

>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=99.90  E-value=5e-24  Score=139.99  Aligned_cols=80  Identities=23%  Similarity=0.336  Sum_probs=74.0

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.+.+|||||||+.+++|++|+++|++||.|++|++..++.++++||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~--g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL--GKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEET--TEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEE
Confidence            3456899999999999999999999999999999999887777779999999999999999999999994  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        83 a~   84 (90)
T d2cqia1          83 AT   84 (90)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.90  E-value=3.6e-23  Score=136.65  Aligned_cols=82  Identities=17%  Similarity=0.239  Sum_probs=74.9

Q ss_pred             CCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           60 SYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        60 ~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....++|||+|||.++++++|+++|++||.|.+|++..++++.++||||+|.+.++|++|++.|||..|+  |+.|+|+
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~--g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVE--GRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            34556789999999999999999999999999999999887777779999999999999999999999995  8999999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      |+..
T Consensus        85 ~A~~   88 (93)
T d2cq3a1          85 NATA   88 (93)
T ss_dssp             ECCS
T ss_pred             ecCc
Confidence            9753

>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=99.90  E-value=2.4e-23  Score=135.40  Aligned_cols=79  Identities=22%  Similarity=0.348  Sum_probs=71.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++||||||+.++|+++|+++|++||.|+++++++++.+++  +||||+|.+.++|++|++.|||..++|+.+.|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            346899999999999999999999999999999998865443  399999999999999999999999976677899988


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.89  E-value=3.1e-23  Score=135.68  Aligned_cols=79  Identities=22%  Similarity=0.293  Sum_probs=71.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||+||+.++++++|+++|++||.|++|++.+++.++.+  ||||+|++.++|++|++.|||..|+  |+.|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~--g~~l~V~   82 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQVD   82 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            45689999999999999999999999999999999988665444  9999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        83 ~a~   85 (88)
T d1rk8a_          83 WCF   85 (88)
T ss_dssp             ESE
T ss_pred             Eec
Confidence            975

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.89  E-value=2.3e-23  Score=134.23  Aligned_cols=77  Identities=23%  Similarity=0.355  Sum_probs=70.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .++|||+|||.++++++|+++|++||.|++|++.+++.++  ++||||+|.+.++|++|++.|||..+.  |+.|+|+|+
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~--g~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR--NKRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEc
Confidence            3679999999999999999999999999999998876544  349999999999999999999999994  899999998


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        80 ~   80 (82)
T d1b7fa1          80 R   80 (82)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.89  E-value=4.5e-23  Score=136.29  Aligned_cols=79  Identities=18%  Similarity=0.263  Sum_probs=71.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.+|||||||+.++++++|+++|++||.|++|++++++.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~   84 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY--GKPIRVN   84 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCS--SCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            345799999999999999999999999999999998876544  349999999999999999999999995  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        85 ~A~   87 (93)
T d1x5ua1          85 KAS   87 (93)
T ss_dssp             ETT
T ss_pred             EcC
Confidence            975

>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=99.89  E-value=6.2e-23  Score=132.06  Aligned_cols=77  Identities=22%  Similarity=0.317  Sum_probs=70.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ++|||||||.+++|++|+++|++||.|.+|++.++...+..  ||||+|.+.++|++|++.|||..|.  |+.|+|+|+.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~--g~~l~v~~Ak   80 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ--TKTIKVSYAR   80 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEee
Confidence            57999999999999999999999999999999987554443  9999999999999999999999994  8999999975


Q ss_pred             C
Q 032280          143 A  143 (144)
Q Consensus       143 ~  143 (144)
                      .
T Consensus        81 P   81 (82)
T d1fxla1          81 P   81 (82)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=6.7e-23  Score=135.43  Aligned_cols=79  Identities=18%  Similarity=0.200  Sum_probs=72.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ..++|||||||+.++|+++|+++|++||.|.+|++..++.++..  ||||+|.+.++|++|++.|||..++  |+.|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--gr~i~V~   82 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DRIIRTD   82 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEET--TEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            45679999999999999999999999999999999988665543  9999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        83 ~a~   85 (93)
T d1h2vz_          83 WDA   85 (93)
T ss_dssp             EES
T ss_pred             EcC
Confidence            975

>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=99.89  E-value=1.1e-22  Score=132.11  Aligned_cols=79  Identities=20%  Similarity=0.390  Sum_probs=71.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..++|||+|||.+++|++|+++|++||.|.++++++++.++++  ||||+|.+.++|++|++.|||..+.+.++.|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            4567999999999999999999999999999999988655444  99999999999999999999999976668899988


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      .
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=7.3e-23  Score=134.34  Aligned_cols=79  Identities=25%  Similarity=0.358  Sum_probs=72.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ++..+|||+||+.++++++|+++|++||.|.+|++..++.++.  +||||+|.+.++|++|++.|||..|+  |+.|+|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~--g~~i~v~   83 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD--HLILNVE   83 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEET--TEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            4567999999999999999999999999999999998865444  39999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        84 ~ak   86 (90)
T d2cq0a1          84 WAK   86 (90)
T ss_dssp             ESS
T ss_pred             eee
Confidence            985

>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=99.88  E-value=5.6e-23  Score=132.13  Aligned_cols=75  Identities=19%  Similarity=0.184  Sum_probs=69.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      +||||||+.++||++|+++|++||.|.+|+|.+++.+++  +||||+|.+.++|.+|++.|||..+.  |+.|+|+|+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~--gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK--GKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEET--TEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEEeC
Confidence            699999999999999999999999999999999866554  39999999999999999999999995  8899999985

>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=99.88  E-value=3.1e-23  Score=135.90  Aligned_cols=77  Identities=18%  Similarity=0.345  Sum_probs=71.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..+|||+||+.++++++|+++|++||.|.++++..++.++++||||+|++.++|++|++.|||..|+  |+.|+|+|+.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~--g~~i~V~~a~   84 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN--DRKVFVGRFK   84 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEET--TEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEECC
Confidence            4689999999999999999999999999999999887777779999999999999999999999994  8999999875

>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=99.88  E-value=3.5e-23  Score=135.61  Aligned_cols=80  Identities=20%  Similarity=0.276  Sum_probs=72.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...+|||||||++++++++|+++|++||.|.+|++.+++.+  .++||||+|.+.++|++|++.|||..++  |+.|+|+
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~--g~~l~v~   80 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF--GRTIRVN   80 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEET--TEEEEEE
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            35689999999999999999999999999999999887553  3449999999999999999999999995  8899999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      |+..
T Consensus        81 ~a~p   84 (89)
T d2cqba1          81 LAKP   84 (89)
T ss_dssp             ECCC
T ss_pred             EeCC
Confidence            9864

>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=99.88  E-value=1.3e-22  Score=131.12  Aligned_cols=75  Identities=20%  Similarity=0.233  Sum_probs=68.0

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      +..++|||+||+.++||++|+++|++||.|++|++.+++.++++  ||||+|.+.++|++|++.|||..|+  |+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEET--TEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEEC--CEEeEC
Confidence            34689999999999999999999999999999999988665443  9999999999999999999999995  888886

>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=99.88  E-value=7e-22  Score=138.85  Aligned_cols=80  Identities=25%  Similarity=0.335  Sum_probs=72.4

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .+..++||||||+.+++|++|+++|++||.|++|+++.++.+++  +||||+|.+.++|++|++.|||..|+  |+.|+|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~--gr~l~V  116 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL--NKRLKV  116 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECS--SCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEEC--CEEEEE
Confidence            34568999999999999999999999999999999998866544  49999999999999999999999995  899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus       117 ~~a~  120 (139)
T d1u6fa1         117 ALAA  120 (139)
T ss_dssp             EESS
T ss_pred             EEcC
Confidence            9974

>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=99.88  E-value=2.1e-22  Score=137.07  Aligned_cols=78  Identities=19%  Similarity=0.333  Sum_probs=70.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +..+|||||||+.++++++|+++|++||.|++|++..+.. .++||||+|.+.++|.+|++.|||..|.  |+.|+|+|+
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~-~kG~afV~f~~~~~A~~Ai~~l~g~~~~--gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE-TRGTAYVVYEDIFDAKNACDHLSGFNVC--NRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT-TTTEEEEEESSHHHHHHHHHHHTTCEET--TEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCC-cCCeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEc
Confidence            3468999999999999999999999999999999986544 3459999999999999999999999995  899999986


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        82 ~   82 (114)
T d2f9da1          82 N   82 (114)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.88  E-value=2.2e-22  Score=133.17  Aligned_cols=79  Identities=23%  Similarity=0.319  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC---CCCcEEEEEeCCHHHHHHHHHHh-cCCccCCCCCeEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ---NSQPFAFAVFSDQQSALGAMYAL-NNFAPSDSACSLL  137 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~---~~~~~aFV~F~~~~~A~~A~~~l-nG~~~~~~g~~l~  137 (144)
                      ...++|||+|||.+++|++|+++|++||.|.+|++..+..   ..++||||+|.+.++|.+|++.| ||..|+  |+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~--Gr~l~   83 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY--GRRLV   83 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSS--SCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEEC--CEEEE
Confidence            4567899999999999999999999999999999977632   33459999999999999999998 899885  88999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        84 V~~A~   88 (94)
T d2cpha1          84 LEWAD   88 (94)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99985

>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=99.87  E-value=2.9e-22  Score=133.49  Aligned_cols=79  Identities=19%  Similarity=0.208  Sum_probs=70.9

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+||++++++++|+++|++||.|++|++.+++.++  ++||||+|.+.++|++|++.|||..|+  |+.|+|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~--gr~i~V~   83 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ--GRMLHVL   83 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESS--SCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            345689999999999999999999999999999998875544  349999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus        84 ~a~   86 (99)
T d1whwa_          84 PST   86 (99)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            875

>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=99.87  E-value=1.1e-22  Score=130.77  Aligned_cols=78  Identities=21%  Similarity=0.239  Sum_probs=67.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .||||+|||.++|+++|+++|++||.|..+.++.+...  .++||||+|.+.++|++|++.|||..++  |+.|+|+||.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~--g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE--GYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEET--TEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEcc
Confidence            48999999999999999999999999988877665433  3449999999999999999999999994  9999999998


Q ss_pred             CC
Q 032280          143 AM  144 (144)
Q Consensus       143 ~~  144 (144)
                      .|
T Consensus        80 P~   81 (81)
T d2ghpa1          80 PL   81 (81)
T ss_dssp             CC
T ss_pred             Cc
Confidence            76

>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=99.87  E-value=3.9e-22  Score=128.95  Aligned_cols=76  Identities=24%  Similarity=0.433  Sum_probs=68.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++||||+||+.++++++|+++|++||.|.+|++..++   ++||||+|.|.++|.+|++.|||+.|. .|+.|+|+|+.
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~-~~~~i~v~~ak   82 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFTTELQSNAAKEALQGFKIT-PTHAMKITFAK   82 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT---CSCEEEEESSHHHHHHHHHHHTTCBSS-TTCBCEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc---ceeEEEecCCHHHHHHHHHHhCCcEeC-CCcEEEEEEec
Confidence            46899999999999999999999999999999997532   349999999999999999999999995 36789999985

>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=99.87  E-value=7.4e-22  Score=131.19  Aligned_cols=78  Identities=15%  Similarity=0.240  Sum_probs=70.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..++||||+||+.++++++|+++|++||.|++|++.+++    .||||+|.+.++|++|++.|||..|.+.++.|+|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~----~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD----SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSS----CCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccc----cEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            456899999999999999999999999999999986543    3999999999999999999999999777789999998


Q ss_pred             cC
Q 032280          142 MA  143 (144)
Q Consensus       142 ~~  143 (144)
                      ..
T Consensus        91 k~   92 (97)
T d1whya_          91 KS   92 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.87  E-value=8e-23  Score=137.30  Aligned_cols=78  Identities=24%  Similarity=0.388  Sum_probs=71.2

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.|||||+||+.++++++|+++|++||.|.+|++..++.+++  +||||+|.+.++|++|++.|||..|.  |+.|+|+|
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~--g~~i~V~~   84 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS--GRALRVDN   84 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCS--SSCBEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEEC--CEEEEEEE
Confidence            468999999999999999999999999999999998866544  39999999999999999999999995  88999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        85 a~   86 (104)
T d1p1ta_          85 AA   86 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            74

>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=99.87  E-value=3.7e-22  Score=133.90  Aligned_cols=78  Identities=22%  Similarity=0.348  Sum_probs=71.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++|||+||++++++++|+++|++||.|.+++++.++.++..  ||||+|.+.++|+.|++.|||..|.  |+.|+|+|
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~--g~~i~V~~   94 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG--MKRLKVQL   94 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEET--TEECEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEEC--CEEEEEEE
Confidence            4578999999999999999999999999999999988665543  9999999999999999999999994  88999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        95 a~   96 (102)
T d2cpza1          95 KR   96 (102)
T ss_dssp             CC
T ss_pred             eC
Confidence            75

>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=99.87  E-value=2.1e-22  Score=130.92  Aligned_cols=77  Identities=21%  Similarity=0.363  Sum_probs=69.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .+|||||||.++||++|+++|++||.|++|++.+|+.++  ++||||+|.+.++|++|++.|||..|.  |+.|+|+|+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~--g~~l~V~~A~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG--DKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCS--SSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEECC
Confidence            469999999999999999999999999999999875533  459999999999999999999999995  8889999986


Q ss_pred             C
Q 032280          143 A  143 (144)
Q Consensus       143 ~  143 (144)
                      .
T Consensus        80 ~   80 (85)
T d2u2fa_          80 V   80 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.87  E-value=2.5e-22  Score=130.17  Aligned_cols=74  Identities=16%  Similarity=0.244  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS-----QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~-----~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      |||+||+.++|+++|+++|++||.|.+|++..++.++     ++||||+|++.++|++|++.|||..++  |+.|+|+|+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~--g~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD--GHKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEET--TEECEEECS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEC
Confidence            8999999999999999999999999999998875433     349999999999999999999999995  889999996


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        79 ~   79 (85)
T d2cpfa1          79 E   79 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.87  E-value=3.3e-22  Score=130.90  Aligned_cols=79  Identities=19%  Similarity=0.318  Sum_probs=70.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+.++|||||||.++++++|+++|++||.|.++.++.+..++  ++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~--g~~l~V~   80 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD--GRQIRVD   80 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTT--SCCCEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            456789999999999999999999999999999988764433  449999999999999999999999994  8899999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        81 ~a~   83 (90)
T d1x5sa1          81 QAG   83 (90)
T ss_dssp             EEE
T ss_pred             EcC
Confidence            864

>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=99.87  E-value=7.3e-22  Score=128.79  Aligned_cols=78  Identities=18%  Similarity=0.214  Sum_probs=68.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++||||+||+.++++++|+++|++||.|.++++...+  +++||||+|++.++|.+|++.|||..+. .|+.|+|+||.
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~--~~~~afV~f~~~~~A~~A~~~l~~~~i~-~g~~l~v~~sk   85 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLG-ENHHLRVSFSK   85 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS--STTCEEEEESSHHHHHHHHHHHTTCBSS-SSCBCEEEECS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec--ccceeEEEECCHHHHHHHHHhccCCEec-CCCEEEEEeCC
Confidence            36899999999999999999999999999888776533  3449999999999999999999999984 37899999997


Q ss_pred             C
Q 032280          143 A  143 (144)
Q Consensus       143 ~  143 (144)
                      .
T Consensus        86 ~   86 (88)
T d2adca2          86 S   86 (88)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.86  E-value=3.6e-22  Score=135.06  Aligned_cols=79  Identities=20%  Similarity=0.176  Sum_probs=71.8

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..+.+|||+||++++||++|+++|++||.|++|++..++  +++||||+|++.++|++|++.|||..|.++++.|+|+||
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~--~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN--NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET--TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC--CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            456789999999999999999999999999999998754  345999999999999999999999999778999999998


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        83 ~   83 (108)
T d2adba1          83 K   83 (108)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.86  E-value=6.2e-22  Score=131.55  Aligned_cols=74  Identities=15%  Similarity=0.211  Sum_probs=68.4

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..++|||+||+.++++++|+++|++||.|++|++..+++    ||||+|++.++|++|++.|||..|.  |+.|+|+|+.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg----~afV~f~~~~~A~~Ai~~l~~~~i~--g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----YSFVRFSTHESAAHAIVSVNGTTIE--GHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTT----EEEEEESSHHHHHHHHHHHTTCEET--TEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecce----EEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEcC
Confidence            357899999999999999999999999999999987643    9999999999999999999999994  8999999975

>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=99.86  E-value=2e-21  Score=128.55  Aligned_cols=79  Identities=22%  Similarity=0.447  Sum_probs=69.9

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ....++|||+|||.++++++|+++|++||.|..+.+..+. ..++||||+|++.++|++|++.|||..|.  |+.|+|+|
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~-~~~g~afV~f~~~e~a~~Ai~~l~g~~~~--g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR-GGPPFAFVEFEDPRDAEDAVYGRDGYDYD--GYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS-SSSCCEEEEESCHHHHHHHHHHHTTCEET--TEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccc-cccceEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEe
Confidence            3445689999999999999999999999999999886543 34559999999999999999999999994  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        88 a~   89 (95)
T d1x4aa1          88 PR   89 (95)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>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=4.9e-22  Score=133.31  Aligned_cols=77  Identities=21%  Similarity=0.323  Sum_probs=69.5

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.+|||||||+.+++|++|+++|+.||.|.+|++++++.+  .++||||+|.+.++|.+|++ |||..|+  |+.|+|.+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~--G~~l~V~~   93 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLL--GVPIIVQA   93 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEET--TEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEEC--CEEEEEEE
Confidence            4689999999999999999999999999999999988554  34499999999999999994 9999995  89999998


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        94 a~   95 (101)
T d2cq4a1          94 SQ   95 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            74

>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=99.86  E-value=1.7e-21  Score=128.91  Aligned_cols=79  Identities=18%  Similarity=0.228  Sum_probs=69.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcC------CccCCCC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNN------FAPSDSA  133 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG------~~~~~~g  133 (144)
                      .+.+|||||||++++||++|+++|++||.|.++++..++.++  ++||||+|.+.++|.+|++.||+      ..+  .|
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~--~g   83 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKL--DG   83 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEES--SS
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEE--CC
Confidence            457899999999999999999999999999999998875544  34999999999999999999984      445  48


Q ss_pred             CeEEEEeec
Q 032280          134 CSLLFPHSM  142 (144)
Q Consensus       134 ~~l~v~~s~  142 (144)
                      +.|+|+|+.
T Consensus        84 r~l~v~~a~   92 (98)
T d1x4ha1          84 RQLKVDLAV   92 (98)
T ss_dssp             CEEEEECCC
T ss_pred             EEEEEEECC
Confidence            899999975

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.86  E-value=1.2e-21  Score=125.25  Aligned_cols=75  Identities=23%  Similarity=0.223  Sum_probs=67.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      +|||+||+.++++++|+++|++||.|.+|++..++.+ .++||||+|.+.++|++|++.|||..+.  |+.|+|++..
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~--g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLD--GRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEET--TEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEee
Confidence            5999999999999999999999999999999887533 3449999999999999999999999995  8999998863

>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=99.85  E-value=2e-21  Score=126.05  Aligned_cols=78  Identities=13%  Similarity=0.268  Sum_probs=68.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ++.++|||||||.++++++|+++|++||.|.++++.+++.+++.  ||||+|.+.++|++|++ ++|..|+  |+.|+|.
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~--Gr~i~V~   80 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVD--GRVVEPK   80 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEET--TEECEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEEC--CEEEEEE
Confidence            35689999999999999999999999999999999988665443  99999999999999996 6999994  8889887


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ..+
T Consensus        81 ~A~   83 (84)
T d1l3ka1          81 RAV   83 (84)
T ss_dssp             ECC
T ss_pred             eee
Confidence            653

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.7e-21  Score=130.75  Aligned_cols=77  Identities=19%  Similarity=0.267  Sum_probs=68.1

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++||||||+++++|++|+++|++||.|.+|+++.++.+  .++||||+|.+.++|++|++.+|+ .|+  |+.|+|+|
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~--Gr~l~V~~   85 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID--GRKANVNL   85 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET--TEECEEEE
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCC--CEEEEEEE
Confidence            4578999999999999999999999999999999888654  344999999999999999999987 574  88999988


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        86 a~   87 (103)
T d2cqda1          86 AY   87 (103)
T ss_dssp             ST
T ss_pred             cC
Confidence            64

>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=99.85  E-value=2.6e-21  Score=123.59  Aligned_cols=75  Identities=19%  Similarity=0.357  Sum_probs=67.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      .|+|||||||+++|+++|+++|++||.|.++++..++.++..  ||||+|.+.++|++|+ .|||..|+  |+.|+|+..
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l~--Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVN--GHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEET--TEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEEC--CEEEEEEEC
Confidence            589999999999999999999999999999999988665543  9999999999999998 58999995  888988754

>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=99.85  E-value=1.3e-21  Score=127.40  Aligned_cols=73  Identities=22%  Similarity=0.311  Sum_probs=67.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..+|||+||+.++++++|+++|++||.|.+|++..+++    ||||+|++.++|++|++.|||..|+  |+.|+|+|+.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~----~afV~f~~~~~A~~A~~~l~g~~i~--g~~l~V~~A~   80 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----FGFIRLETRTLAEIAKVELDNMPLR--GKQLRVRFAC   80 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTT----EEEEECSSSHHHHHHHHHHTTCCBT--TBCCEEEESS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccc----eEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEECC
Confidence            45799999999999999999999999999999976543    9999999999999999999999995  8899999974

>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=99.85  E-value=1.2e-21  Score=132.40  Aligned_cols=74  Identities=18%  Similarity=0.143  Sum_probs=66.8

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ..+||||+|||.++++++|+++|++||.|.+|.|...    ++||||+|.+.++|.+|++.|||..|.  |+.|+|+|..
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~----kg~afV~f~~~~~A~~A~~~lng~~~~--gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG----GITAIVEFLEPLEARKAFRHLAYSKFH--HVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS----SSCEEEEESCHHHHHHHHHHHTTCBSS--SSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeecc----CceEEEEEcCHHHHHHHHHHHcCCccC--CCeEEEEECC
Confidence            4578999999999999999999999999999988432    349999999999999999999999995  8899999974

>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=99.85  E-value=1.5e-21  Score=131.61  Aligned_cols=74  Identities=22%  Similarity=0.253  Sum_probs=67.1

Q ss_pred             cceEEEcCCC-CCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           64 VRTLFVAGLP-EDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        64 ~~tLfVgnLp-~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++|||+||+ ..++|++|+++|++||.|++|++++++   ++||||+|++.++|.+|++.|||..|.  |+.|+|+|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~---kg~afV~f~~~~~A~~ai~~lng~~l~--g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLH--GKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT---SCCEEEEESCHHHHHHHHHHHTTCBCS--SSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc---cceEEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEECC
Confidence            4799999995 569999999999999999999998764   349999999999999999999999995  8899999974

>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=99.85  E-value=4.4e-21  Score=124.51  Aligned_cols=76  Identities=21%  Similarity=0.267  Sum_probs=68.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+.++++++|+++|++||.+..+++...+    +||||+|.+.++|.+|++.|||..|.  |+.|+|+|+
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~r----g~afV~f~~~~~A~~Ai~~l~~~~i~--g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR----DYAFVHFSNREDAVEAMKALNGKVLD--GSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECS----SEEEEEESSHHHHHHHHHHHSSEEET--TEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcccc----EEEEEEeCCHHHHHHHHHHcCCCEEC--CEEEEEEec
Confidence            346899999999999999999999999999888875543    39999999999999999999999994  899999998


Q ss_pred             cC
Q 032280          142 MA  143 (144)
Q Consensus       142 ~~  143 (144)
                      ..
T Consensus        80 kP   81 (86)
T d2cpda1          80 KP   81 (86)
T ss_dssp             CC
T ss_pred             cC
Confidence            63

>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=99.84  E-value=2.9e-21  Score=123.75  Aligned_cols=73  Identities=21%  Similarity=0.236  Sum_probs=65.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...+||||+||+  +||++|+++|++||.|.+|++..+++    ||||+|++.++|.+|++.|||..+.  |+.|+|+|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~----~afV~f~~~~~A~~Ai~~lng~~~~--g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRN----CAFVTYEKMESADQAVAELNGTQVE--SVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTT----EEEEECSSHHHHHHHHHHHTTCBCS--SCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCC----EEEEEEcccHHHHHHHHHhCCCEEC--CEEEEEEEe
Confidence            346899999985  99999999999999999999865433    9999999999999999999999995  889999998


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        75 ~   75 (79)
T d2bz2a1          75 R   75 (79)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.84  E-value=2.5e-21  Score=129.05  Aligned_cols=74  Identities=15%  Similarity=0.203  Sum_probs=65.6

Q ss_pred             CCCcceEEEcCCC-CCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLP-EDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp-~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....+|||+||+ ..+++++|+++|++||.|++|++.      ++||||+|++.++|++|++.|||+.|.  |+.|+|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~------rg~aFV~f~~~~~A~~Ai~~lng~~~~--g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH------KGFAFVQYVNERNARAAVAGEDGRMIA--GQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE------TEEEEEEESSHHHHHHHHHTTTTCEET--TEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe------CCeEEEEECCHHHHHHHHHHcCCCEEC--CEEEEEE
Confidence            3445679999996 678999999999999999999983      239999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        84 ~a~   86 (98)
T d1wf2a_          84 LAA   86 (98)
T ss_dssp             ETT
T ss_pred             ECC
Confidence            975

>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=4.4e-21  Score=128.26  Aligned_cols=80  Identities=14%  Similarity=0.212  Sum_probs=68.7

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+.++||||||+.++++++|+++|++||.|.++++..+..+ .++||||+|.+.++|++|++.|||..|.  |+.+++.+
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~--gr~~~v~~   93 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIK--TPPGVSAP   93 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCC--CCTTSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEEC--CcCCccCC
Confidence            34578999999999999999999999999999998876432 2349999999999999999999999995  77777776


Q ss_pred             ecC
Q 032280          141 SMA  143 (144)
Q Consensus       141 s~~  143 (144)
                      +..
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.84  E-value=1.8e-21  Score=125.51  Aligned_cols=74  Identities=15%  Similarity=0.302  Sum_probs=65.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEE-EEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESS-HLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v-~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      ||||||+.+++|++|+++|++||.|.++ ++.+++.++  ++||||+|++.++|++|++.|||..++  |+.|+|+|+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~--gr~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLC--NRPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEET--TEECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEEC--CEEEEEEEec
Confidence            8999999999999999999999998664 677665443  459999999999999999999999995  8899999864

>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=99.84  E-value=4.4e-21  Score=121.99  Aligned_cols=73  Identities=19%  Similarity=0.313  Sum_probs=67.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .||||+|||.++++++|+++|++||.|.+|++..++.++++||||+|++.++|++|+ .+||..|+  |+.|.|+.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al-~~~~~~i~--g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI-TKTHKVVG--QNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHH-TTTTCEET--TEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHH-HhcCcEEC--CEEEEEEE
Confidence            489999999999999999999999999999999887776679999999999999998 58999995  88888875

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.8e-21  Score=127.03  Aligned_cols=80  Identities=14%  Similarity=0.195  Sum_probs=67.4

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeE--------EEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCC
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYE--------SSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSD  131 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~--------~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~  131 (144)
                      .+.++|||+||+.++++++|+++|++||.|.        .+.+..++.++  ++||||+|.+.++|.+|++.|||..|. 
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~-   84 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ-   84 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET-
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC-
Confidence            4568999999999999999999999999874        34444444333  349999999999999999999999994 


Q ss_pred             CCCeEEEEeecC
Q 032280          132 SACSLLFPHSMA  143 (144)
Q Consensus       132 ~g~~l~v~~s~~  143 (144)
                       |+.|+|+|+..
T Consensus        85 -gr~i~V~~a~~   95 (101)
T d2cpea1          85 -GSKLKVSLARK   95 (101)
T ss_dssp             -TEECEEECSSC
T ss_pred             -CEEEEEEEcCC
Confidence             89999999753

>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=99.84  E-value=4.6e-21  Score=128.95  Aligned_cols=77  Identities=16%  Similarity=0.264  Sum_probs=68.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +.++||||||++++++++|+++|++||.|.+++|.+++.++  ++||||+|.+.++|++|++ +||..|  +|+.|+|++
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l--~G~~i~V~~   95 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSI--DGRVVEPKR   95 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEE--TTEEEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeE--CCEEEEEEE
Confidence            45899999999999999999999999999999998885543  4499999999999999995 799999  489999988


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      ..
T Consensus        96 a~   97 (103)
T d1x4ba1          96 AV   97 (103)
T ss_dssp             CS
T ss_pred             Cc
Confidence            64

>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=99.84  E-value=1.6e-21  Score=125.39  Aligned_cols=72  Identities=18%  Similarity=0.232  Sum_probs=64.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCC-ccCCCCCeEEEEeec
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF-APSDSACSLLFPHSM  142 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~-~~~~~g~~l~v~~s~  142 (144)
                      .+|||||||.++|+++|+++|++||.+.++++..+++    ||||+|.+.++|++|++.|||. .+  +|+.|+|+|+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg----~aFV~f~~~~~A~~Ai~~lng~~~~--~G~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG----YAFVDYPDQNWAIRAIETLSGKVEL--HGKIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETT----EEEECCSCHHHHHHHHHHHTTTCEE--TTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccc----eEEEEECCHHHHHHHHHHhCCCeEE--CCEEEEEEEcC
Confidence            4699999999999999999999999998887766443    9999999999999999999996 58  48999999985

>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=99.83  E-value=4.1e-21  Score=121.31  Aligned_cols=72  Identities=14%  Similarity=0.252  Sum_probs=64.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +|||||||.++||++|+++|++||.+.++.+..++.++.  +||||+|.+.++|++|++ |||..|+  |+.|+|.+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~--gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEIN--NKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBT--TBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEEC--CeEEEEEE
Confidence            499999999999999999999999999999888765443  399999999999999996 9999995  88898875

>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=99.83  E-value=1.8e-20  Score=125.82  Aligned_cols=81  Identities=15%  Similarity=0.087  Sum_probs=69.2

Q ss_pred             CCCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           58 YGSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        58 ~~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      +.....+++|||+||+.+++|++|+++|++||.|+++++.++++    ||||+|++.++|++|++.|++..+...|+.|+
T Consensus         9 ~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~----~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_           9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR----QALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTT----EEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecce----eEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            33445688999999999999999999999999999999875433    99999999999999999986554433589999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+|+.
T Consensus        85 v~~s~   89 (104)
T d1wexa_          85 FNYST   89 (104)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            99985

>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=99.83  E-value=1.1e-20  Score=124.19  Aligned_cols=77  Identities=14%  Similarity=0.211  Sum_probs=67.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ...++|||+|||+++||++|+++|++||.|.+|+|.+|+.+++  +||||+|.+.++|++|++.+  ..|+  |+.|+|.
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~--Gr~i~v~   81 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMID--GRWCDCK   81 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEET--TEEEEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccC--CEEeEEE
Confidence            4567899999999999999999999999999999999865544  49999999999999999854  3664  8899998


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      ++.
T Consensus        82 ~a~   84 (90)
T d2cqga1          82 LPN   84 (90)
T ss_dssp             CCC
T ss_pred             eCC
Confidence            864

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.83  E-value=2.6e-21  Score=125.84  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=66.6

Q ss_pred             CcceEEEcCCCCCCC-HHHHHHHhhcCCCeEEEEEeecC---CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           63 EVRTLFVAGLPEDVK-PREIYNLFREFPGYESSHLRSST---QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        63 ~~~tLfVgnLp~~vt-e~~L~~~F~~~G~v~~v~l~~~~---~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      +.++|||+||+.+++ |++|+++|++||.|++|++..+.   +..++||||+|.+.++|++|++ |||..|+  |+.|+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~--gr~l~V   79 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLG--NREISV   79 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEET--TEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEEC--CEEEEE
Confidence            578999999999975 66799999999999999986642   2234499999999999999995 9999995  899999


Q ss_pred             EeecC
Q 032280          139 PHSMA  143 (144)
Q Consensus       139 ~~s~~  143 (144)
                      +|+..
T Consensus        80 ~~a~~   84 (86)
T d2ghpa3          80 SLADK   84 (86)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99853

>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=99.83  E-value=7.7e-21  Score=123.93  Aligned_cols=76  Identities=16%  Similarity=0.136  Sum_probs=67.2

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc--CCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN--NFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln--G~~~~~~g~~l~v  138 (144)
                      ...+++||||||+.++++++|+++|++||.|.++++..+++    ||||+|++.++|++|++.++  +..+  +|+.|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~----~afV~f~~~e~A~~a~~~~~~~~~~~--~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN----QAFLELATEEAAITMVNYYSAVTPHL--RNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTT----EEEEEESSHHHHHHHHHHHHHSCCEE--TTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccce----EEEEEeCCHHHHHHHHHHHccCCCcc--CCCEEEE
Confidence            45678999999999999999999999999999999875443    99999999999999999775  4566  5899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +||.
T Consensus        79 ~~sk   82 (88)
T d2cq1a1          79 QYSN   82 (88)
T ss_dssp             EECS
T ss_pred             EECC
Confidence            9985

>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=99.83  E-value=9.2e-21  Score=120.33  Aligned_cols=71  Identities=17%  Similarity=0.297  Sum_probs=63.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +||||||+++++|++|+++|++||.|.+|++..++.++  ++||||+|.+.++|++|++ ++|..|+  |+.|+|.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~--Gr~i~V~   73 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLN--GKVIDPK   73 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBT--TBCCEEC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEEC--CCEEEee
Confidence            49999999999999999999999999999999876544  3499999999999999996 7999884  7888774

>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=99.83  E-value=4.2e-21  Score=125.77  Aligned_cols=75  Identities=21%  Similarity=0.325  Sum_probs=65.9

Q ss_pred             CcceEEEcCCCCCCCHHHH---HHHhhcCCCeEEEEEeecCCCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCC
Q 032280           63 EVRTLFVAGLPEDVKPREI---YNLFREFPGYESSHLRSSTQNS-----QPFAFAVFSDQQSALGAMYALNNFAPSDSAC  134 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L---~~~F~~~G~v~~v~l~~~~~~~-----~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~  134 (144)
                      +.++|||+||+.+++++||   +++|++||.|.+|.+..++.++     ++||||+|++.++|.+|++.|||..|+  |+
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~--gr   84 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD--GR   84 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET--TE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEEC--CE
Confidence            4568999999999999999   7789999999999998874332     249999999999999999999999995  88


Q ss_pred             eEEEE
Q 032280          135 SLLFP  139 (144)
Q Consensus       135 ~l~v~  139 (144)
                      .||+.
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            89874

>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=99.83  E-value=1e-21  Score=129.25  Aligned_cols=78  Identities=12%  Similarity=0.137  Sum_probs=68.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...++|||+||+.++++++|+++|++||.|.+++++.+. +..++||||+|.+.++|++|++ |||..+.  |+.|+|++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~--g~~i~V~~   87 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVF--GNEIKLEK   87 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEET--TEEEEEEC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEEC--CEEEEEEe
Confidence            456799999999999999999999999999888776542 3344599999999999999995 9999995  99999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        88 ak   89 (91)
T d1fjeb1          88 PK   89 (91)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.83  E-value=7.8e-21  Score=124.20  Aligned_cols=73  Identities=15%  Similarity=0.297  Sum_probs=62.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .+++|||+|||.+++++||+++|++|| ++.+.+...    ++||||+|++.++|++|++.|||+.|.  |+.|+|+|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~~----kg~afV~f~~~~~A~~Ai~~ln~~~~~--G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRN----KRTAFVTLLNGEQAQNAIQMFHQYSFR--GKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEGG----GTEEEECCSCHHHHHHHHHHHTTEEET--TEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeecc----CCceEEEECCHHHHHHHHHHhCCCEEC--CEEEEEEEcC
Confidence            457899999999999999999999999 334444322    339999999999999999999999994  9999999975

>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=99.83  E-value=3.1e-20  Score=123.70  Aligned_cols=73  Identities=11%  Similarity=0.064  Sum_probs=65.6

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++|||+||+++++++||+++|++||.|++|++..+     +||||+|.+.++|++|++.|||..|.  |+.|+|.|.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~lng~~~~--g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-----GMGMVEYLRKEDMEYALRKLDDTKFR--SHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT-----TEEEEEESSHHHHHHHHHHHSSEEEE--CTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhccccccccccc-----ceEEEEECCHHHHHHHHHHhCCCEeC--CeEEEEEEE
Confidence            45678999999999999999999999999999998632     39999999999999999999999995  777888875

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.5e-21  Score=129.18  Aligned_cols=79  Identities=18%  Similarity=0.303  Sum_probs=70.1

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +.++||||+||+.++++++|+++|++||.|.++.+..+.  +..++||||+|.+.++|++|++.|||..|.  |+.|+|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~--g~~l~V~   93 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY--GKILVIE   93 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCS--SCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            346899999999999999999999999999988887653  334459999999999999999999999994  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        94 ~ak   96 (102)
T d2cpxa1          94 FGK   96 (102)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            985

>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=99.82  E-value=7.9e-21  Score=125.83  Aligned_cols=77  Identities=14%  Similarity=0.126  Sum_probs=67.1

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ..+.++|||+||+.++++++|+++|++||.|..++.   .+..++||||+|.+.++|++|++.|||..|+  |+.|+|+|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~---~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~--gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ---DGKSKGIAYIEFKSEADAEKNLEEKQGAEID--GRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE---TTEEEEEEEEEESSHHHHHHHHHHTTEEEET--TEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee---cCccccEEEEEeCCHHHHHHHHHHcCCCEEC--CEEEEEEE
Confidence            345789999999999999999999999998876643   2334459999999999999999999999995  89999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        88 a~   89 (96)
T d1fjca_          88 TG   89 (96)
T ss_dssp             CS
T ss_pred             eC
Confidence            75

>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=99.82  E-value=5.5e-21  Score=122.17  Aligned_cols=72  Identities=14%  Similarity=0.215  Sum_probs=64.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      +|||||||+++||++|+++|++||.|+++++.+|+.++  ++||||+|.+.++|++|++ +||..++  |+.|+|..
T Consensus         2 klfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~--Gr~i~V~~   75 (77)
T d1uawa_           2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELD--SKTIDPKV   75 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCS--SCCCEEEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEEC--CeEEEEEE
Confidence            69999999999999999999999999999999886544  3499999999999999996 7999995  77787765

>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=99.82  E-value=3.6e-20  Score=120.28  Aligned_cols=77  Identities=17%  Similarity=0.213  Sum_probs=67.7

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +.|||||+|||.++|+++|+++|++||.|.+|++..+..+ .++||||+|.+.++|++|++ +||..|  .|+.|+|.|+
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~--~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKY--KETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEE--TTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEE--CCEEEEEEEc
Confidence            3589999999999999999999999999999999876432 23499999999999999995 799999  4889999886


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        82 ~   82 (85)
T d1zh5a2          82 D   82 (85)
T ss_dssp             G
T ss_pred             C
Confidence            3

>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=99.82  E-value=6.3e-21  Score=119.85  Aligned_cols=69  Identities=17%  Similarity=0.249  Sum_probs=61.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      |||+|||.++|+++|+++|++||.|.++++.+++.++  ++||||+|.+.++|++|++.|||..|.  |+.||
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~--Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ--AQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCC--EESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEEC--CEECc
Confidence            7999999999999999999999999999998875443  349999999999999999999999994  65553

>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=99.81  E-value=7.9e-21  Score=123.78  Aligned_cols=69  Identities=14%  Similarity=0.069  Sum_probs=62.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      +|||||||.++++++|+++|++||.|.++++..+     +||||+|.+.++|++||+.|||..|.  |+.|+|++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~--g~~i~v~~~   70 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFR--SHEGETAYI   70 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCC--CTTSCCCBC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-----ceeeEEeCCHHHHHHHHHHhCCCEEC--CcEeEEeEE
Confidence            6999999999999999999999999999998543     39999999999999999999999995  777776653

>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=99.81  E-value=9.2e-20  Score=115.74  Aligned_cols=69  Identities=17%  Similarity=0.293  Sum_probs=61.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           67 LFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        67 LfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      |||||||.+++++||+++|++|| +..+++..    .++||||+|.+.++|++|++.|||..+.  |+.|+|+|+.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~----~~g~afv~f~~~~~A~~Ai~~ln~~~~~--g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK----YKGTAFVTLLNGEQAEAAINTFHQSRLR--ERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTEESS--SCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc----cceeEEEEECCHHHHHHHHHHhCCccCC--CCEEEEEEeC
Confidence            79999999999999999999999 56655533    2349999999999999999999999994  8999999974

>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=99.81  E-value=2e-20  Score=122.76  Aligned_cols=76  Identities=20%  Similarity=0.297  Sum_probs=66.2

Q ss_pred             cceEEEcCCCCCCCHHHHHH----HhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           64 VRTLFVAGLPEDVKPREIYN----LFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~----~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      ++|||||||+.+++++||++    +|++||.|.+|++..+. ..++||||+|++.++|.+|++.|||..++  |+.|+|+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~-~~~g~afV~F~~~~~A~~A~~~~~~~~~~--g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL-KMRGQAFVIFKEVSSATNALRSMQGFPFY--DKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHH-HHTTCEEEEESSHHHHHHHHHHHTTCEET--TEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeec-cCCCceEEEECCHHHHHHHHHHhCCCEEC--CEEEEEE
Confidence            58999999999999999864    68999999999875432 23449999999999999999999999995  8999999


Q ss_pred             eec
Q 032280          140 HSM  142 (144)
Q Consensus       140 ~s~  142 (144)
                      |+.
T Consensus        80 ~ak   82 (91)
T d1nu4a_          80 YAK   82 (91)
T ss_dssp             ECS
T ss_pred             EeC
Confidence            985

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.2e-19  Score=121.47  Aligned_cols=77  Identities=25%  Similarity=0.325  Sum_probs=65.3

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-C--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-N--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ...+||||+||+++++|++|+++|++|| +++++++.+.. +  .++||||+|.+.++|++|+ .|||..|+  |+.|+|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~--gr~l~V   88 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NKRIRV   88 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEET--TEECEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEEC--CEEEEE
Confidence            3458999999999999999999999998 77888776532 2  2349999999999998776 69999995  889999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      +|+.
T Consensus        89 ~~a~   92 (104)
T d1wi8a_          89 DVAD   92 (104)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9874

>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=4.4e-20  Score=122.09  Aligned_cols=78  Identities=18%  Similarity=0.162  Sum_probs=67.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCC-eEEEEEeecC---CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPG-YESSHLRSST---QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~-v~~v~l~~~~---~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+|||||||.++++++|+++|++||. |.++++..+.   +..++||||+|++.++|.+|++.|++..+...|+.|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            36999999999999999999999995 8999987663   3344599999999999999999998766633588999999


Q ss_pred             ec
Q 032280          141 SM  142 (144)
Q Consensus       141 s~  142 (144)
                      +.
T Consensus        82 A~   83 (96)
T d2disa1          82 AE   83 (96)
T ss_dssp             SC
T ss_pred             cC
Confidence            75

>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=99.80  E-value=1.5e-19  Score=120.47  Aligned_cols=76  Identities=12%  Similarity=0.106  Sum_probs=66.8

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHH--HhcCCccCCCCCeEE
Q 032280           61 YDEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMY--ALNNFAPSDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~--~lnG~~~~~~g~~l~  137 (144)
                      ...+++|||+|||.+ +|+++|+++|++||.|.++++..+++    ||||+|++.++|.+|++  .+|+..|  .|+.|+
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~----~afV~f~~~~~A~~Ai~~~~~~~~~~--~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS----QAFIEMETREDAMAMVDHCLKKALWF--QGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTT----EEEEECSSHHHHHHHHHHHHHSCCCS--SSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCC----cEEEEecchHHHHHHHHHHhcCCceE--CCEEEE
Confidence            355789999999985 89999999999999999999976543    99999999999999998  5677788  489999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+||.
T Consensus        89 V~~s~   93 (99)
T d1x4fa1          89 VDLSE   93 (99)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            99985

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.3e-19  Score=121.18  Aligned_cols=79  Identities=16%  Similarity=0.172  Sum_probs=66.6

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC-CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN-SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~-~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .....+|||+|||+++||+||+++|+.|| +++|+++.+..+ .++||||+|++.++|++|++ |||..|.  |+.|+|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~--gR~I~V~   87 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQ--HRYVELF   87 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSS--SSCCEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEEC--CEEEEEE
Confidence            35567999999999999999999999997 457777776443 34499999999999999985 8999995  8889999


Q ss_pred             eecC
Q 032280          140 HSMA  143 (144)
Q Consensus       140 ~s~~  143 (144)
                      |+..
T Consensus        88 ~s~~   91 (102)
T d1weza_          88 LNST   91 (102)
T ss_dssp             EECC
T ss_pred             EcCC
Confidence            8753

>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=99.80  E-value=5.7e-20  Score=120.37  Aligned_cols=76  Identities=11%  Similarity=0.048  Sum_probs=67.1

Q ss_pred             CCCcceEEEcCCCCC-CCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHh--cCCccCCCCCeEE
Q 032280           61 YDEVRTLFVAGLPED-VKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYAL--NNFAPSDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~-vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~l--nG~~~~~~g~~l~  137 (144)
                      .+.+|+|||+||+.. +|++||+++|+.||.|.+|.+..+++    +|||+|++.++|.+|++.|  ++..+  .|+.|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~----~afV~f~~~~~A~~A~~~l~~~~~~~--~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN----EAFIEMATTEDAQAAVDYYTTTPALV--FGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSS----CEEEEESSHHHHHHHHHHHHHSCCEE--TTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccce----EEEEEEcchhhHHHHHHHHhhCCCcc--CCceEE
Confidence            467899999999996 88999999999999999999976543    9999999999999999977  45667  599999


Q ss_pred             EEeec
Q 032280          138 FPHSM  142 (144)
Q Consensus       138 v~~s~  142 (144)
                      |+||.
T Consensus        79 V~~s~   83 (89)
T d1x4da1          79 VHLSQ   83 (89)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            99985

>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=99.79  E-value=5e-19  Score=118.59  Aligned_cols=81  Identities=16%  Similarity=0.055  Sum_probs=66.8

Q ss_pred             CCCCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           59 GSYDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        59 ~~~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ++..+..+|||+|||+++||+||+++|+.+|.+..+.++.+...+  ++||||+|.+.++|++|++ +||..|.  |+.|
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~--gR~i   86 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIG--HRYI   86 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSS--SSCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEc--ceEE
Confidence            344556689999999999999999999999998876555543333  3499999999999999995 9999994  8889


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|.++.
T Consensus        87 ~V~~~~   92 (104)
T d1wg5a_          87 EIFKSS   92 (104)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            998764

>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=99.79  E-value=4.2e-20  Score=120.53  Aligned_cols=74  Identities=18%  Similarity=0.271  Sum_probs=64.2

Q ss_pred             CCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           62 DEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        62 ~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ...++||||||++++||++|+++|++||.|.+|++..   ..++||||+|++.++|++|++  ||..|+  |+.|+|+|+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~---~~~gfafV~f~~~~~a~~a~~--~~~~i~--g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK---PFRAFAFVTFADDQIAQSLCG--EDLIIK--GISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS---SCCSCCEEECSCHHHHHHTTT--CEEEET--TEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee---ccCceEEEEECCHHHHHHHHh--CCCEEC--CEEeEEEeC
Confidence            4568999999999999999999999999999988643   233499999999999999984  788884  899999987


Q ss_pred             c
Q 032280          142 M  142 (144)
Q Consensus       142 ~  142 (144)
                      .
T Consensus        76 ~   76 (88)
T d1wf0a_          76 E   76 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.79  E-value=5.5e-20  Score=116.95  Aligned_cols=71  Identities=21%  Similarity=0.315  Sum_probs=61.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCC--CcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           66 TLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNS--QPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        66 tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~--~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      +||||||++++|+++|+++|++||.|++|++..++.++  ++||||+|++.++|++|++ +++..++  |+.|+|.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~--g~~i~vk   73 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVG--LSKCEIK   73 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBT--TBCCEEE
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEEC--CEEeEEE
Confidence            59999999999999999999999999999998886543  4499999999999999996 4777775  6666664

>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=99.77  E-value=3.4e-19  Score=115.35  Aligned_cols=76  Identities=17%  Similarity=0.187  Sum_probs=63.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEE-EEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYES-SHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~-v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...+|||+|||++++++||+++|+.||.+.. +.+..+.. ..++||||+|.+.++|++|++.|||..+.  |+.|+|++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~--gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIG--SRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEET--TEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEEC--CEEEEEEE
Confidence            3467999999999999999999999999866 34444432 22349999999999999999999999994  88888875

>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=99.75  E-value=2.9e-19  Score=120.25  Aligned_cols=75  Identities=17%  Similarity=0.097  Sum_probs=65.5

Q ss_pred             CCcceEEEcCCCCCC-CH----HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeE
Q 032280           62 DEVRTLFVAGLPEDV-KP----REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSL  136 (144)
Q Consensus        62 ~~~~tLfVgnLp~~v-te----~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l  136 (144)
                      ....+|||+||+.++ ++    ++|+++|++||.|+++++.++++    ||||+|++.++|.+|++.|||..|.  |+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~----~afV~f~~~~~A~~Ai~~lng~~~~--g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK----RVRINFSNPLSAADARLRLHKTEFL--GKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT----EEEEECSSTTHHHHHHHTSTTSEET--TEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCC----EEEEEECCHHHHHHHHHHhcccccC--CCEe
Confidence            346789999999987 33    56999999999999999975433    9999999999999999999999994  8999


Q ss_pred             EEEeec
Q 032280          137 LFPHSM  142 (144)
Q Consensus       137 ~v~~s~  142 (144)
                      +|+|+.
T Consensus        77 ~v~~a~   82 (104)
T d1weya_          77 KLYFAQ   82 (104)
T ss_dssp             EEECCC
T ss_pred             EEeecc
Confidence            999975

>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=99.75  E-value=1.4e-18  Score=116.18  Aligned_cols=74  Identities=15%  Similarity=0.232  Sum_probs=62.3

Q ss_pred             CCCcceEEE--cCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeEE
Q 032280           61 YDEVRTLFV--AGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAP-SDSACSLL  137 (144)
Q Consensus        61 ~~~~~tLfV--gnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l~  137 (144)
                      ....++|||  |||+.++||++|+++|++||.|++|++..+++    ||||+|++.++|.+|++.|||+.+ ++.+..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~----~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i~   90 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP----YSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCS----CEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCcc----EEEEEECCHHHHHHHHHHhCCCCCCCCCCcEEE
Confidence            345678999  55999999999999999999999998865433    999999999999999999999988 54455443


Q ss_pred             E
Q 032280          138 F  138 (144)
Q Consensus       138 v  138 (144)
                      +
T Consensus        91 ~   91 (101)
T d2cq2a1          91 L   91 (101)
T ss_dssp             C
T ss_pred             E
Confidence            3

>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=99.75  E-value=1e-18  Score=116.67  Aligned_cols=76  Identities=11%  Similarity=0.143  Sum_probs=63.6

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEE-EEeecC-CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESS-HLRSST-QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v-~l~~~~-~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      ...+|||+|||+++|+++|+++|+.||.+..+ .+..+. +..++||||+|.+.++|++|++ |||..|.  |+.|+|.+
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~--gr~i~V~~   83 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLN--GREAFVHV   83 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEET--TEEEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeEC--CcEEEEEE
Confidence            34689999999999999999999999998764 444432 2334599999999999999995 9999994  88999987


Q ss_pred             e
Q 032280          141 S  141 (144)
Q Consensus       141 s  141 (144)
                      +
T Consensus        84 ~   84 (103)
T d2cpya1          84 V   84 (103)
T ss_dssp             E
T ss_pred             C
Confidence            5

>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=99.72  E-value=7.2e-18  Score=114.36  Aligned_cols=78  Identities=13%  Similarity=0.160  Sum_probs=63.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCC--CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQN--SQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~--~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      .....+|||+|||+++|++||+++|+.||.+..+.++.+...  ..+||||+|.+.++|++|++ |||..|.  |+.|+|
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~--gR~i~V   91 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMG--NRFIQV   91 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCST--TSCBEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCC--CEEEEE
Confidence            345679999999999999999999999999866544433333  33499999999999999995 9999995  788888


Q ss_pred             Eee
Q 032280          139 PHS  141 (144)
Q Consensus       139 ~~s  141 (144)
                      ..+
T Consensus        92 ~~~   94 (112)
T d1wela1          92 HPI   94 (112)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            764

>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=99.71  E-value=5.6e-20  Score=120.14  Aligned_cols=73  Identities=19%  Similarity=0.303  Sum_probs=60.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEee-----cC--CCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEE
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRS-----ST--QNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLL  137 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~-----~~--~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~  137 (144)
                      |+||||||+.++||++|+++|++||.+.++.+..     +.  ...++||||+|++.++|++|+ .|||..|.  |+.|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~--Gr~l~   78 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQ--GQSLK   78 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSS--SSCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEEC--CEEEE
Confidence            7899999999999999999999999887665532     11  233459999999999999998 59999995  78888


Q ss_pred             EEe
Q 032280          138 FPH  140 (144)
Q Consensus       138 v~~  140 (144)
                      |..
T Consensus        79 V~r   81 (90)
T d1u2fa_          79 IRR   81 (90)
T ss_dssp             CBC
T ss_pred             ECC
Confidence            864

>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=3.7e-17  Score=117.86  Aligned_cols=79  Identities=18%  Similarity=0.321  Sum_probs=69.7

Q ss_pred             CCCcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCC--cEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEE
Q 032280           61 YDEVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQ--PFAFAVFSDQQSALGAMYALNNFAPSDSACSLLF  138 (144)
Q Consensus        61 ~~~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~--~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v  138 (144)
                      ....++|||+||+.++++++|+++|+.||.|..+.+..+..++.  +||||+|.+.++|++|++ ++|..+  +|+.|+|
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~--~G~~i~V  170 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTV--NGHNCEV  170 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEE--TTEEEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeE--CCEEEEE
Confidence            45568999999999999999999999999999999998765444  399999999999999996 799888  4899999


Q ss_pred             Eeec
Q 032280          139 PHSM  142 (144)
Q Consensus       139 ~~s~  142 (144)
                      .|++
T Consensus       171 ~~A~  174 (183)
T d1u1qa_         171 RKAL  174 (183)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9864

>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=99.70  E-value=6.5e-17  Score=109.83  Aligned_cols=74  Identities=14%  Similarity=0.110  Sum_probs=62.9

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCH-HHHHHHHHHhcCCccCCCCCeEEEEe
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQ-QSALGAMYALNNFAPSDSACSLLFPH  140 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~-~~A~~A~~~lnG~~~~~~g~~l~v~~  140 (144)
                      .+..+|||||+.++|+++|+++|++||.|.+|+++.++    +||||.|.+. ++|..|++.|||..+.+++..+.+.+
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~k----g~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA----KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC----SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCC----ceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            36678999999999999999999999999999997543    3999999984 78999999999999965565555544

>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=99.66  E-value=5.3e-18  Score=113.95  Aligned_cols=75  Identities=11%  Similarity=0.025  Sum_probs=67.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCC-CCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEee
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQ-NSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHS  141 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~-~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s  141 (144)
                      ..++|+++..+++|++|+++|++||.|++|+|..+.. ..++||||+|++.++|.+|++.|||+.|+  |+.|+|+||
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~--gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN--GQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEET--TEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEEC--CEEEEEEEC
Confidence            4688999999999999999999999999999976633 23449999999999999999999999995  999999997

>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=99.60  E-value=1.9e-15  Score=108.72  Aligned_cols=65  Identities=17%  Similarity=0.336  Sum_probs=57.3

Q ss_pred             CcceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc--EEEEEeCCHHHHHHHHHHhcCC
Q 032280           63 EVRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP--FAFAVFSDQQSALGAMYALNNF  127 (144)
Q Consensus        63 ~~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~--~aFV~F~~~~~A~~A~~~lnG~  127 (144)
                      ..||||||||+.++|+++|+++|++||.|.++.++++..++..  ||||+|.+.++|.+|++.+++.
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~   71 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHK   71 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCc
Confidence            4589999999999999999999999999999999987555443  9999999999999999765544

>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=99.56  E-value=4.4e-15  Score=98.50  Aligned_cols=76  Identities=13%  Similarity=0.092  Sum_probs=63.9

Q ss_pred             CCcceEEEcCC--CCCCC---------HHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           62 DEVRTLFVAGL--PEDVK---------PREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        62 ~~~~tLfVgnL--p~~vt---------e~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      ...++|+|.||  +.++.         ++||++.|++||.|.+|++..+.  .++||||+|++.++|.+|++.|||..|+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~--~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC--TTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC--CccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            45789999999  54432         26799999999999999886543  3459999999999999999999999995


Q ss_pred             CCCCeEEEEee
Q 032280          131 DSACSLLFPHS  141 (144)
Q Consensus       131 ~~g~~l~v~~s  141 (144)
                        |+.|+|+|-
T Consensus        84 --gr~i~v~~~   92 (99)
T d2dita1          84 --GRQITAQAW   92 (99)
T ss_dssp             --TEECEEEEC
T ss_pred             --CEEEEEEEe
Confidence              899999974

>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=99.53  E-value=9.2e-15  Score=93.75  Aligned_cols=61  Identities=10%  Similarity=0.086  Sum_probs=52.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccC
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPS  130 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~  130 (144)
                      .+.|+|++|+.+.+++.| +.|++||.|.++++..+    ++||||+|++.++|++|++ +||..|.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~----~~~~fV~f~~~~~A~~Al~-~nG~~~~   64 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT----GNWMHIRYQSKLQARKALS-KDGRIFG   64 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS----SSEEEEEESSHHHHHHHHT-TTTCEET
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC----CCEEEEEEcccHHHHHHHh-cCCCeEC
Confidence            467999999999987655 57999999999987433    3399999999999999995 9999994

>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=99.48  E-value=3.1e-14  Score=95.00  Aligned_cols=77  Identities=12%  Similarity=0.117  Sum_probs=63.7

Q ss_pred             CcceEEEcCC--CCCCC--------HHHHHHHhhcCCCeEEEEEeecCCC----CCcEEEEEeCCHHHHHHHHHHhcCCc
Q 032280           63 EVRTLFVAGL--PEDVK--------PREIYNLFREFPGYESSHLRSSTQN----SQPFAFAVFSDQQSALGAMYALNNFA  128 (144)
Q Consensus        63 ~~~tLfVgnL--p~~vt--------e~~L~~~F~~~G~v~~v~l~~~~~~----~~~~aFV~F~~~~~A~~A~~~lnG~~  128 (144)
                      .+++|.|.||  +.++.        .+||++.|++||.|++|.+.++...    ..+++||+|++.++|.+|++.|||+.
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3688999999  55443        3568999999999999998765332    22499999999999999999999999


Q ss_pred             cCCCCCeEEEEee
Q 032280          129 PSDSACSLLFPHS  141 (144)
Q Consensus       129 ~~~~g~~l~v~~s  141 (144)
                      |+  |+.|+++|.
T Consensus        83 f~--gR~v~v~f~   93 (104)
T d1o0pa_          83 FA--NRVVVTKYC   93 (104)
T ss_dssp             SS--SSCCEEEEE
T ss_pred             EC--CeEEEEEEc
Confidence            95  899999885

>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=98.33  E-value=4.1e-06  Score=53.72  Aligned_cols=76  Identities=11%  Similarity=0.209  Sum_probs=61.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCc----EEEEEeCCHHHHHHHHHHhcCCcc-CCCCCeE--E
Q 032280           65 RTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQP----FAFAVFSDQQSALGAMYALNNFAP-SDSACSL--L  137 (144)
Q Consensus        65 ~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~----~aFV~F~~~~~A~~A~~~lnG~~~-~~~g~~l--~  137 (144)
                      .+|-|++||.++||+++.+.++..|++.-......+.+.+.    .|||.|.+.++...-.+.++|..| |++|..-  .
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            46889999999999999999999999887776654333222    899999999999999999999999 6566543  3


Q ss_pred             EEe
Q 032280          138 FPH  140 (144)
Q Consensus       138 v~~  140 (144)
                      ||+
T Consensus        82 VE~   84 (91)
T d1uw4a_          82 VEF   84 (91)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            444

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=3.5e-05  Score=49.07  Aligned_cols=52  Identities=12%  Similarity=0.236  Sum_probs=44.6

Q ss_pred             HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEE
Q 032280           79 REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFP  139 (144)
Q Consensus        79 ~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~  139 (144)
                      .+|-+.|.+||+|.-+|++.+      -..|+|.|-++|.+|+ .++|.++  +|++|+|.
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d------~mwVTF~dG~SAL~al-~l~g~~v--~G~~l~It   90 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG------QMLVTFADSHSALSVL-DVDGMKV--KGRAVKIS   90 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT------EEEEECSCSHHHHHHH-HGGGSEE--TTEEEEEE
T ss_pred             HHHHHHHhhCCeEEEEEEeCC------eEEEEECCcHHHHHHh-ccCCeEE--cceEEEEe
Confidence            357788999999998888643      5799999999999998 7999999  58888875

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.39  E-value=0.00044  Score=41.83  Aligned_cols=65  Identities=18%  Similarity=0.251  Sum_probs=52.1

Q ss_pred             CCCHHH----HHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCCeEEEEeec
Q 032280           75 DVKPRE----IYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNFAPSDSACSLLFPHSM  142 (144)
Q Consensus        75 ~vte~~----L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~~~~~~g~~l~v~~s~  142 (144)
                      .++++|    |.++|+++|.|.++.+....++. ..|-|.-.+..+|..|+..|+-.++.  ++.|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg~-~~A~V~v~~~q~A~~~v~~LhR~KiG--~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ-LKAVVQMENLQDAIGAVNSLHRYKIG--SKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTT-CCEEEEESSHHHHHHHHHHHTTEEET--TEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCCc-EEEEEEcCCHHHHHHHHHHHHHHhcC--CeEEEEEEec
Confidence            345555    55688999999999986544332 38999999999999999999999994  7788888764

>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=95.72  E-value=0.039  Score=34.98  Aligned_cols=56  Identities=18%  Similarity=0.285  Sum_probs=45.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           64 VRTLFVAGLPEDVKPREIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        64 ~~tLfVgnLp~~vte~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ...||.-..|......||.++|+.||.|.- ..+ |..    -|||.-.+.++|..+++.++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swI-ddT----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWI-DDT----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEE-ETT----EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEE-EEe-cCc----eEEEEecCHHHHHHHHHHhc
Confidence            346888899999999999999999998743 333 222    69999999999999987765

>d1oj4a2 d.58.26.5 (A:164-283) 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: GHMP Kinase, C-terminal domain
family: 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE
domain: 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE
species: Escherichia coli [TaxId: 562]

Probab=89.83  E-value=0.39  Score=30.71  Aligned_cols=39  Identities=21%  Similarity=0.284  Sum_probs=28.8

Q ss_pred             HHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhc
Q 032280           80 EIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALN  125 (144)
Q Consensus        80 ~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~ln  125 (144)
                      ++++.++++|.   +++   .+ +++.+|..|+|.++|.+|.+.+.
T Consensus        61 ~~~~~L~~~g~---~~M---SG-SGstvF~~f~~~~~a~~~~~~l~   99 (120)
T d1oj4a2          61 AVLSWLLEYAP---SRL---TG-TGACVFAEFDTESEARQVLEQAP   99 (120)
T ss_dssp             HHHHHHTTTSC---EEE---CT-TSSCEEEEESSHHHHHHHHHHSC
T ss_pred             HHHHHHhhccc---cee---cC-CCCEEEEEeCCHHHHHHHHHHcC
Confidence            45666678885   333   23 33389999999999999999885

>d1ueka2 d.58.26.5 (A:149-268) 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: GHMP Kinase, C-terminal domain
family: 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE
domain: 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE
species: Thermus thermophilus [TaxId: 274]

Probab=87.82  E-value=0.8  Score=28.80  Aligned_cols=44  Identities=18%  Similarity=0.155  Sum_probs=31.9

Q ss_pred             HHHHHHhhcCCCeEEEEEeecCCCCCcEEEEEeCCHHHHHHHHHHhcCC
Q 032280           79 REIYNLFREFPGYESSHLRSSTQNSQPFAFAVFSDQQSALGAMYALNNF  127 (144)
Q Consensus        79 ~~L~~~F~~~G~v~~v~l~~~~~~~~~~aFV~F~~~~~A~~A~~~lnG~  127 (144)
                      +++++.+.++|.. .+.+    .++++..|..|++.++|++|.+.|...
T Consensus        66 ~~~~~~l~~~g~~-~~~m----SGSGst~F~l~~~~~~a~~~~~~l~~~  109 (120)
T d1ueka2          66 KEVRGRMRALGLR-GVLM----SGSGSAFFGLAEGPDHARRAAEALRAW  109 (120)
T ss_dssp             HHHHHHHHHTTCE-EEEE----CTTSSCEEEECSSHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHhhhh-heee----cCCCCeEEEEeCCHHHHHHHHHHHHHh
Confidence            4566667788763 3444    223348999999999999999998754