Psyllid ID: psy2347

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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-------150-------160-------170-------180-------190-------200-------
Protein Sequence
MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYNVDEY
Secondary Structure (PSIPRED)
ccccccccccEEEEccccccccHHHHHHHHHHcccccEEEEccccccEEEEEEccHHHHHHHHHHcccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEccccccccHHHHHHHHHHccccEEEEcccccccEEEEEEccHccHHHHHHcccccEEccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccEEEcccccc
Coil and Loop (DISEMBL)
msdgmmergtrVYVGGLTETVKKEDLELEFEKFGKLNSVWvafnppgfafvefsNQIDaeaacdsmndqdlmgsKLRVEISrgrgrgrggggrggrfdsrggrggyrgggggyggggyrdggdrfggggrgrgdggfrgsrggggyrggrdeygggrggggyrggrdsrgfdggkpdyyngggggrggggrfrsrspvqrrynvdey
Flexible Loop (DISEMBL)
msdgmmergtrvyvggltetvkkEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRveisrgrgrgrggggrggrfdsrggrggyrgggggyggggYRDGGDRFGGggrgrgdggfrgsrggggyrggrdeygggrggggyrggrdsrgfdGGKPDYyngggggrggggrfrsrspvqrrynvdey
Low Complexity Region (SEG)
MSDGMMERGTRVYVGGLTETVkkedlelefekfgklNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIsrgrgrgrggggrggrfdsrggrggyrgggggyggggyrdggdrfggggrgrgdggfrgsrggggyrggrdeygggrggggyrggrdsrgfdggKPDYYNgggggrggggrFRSRSPVQRRYNVDEY
Disordered region (IsUnstruct)
**********RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAE***************************************************************************************************************************************************
Disordered Region (DISOPRED)
*************VGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK************************************************************************************************************************************
Disordered Region (DISEMBL)
MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG************RFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYNVDEY
Disordered Region (DISPRO)
********GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR*************************************D**********************************GGRGG*******D***FDGGKPD*************RFRSRSPVQRRYN****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQRRYNVDEY
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	207	2.2.26 [Sep-21-2011]
Q24491	197	RNA-binding protein Rsf1	yes	N/A	0.367	0.385	0.710	2e-27
Q69KL9	185	Serine/arginine-rich spli	yes	N/A	0.415	0.464	0.467	4e-12
Q02427	144	RNA-binding protein 1 OS=	no	N/A	0.347	0.5	0.458	1e-10
Q18409	179	Probable splicing factor,	yes	N/A	0.342	0.396	0.450	3e-10
O81126	200	Serine/arginine-rich spli	yes	N/A	0.280	0.29	0.465	2e-08
Q9SJA6	196	Serine/arginine-rich spli	no	N/A	0.256	0.270	0.509	3e-08
Q7SXP4	257	Serine/arginine-rich spli	no	N/A	0.357	0.287	0.368	0.0001
P60825	172	Cold-inducible RNA-bindin	no	N/A	0.410	0.494	0.333	0.0001
P60824	172	Cold-inducible RNA-bindin	no	N/A	0.410	0.494	0.333	0.0001
P60826	172	Cold-inducible RNA-bindin	no	N/A	0.410	0.494	0.333	0.0001

>sp|Q24491|RX21_DROME RNA-binding protein Rsf1 OS=Drosophila melanogaster GN=Rsf1 PE=1 SV=1

 Score =  122 bits (306), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 54/76 (71%), Positives = 66/76 (86%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          +RGTRVYVG LT+ VKK+DLE EF K+GKLNSVW+AFNPPGFAFVEF ++ DAE ACD +
Sbjct: 4  QRGTRVYVGNLTDKVKKDDLEGEFTKYGKLNSVWIAFNPPGFAFVEFEHRDDAEKACDIL 63

Query: 67 NDQDLMGSKLRVEISR 82
          N  +L+GS+LRVEIS+
Sbjct: 64 NGSELLGSQLRVEISK 79

May control important aspects of development.
Drosophila melanogaster (taxid: 7227)

>sp|Q69KL9|RZ21A_ORYSJ Serine/arginine-rich splicing factor RSZ21A OS=Oryza sativa subsp. japonica GN=RSZ21A PE=2 SV=1

 Score = 71.2 bits (173), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 43/92 (46%), Positives = 54/92 (58%), Gaps = 6/92 (6%)

Query: 10  TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
            RVYVG L   V   +LE EF  FG L SVWVA  PPGFAF++F ++ DA+ A      +
Sbjct: 2   ARVYVGNLDPRVTARELEDEFRVFGVLRSVWVARKPPGFAFIDFDDRRDAQDAI-----R 56

Query: 70  DLMGSK-LRVEISRGRGRGRGGGGRGGRFDSR 100
           D+ G    RVE+SR    GRGG  R G  +S+
Sbjct: 57  DIDGKNGWRVELSRNASSGRGGRDRYGSSESK 88

Involved in pre-mRNA splicing.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q02427|RBP1_DROME RNA-binding protein 1 OS=Drosophila melanogaster GN=Rbp1 PE=2 SV=3

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 33/72 (45%), Positives = 48/72 (66%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
            +VYVG L  +  K ++E  F K+G L +VWVA NPPGFAFVEF ++ DAE A  +++ 
Sbjct: 10 ACKVYVGNLGSSASKHEIEGAFAKYGPLRNVWVARNPPGFAFVEFEDRRDAEDATRALDG 69

Query: 69 QDLMGSKLRVEI 80
              G+++RVE+
Sbjct: 70 TRCCGTRIRVEM 81

Contributes to the activation of female-specific DSX splicing in vivo by recognizing the RBP1 target sequences within the purine-rich polypyrimidine tract of the female-specific 3' splice site.

Drosophila melanogaster (taxid: 7227)

>sp|Q18409|RSP6_CAEEL Probable splicing factor, arginine/serine-rich 6 OS=Caenorhabditis elegans GN=rsp-6 PE=3 SV=1

 Score = 65.1 bits (157), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/71 (45%), Positives = 47/71 (66%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +VYVGGL      ++LE  F++FG++  VWVA  PPGFAFVE+ +  DAE A  +++   
Sbjct: 4  KVYVGGLPSDATSQELEEIFDRFGRIRKVWVARRPPGFAFVEYDDVRDAEDAVRALDGSR 63

Query: 71 LMGSKLRVEIS 81
          + G + RVE+S
Sbjct: 64 ICGVRARVELS 74

Plays a functionally redundant role in shifting germ cell sexual differentiation in hermaprodites. Required for the development of somatic gonad structures and for progression from larval stage to adulthood.

Caenorhabditis elegans (taxid: 6239)

>sp|O81126|RZP22_ARATH Serine/arginine-rich splicing factor RSZ22 OS=Arabidopsis thaliana GN=RSZ22 PE=1 SV=1

 Score = 59.3 bits (142), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/58 (46%), Positives = 38/58 (65%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +RVYVG L   V + +LE EF  FG + SVWVA  PPG+AF++F +  DA  A  +++
Sbjct: 2  SRVYVGNLDPRVTERELEDEFRAFGVVRSVWVARRPPGYAFLDFEDPRDARDAIRALD 59

Sequence-specific RNA-binding protein probably involved in pre-mRNA splicing. In vitro, can complement efficiently splicing-deficient mammalian SRSF7-depleted HeLa cell extract.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJA6|RZ22A_ARATH Serine/arginine-rich splicing factor RSZ22A OS=Arabidopsis thaliana GN=RSZ22A PE=1 SV=1

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 35/53 (66%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAA 62
          +RVYVG L   V + +LE EF  FG + SVWVA  PPG+AF++F +  DA  A
Sbjct: 2  SRVYVGNLDPRVTERELEDEFRSFGVIRSVWVARRPPGYAFLDFEDSRDARDA 54

Involved in pre-mRNA splicing.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7SXP4|SRS1A_DANRE Serine/arginine-rich splicing factor 1A OS=Danio rerio GN=srsf1a PE=2 SV=2

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP--PGFAFVEFSNQIDAEAACDSMN 67
           R+YVG L   ++ +D+E  F K+G +  + +      P FAFVEF +  DAE A  + +
Sbjct: 15 CRIYVGNLPPDIRTKDVEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYARD 74

Query: 68 DQDLMGSKLRVEISRG 83
            D  G +LRVE  R 
Sbjct: 75 GYDYDGYRLRVEFPRS 90

May play a role in preventing exon skipping, ensuring the accuracy of splicing and regulating alternative splicing.

Danio rerio (taxid: 7955)

>sp|P60825|CIRBP_RAT Cold-inducible RNA-binding protein OS=Rattus norvegicus GN=Cirbp PE=2 SV=1

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 5/90 (5%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
          +++VGGL+    ++ LE  F K+G+++ V V  +       GF FV F N  DA+ A  +
Sbjct: 7  KLFVGGLSFDTNEQALEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 66 MNDQDLMGSKLRVEISRGRGRGRGGGGRGG 95
          MN + + G ++RV+ +      R  G RGG
Sbjct: 67 MNGKSVDGRQIRVDQAGKSSDNRSRGYRGG 96

Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Acts as a translational activator. Seems to play an essential role in cold-induced suppression of cell proliferation. Binds specifically to the 3'-untranslated regions (3'-UTRs) of stress-responsive transcripts RPA2 and TXN. Acts as a translational repressor. Promotes assembly of stress granules (SGs), when overexpressed.

Rattus norvegicus (taxid: 10116)

>sp|P60824|CIRBP_MOUSE Cold-inducible RNA-binding protein OS=Mus musculus GN=Cirbp PE=1 SV=1

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 5/90 (5%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
          +++VGGL+    ++ LE  F K+G+++ V V  +       GF FV F N  DA+ A  +
Sbjct: 7  KLFVGGLSFDTNEQALEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 66 MNDQDLMGSKLRVEISRGRGRGRGGGGRGG 95
          MN + + G ++RV+ +      R  G RGG
Sbjct: 67 MNGKSVDGRQIRVDQAGKSSDNRSRGYRGG 96

Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Promotes assembly of stress granules (SGs), when overexpressed. Seems to play an essential role in cold-induced suppression of cell proliferation. Acts as a translational repressor. Acts as a translational activator. Binds specifically to the 3'-untranslated regions (3'-UTRs) of stress-responsive transcripts RPA2 and TXN.

Mus musculus (taxid: 10090)

>sp|P60826|CIRBP_CRIGR Cold-inducible RNA-binding protein OS=Cricetulus griseus GN=CIRBP PE=2 SV=1

 Score = 46.6 bits (109), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 5/90 (5%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
          +++VGGL+    ++ LE  F K+G+++ V V  +       GF FV F N  DA+ A  +
Sbjct: 7  KLFVGGLSFDTNEQALEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 66 MNDQDLMGSKLRVEISRGRGRGRGGGGRGG 95
          MN + + G ++RV+ +      R  G RGG
Sbjct: 67 MNGKSVDGRQIRVDQAGKSSDNRSRGYRGG 96

Cold-inducible mRNA binding protein that plays a protective role in the genotoxic stress response by stabilizing transcripts of genes involved in cell survival. Acts as a translational activator. Seems to play an essential role in cold-induced suppression of cell proliferation. Binds specifically to the 3'-untranslated regions (3'-UTRs) of stress-responsive transcripts RPA2 and TXN. Acts as a translational repressor. Promotes assembly of stress granules (SGs), when overexpressed.

Cricetulus griseus (taxid: 10029)

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	207
126002576	196	GA19037 [Drosophila pseudoobscura pseudo	0.874	0.923	0.471	8e-31
91080449	185	PREDICTED: similar to conserved hypothet	0.381	0.427	0.759	7e-30
403183501	193	AAEL017030-PA [Aedes aegypti]	0.405	0.435	0.738	2e-29
195119159	196	GI19446 [Drosophila mojavensis] gi|19391	0.874	0.923	0.475	3e-28
312384272	556	hypothetical protein AND_02328 [Anophele	0.400	0.149	0.722	4e-28
170035265	197	conserved hypothetical protein [Culex qu	0.367	0.385	0.736	2e-27
242025305	216	arginine/serine-rich splicing factor, pu	0.357	0.342	0.770	7e-27
322798568	199	hypothetical protein SINV_12527 [Solenop	0.830	0.864	0.487	9e-27
2815290	191	P23 protein [Chironomus tentans] gi|3954	0.376	0.408	0.717	1e-26
380011044	201	PREDICTED: uncharacterized protein LOC10	0.864	0.890	0.513	2e-26

>gi|126002576|ref|XP_001382208.1| GA19037 [Drosophila pseudoobscura pseudoobscura] gi|195146834|ref|XP_002014389.1| GL18979 [Drosophila persimilis] gi|54640338|gb|EAL29321.1| GA19037 [Drosophila pseudoobscura pseudoobscura] gi|194106342|gb|EDW28385.1| GL18979 [Drosophila persimilis]

 Score =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 98/208 (47%), Positives = 116/208 (55%), Gaps = 27/208 (12%)

Query: 1   MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAE 60
           M+    +RGTRVYVG LT+ VKK+DLE EF K+GKLNSVW+AFNPPGFAFVEF ++ DAE
Sbjct: 1   MTSMTDQRGTRVYVGNLTDKVKKDDLEGEFTKYGKLNSVWIAFNPPGFAFVEFEHRDDAE 60

Query: 61  AACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRD 120
            ACD +N  +L+GS+LRVEIS+GR R    GG       RG RG +         GG+R 
Sbjct: 61  KACDILNGSELLGSQLRVEISKGRPRQSRRGGSS----ERGRRGDFGRHSINSSNGGFRQ 116

Query: 121 GGDRFGGGGRGRGDGGFRGSRGGGGYRG---------GRDEYGGGRGGGGYRGGRD-SRG 170
                 G      + G+   R G GY G          RD YGGGR G  Y  G   S G
Sbjct: 117 VRGS-SGSSSRHAERGYSSGRSGAGYSGRDSGSNGFSRRDVYGGGRDGSRYSSGNSTSYG 175

Query: 171 FDGGKPDYYNGGGGGRGGGGRFRSRSPV 198
             GG+            GG RFRSRSPV
Sbjct: 176 RSGGQ------------GGCRFRSRSPV 191

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91080449|ref|XP_969323.1| PREDICTED: similar to conserved hypothetical protein [Tribolium castaneum] gi|270005570|gb|EFA02018.1| hypothetical protein TcasGA2_TC007641 [Tribolium castaneum]

 Score =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 60/79 (75%), Positives = 69/79 (87%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          ER  RVYVGGLT++VKKEDLE EFEK+GKLNSVWVAFNPPGFAF+EF N  DAE+ACDS+
Sbjct: 6  ERSARVYVGGLTDSVKKEDLETEFEKYGKLNSVWVAFNPPGFAFIEFINHSDAESACDSL 65

Query: 67 NDQDLMGSKLRVEISRGRG 85
          N  D +GSKLRVEI+RG+ 
Sbjct: 66 NGTDFLGSKLRVEIARGKS 84

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|403183501|gb|EJY58142.1| AAEL017030-PA [Aedes aegypti]

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 62/84 (73%), Positives = 74/84 (88%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          E+GTRVYVG LT+ VKKEDLE EF K+GKLNSVWVAFNPPGFAF+EF N+ +AE+ACD++
Sbjct: 4  EKGTRVYVGNLTDKVKKEDLEGEFTKYGKLNSVWVAFNPPGFAFIEFENKEEAESACDNL 63

Query: 67 NDQDLMGSKLRVEISRGRGRGRGG 90
          N QD++GSKLRVEIS+GR   RGG
Sbjct: 64 NGQDILGSKLRVEISKGRRNPRGG 87

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195119159|ref|XP_002004099.1| GI19446 [Drosophila mojavensis] gi|193914674|gb|EDW13541.1| GI19446 [Drosophila mojavensis]

 Score =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 99/208 (47%), Positives = 117/208 (56%), Gaps = 27/208 (12%)

Query: 1   MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAE 60
           M+D   +RGTRVYVG LT+ VKK+DLE EF K+GKLNSVW+AFNPPGFAFVEF ++ DAE
Sbjct: 1   MTD---QRGTRVYVGNLTDKVKKDDLEGEFTKYGKLNSVWIAFNPPGFAFVEFEHRDDAE 57

Query: 61  AACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRD 120
            ACD +N  +L+GS+LRVEIS+GR R    GG G     R G  G          GG+R 
Sbjct: 58  KACDILNGSELLGSQLRVEISKGRPRQGRRGGPGE--RGRRGDVGRHSITSSSSNGGFR- 114

Query: 121 GGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDE--YGGGRGGGG--------YRGGRDSRG 170
                    + RG           GY  GR    YGG R GG         Y G R+S  
Sbjct: 115 ---------QQRGSSSSSSRHLDRGYSSGRSSTAYGGARDGGSNGFNRRDIYNGTRESSR 165

Query: 171 FDGGKPDYYNGGGGGRGGGGRFRSRSPV 198
           + GG    Y+  GG    GGRFRSRSPV
Sbjct: 166 YGGGTSSSYSRSGG--QSGGRFRSRSPV 191

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312384272|gb|EFR29035.1| hypothetical protein AND_02328 [Anopheles darlingi]

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 60/83 (72%), Positives = 71/83 (85%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +GTRVYVG LT+ VKKEDLE EF K+GKLNSVWVAFNPPGFAF+EF N+ +AE ACD++N
Sbjct: 5  KGTRVYVGNLTDKVKKEDLEGEFTKYGKLNSVWVAFNPPGFAFIEFENKDEAETACDNLN 64

Query: 68 DQDLMGSKLRVEISRGRGRGRGG 90
           QD++GSKLRVEIS+GR   RG 
Sbjct: 65 GQDILGSKLRVEISKGRRNPRGA 87

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170035265|ref|XP_001845491.1| conserved hypothetical protein [Culex quinquefasciatus] gi|167877141|gb|EDS40524.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 56/76 (73%), Positives = 69/76 (90%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          ++GTRVYVG LT+ VKKEDLE EF K+GKLNSVWVAFNPPGFAF+EF N+ +AE+ACD++
Sbjct: 4  QKGTRVYVGNLTDKVKKEDLEGEFTKYGKLNSVWVAFNPPGFAFIEFENKEEAESACDNL 63

Query: 67 NDQDLMGSKLRVEISR 82
          N QD++GSKLRVEIS+
Sbjct: 64 NGQDILGSKLRVEISK 79

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242025305|ref|XP_002433066.1| arginine/serine-rich splicing factor, putative [Pediculus humanus corporis] gi|212518582|gb|EEB20328.1| arginine/serine-rich splicing factor, putative [Pediculus humanus corporis]

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 57/74 (77%), Positives = 66/74 (89%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          +RGTRVYVGGL++  KKEDLE EFEKFGKLN+VWVAFNPPGFAF+EFSN+ DAE ACDSM
Sbjct: 15 QRGTRVYVGGLSQGTKKEDLESEFEKFGKLNNVWVAFNPPGFAFIEFSNKTDAENACDSM 74

Query: 67 NDQDLMGSKLRVEI 80
          N  +L+G KLRVE+
Sbjct: 75 NGTELLGGKLRVEL 88

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322798568|gb|EFZ20180.1| hypothetical protein SINV_12527 [Solenopsis invicta]

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 99/203 (48%), Positives = 113/203 (55%), Gaps = 31/203 (15%)

Query: 10  TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
           TRVYVGGL E++KKEDL++EFEK+GKLN VWVAFNPPGFAF+EF N  +AE AC +MN  
Sbjct: 11  TRVYVGGLNESIKKEDLQMEFEKYGKLNKVWVAFNPPGFAFIEFFNMNEAELACCNMNGM 70

Query: 70  DLMGSKLRVEISRGRGRG----------RGGGGRGGR-FDSRGG-RGGYRGGG-GGYGGG 116
           ++MG+KLRVEISRGRGRG          R   G G R F SRGG   GYRG     YGG 
Sbjct: 71  EIMGAKLRVEISRGRGRGGGRGGGAGGFRSNRGVGSRDFGSRGGTTAGYRGSTYADYGGS 130

Query: 117 GYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRG-GRDEYGGGRGGGGYRGGRDSRGFDGGK 175
            Y   G    G GR   D  +  S G     G  +D YGG  G  G              
Sbjct: 131 YYTGRGGASRGRGRYGEDYMYNRSSGYVTRDGYTQDVYGGSSGDTG-------------- 176

Query: 176 PDYYNGGGGGRGGGGRFRSRSPV 198
            DYY G         R+RSRSP 
Sbjct: 177 ADYYTGKDTST---ARYRSRSPA 196

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|2815290|emb|CAA05719.1| P23 protein [Chironomus tentans] gi|3954793|emb|CAA06034.1| hnRNP protein [Chironomus tentans]

 Score =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 56/78 (71%), Positives = 69/78 (88%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          ERGTRVYVG LT+ VKKE LE EF +FGKLNSVW+A NPPGFAF+EF+N+ +A +ACDS+
Sbjct: 4  ERGTRVYVGNLTDKVKKEQLEEEFTRFGKLNSVWLAHNPPGFAFIEFANKDEAISACDSL 63

Query: 67 NDQDLMGSKLRVEISRGR 84
          N Q+L+GSKLRVEIS+G+
Sbjct: 64 NGQELLGSKLRVEISKGK 81

Source: Chironomus tentans

Species: Chironomus tentans

Genus: Chironomus

Family: Chironomidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380011044|ref|XP_003689623.1| PREDICTED: uncharacterized protein LOC100871916 [Apis florea]

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 98/191 (51%), Positives = 112/191 (58%), Gaps = 12/191 (6%)

Query: 10  TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
           TRVYVGGL E++KKEDL+ EFEK+GKLN VWVAFNPPGFAF+EF N  +AE AC SMN  
Sbjct: 7   TRVYVGGLNESIKKEDLQTEFEKYGKLNKVWVAFNPPGFAFIEFLNMNEAELACSSMNGT 66

Query: 70  DLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRG-GYRGGGGGYGGGGYRDGGDRFGGG 128
           ++MG+KLRVEISRGRGRG G GG GG   +RGG   GY  G        YR  G+     
Sbjct: 67  EIMGAKLRVEISRGRGRGGGRGGMGGFRGNRGGAARGY--GSAASIAFNYR--GNNMYAD 122

Query: 129 GRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKP--DYYNGGGGGR 186
             G   G   GSR    Y  G D       G   R G     ++ G P  DYYN  G   
Sbjct: 123 YGGYYAGKGGGSRSRDYY--GEDYMTNRASGYVTRDGYTQDVYNSGDPNADYYNNKG--- 177

Query: 187 GGGGRFRSRSP 197
            G  R+RSRSP
Sbjct: 178 TGTSRYRSRSP 188

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	207
FB|FBgn0011305	197	Rsf1 "Repressor splicing facto	0.357	0.375	0.567	4.5e-20
ZFIN|ZDB-GENE-040426-1798	258	zgc:77155 "zgc:77155" [Danio r	0.338	0.271	0.414	2.2e-10
FB|FBgn0030479	158	Rbp1-like "Rbp1-like" [Drosoph	0.338	0.443	0.385	3.3e-10
UNIPROTKB|E1C8Y9	164	SRSF3 "Uncharacterized protein	0.338	0.426	0.4	8.6e-10
UNIPROTKB|Q3SZR8	164	SRSF3 "Serine/arginine-rich sp	0.338	0.426	0.4	8.6e-10
UNIPROTKB|F2Z4N6	164	SRSF3 "Uncharacterized protein	0.338	0.426	0.4	8.6e-10
UNIPROTKB|B4E241	124	SFRS3 "Splicing factor, argini	0.338	0.564	0.4	8.6e-10
UNIPROTKB|P84103	164	SRSF3 "Serine/arginine-rich sp	0.338	0.426	0.4	8.6e-10
UNIPROTKB|I3LAE9	164	LOC100523801 "Uncharacterized	0.338	0.426	0.4	8.6e-10
MGI|MGI:98285	164	Srsf3 "serine/arginine-rich sp	0.338	0.426	0.4	8.6e-10

FB|FBgn0011305 Rsf1 "Repressor splicing factor 1" [Drosophila melanogaster (taxid:7227)]

 Score = 217 (81.4 bits), Expect = 4.5e-20, Sum P(2) = 4.5e-20
 Identities = 42/74 (56%), Positives = 51/74 (68%)

Query:     7 ERGTRVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
             +RGTRVYVG LT+ V               NSVW+AFNPPGFAFVEF ++ DAE ACD +
Sbjct:     4 QRGTRVYVGNLTDKVKKDDLEGEFTKYGKLNSVWIAFNPPGFAFVEFEHRDDAEKACDIL 63

Query:    67 NDQDLMGSKLRVEI 80
             N  +L+GS+LRVEI
Sbjct:    64 NGSELLGSQLRVEI 77

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0003729 "mRNA binding" evidence=ISS;TAS

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=TAS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1798 zgc:77155 "zgc:77155" [Danio rerio (taxid:7955)]

 Score = 131 (51.2 bits), Expect = 2.2e-10, Sum P(2) = 2.2e-10
 Identities = 29/70 (41%), Positives = 38/70 (54%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVE+ +  DAE A   M+ + 
Sbjct:    15 KVYVGDLGNGAAKGELERAFSYYGPLRSVWVARNPPGFAFVEYEDARDAEDAVKGMDGKV 74

Query:    71 LMGSKLRVEI 80
             L G+++RVE+
Sbjct:    75 LCGARVRVEL 84

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

FB|FBgn0030479 Rbp1-like "Rbp1-like" [Drosophila melanogaster (taxid:7227)]

 Score = 127 (49.8 bits), Expect = 3.3e-10, Sum P(2) = 3.3e-10
 Identities = 27/70 (38%), Positives = 38/70 (54%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L  +                 +VWVA NPPGFAFVEF ++ DAE A   ++   
Sbjct:    12 KVYVGNLGSSASKYEIENAFSKYGPLRNVWVARNPPGFAFVEFEDRRDAEDATRGLDGTR 71

Query:    71 LMGSKLRVEI 80
               G+++RVE+
Sbjct:    72 CCGTRIRVEM 81

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0006376 "mRNA splice site selection" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|E1C8Y9 SRSF3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0043274 "phospholipase binding" evidence=IEA

UNIPROTKB|Q3SZR8 SRSF3 "Serine/arginine-rich splicing factor 3" [Bos taurus (taxid:9913)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0043274 "phospholipase binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F2Z4N6 SRSF3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0043274 "phospholipase binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|B4E241 SFRS3 "Splicing factor, arginine/serine-rich 3, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|P84103 SRSF3 "Serine/arginine-rich splicing factor 3" [Homo sapiens (taxid:9606)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0043274 "phospholipase binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

UNIPROTKB|I3LAE9 LOC100523801 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0043274 "phospholipase binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:98285 Srsf3 "serine/arginine-rich splicing factor 3" [Mus musculus (taxid:10090)]

 Score = 123 (48.4 bits), Expect = 8.6e-10, Sum P(2) = 8.6e-10
 Identities = 28/70 (40%), Positives = 36/70 (51%)

Query:    11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
             +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct:    11 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 70

Query:    71 LMGSKLRVEI 80
             L G ++RVE+
Sbjct:    71 LCGCRVRVEL 80

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=TAS

GO:0005634 "nucleus" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008286 "insulin receptor signaling pathway" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0016607 "nuclear speck" evidence=IDA

GO:0043274 "phospholipase binding" evidence=IPI

---

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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	207
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	7e-25
smart00360	73	smart00360, RRM, RNA recognition motif	4e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-17
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-14
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-14
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	2e-13
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-13
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-12
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-12
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	4e-11
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	4e-11
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	8e-11
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	1e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-09
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-09
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-09
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	8e-09
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	9e-09
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-08
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	2e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-08
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	3e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	7e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	9e-08
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	1e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-07
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-07
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	3e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	3e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-07
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	4e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-07
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	6e-07
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	6e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	6e-07
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	6e-07
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-07
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	9e-07
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	9e-07
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-06
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	1e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-06
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-06
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-06
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	3e-06
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	4e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	4e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	5e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	7e-06
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	7e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	8e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	8e-06
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	9e-06
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	9e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	1e-05
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	2e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	2e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	2e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-05
PRK12678	672	PRK12678, PRK12678, transcription termination fact	3e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	3e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	3e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	4e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-05
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	4e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	5e-05
PRK12678	672	PRK12678, PRK12678, transcription termination fact	5e-05
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	6e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	6e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	6e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-05
cd12248	74	cd12248, RRM_RBM44, RNA recognition motif in RNA-b	6e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	8e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-05
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	8e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	1e-04
cd12529	71	cd12529, RRM2_MEI2_like, RNA recognition motif 2 i	1e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-04
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-04
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	2e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	2e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	2e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	2e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-04
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	3e-04
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	3e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	3e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	4e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-04
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	5e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	5e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	6e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-04
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	7e-04
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	8e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	8e-04
cd12605	69	cd12605, RRM_RALYL, RNA recognition motif in verte	8e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	9e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	9e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.001
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	0.001
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.001
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.001
COG1512	271	COG1512, COG1512, Beta-propeller domains of methan	0.001
cd12498	83	cd12498, RRM3_ACF, RNA recognition motif 3 in vert	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	0.002
cd12434	75	cd12434, RRM_RCAN_like, RNA recognition motif in r	0.002
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.002
PRK14279	392	PRK14279, PRK14279, chaperone protein DnaJ; Provis	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	0.002
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.002
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.002
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	0.002
COG1512	271	COG1512, COG1512, Beta-propeller domains of methan	0.003
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.003
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.003
PRK07772	186	PRK07772, PRK07772, single-stranded DNA-binding pr	0.003
cd12496	74	cd12496, RRM3_RBM46, RNA recognition motif 3 in ve	0.003
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.003
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.003
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	0.004
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.004
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.004
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.004
pfam03276	582	pfam03276, Gag_spuma, Spumavirus gag protein	0.004

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 92.3 bits (230), Expect = 7e-25
 Identities = 40/73 (54%), Positives = 53/73 (72%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +VYVG L     K +LE EFEK+G L SVWVA NPPGFAFVEF +  DAE A  +++ + 
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRALDGRR 60

Query: 71 LMGSKLRVEISRG 83
          + G+++RVE+SRG
Sbjct: 61 ICGNRVRVELSRG 73

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

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

 Score = 74.6 bits (184), Expect = 4e-18
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 5/73 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
           ++VG L     +E+L   F KFGK+ SV +  +       GFAFVEF ++ DAE A ++
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 66 MNDQDLMGSKLRV 78
          +N ++L G  L+V
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

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

 Score = 72.3 bits (178), Expect = 3e-17
 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 4/72 (5%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMN 67
          ++VG L     +EDL   F KFG++ SV +  +      GFAFVEF +  DAE A +++N
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 68 DQDLMGSKLRVE 79
           ++L G KL+V 
Sbjct: 61 GKELDGRKLKVS 72

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

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

 Score = 73.4 bits (179), Expect = 1e-15
 Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 5/84 (5%)

Query: 10  TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
             ++VG L   V +EDL   F+KFG +  V +  +       GFAFVEF ++  AE A +
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIE 175

Query: 65  SMNDQDLMGSKLRVEISRGRGRGR 88
            +N ++L G  LRV+ ++   + R
Sbjct: 176 ELNGKELEGRPLRVQKAQPASQPR 199

Length = 306

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

 Score = 65.7 bits (161), Expect = 1e-14
 Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 4/70 (5%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMN 67
          ++VG L     +EDL+  F KFG + S+ +  +      GFAFVEF ++ DAE A +++N
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 68 DQDLMGSKLR 77
           ++L G +LR
Sbjct: 61 GKELGGRELR 70

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

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

 Score = 64.2 bits (157), Expect = 5e-14
 Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 5/79 (6%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAAC 63
          G +++V GL+    +++LE  F KFG++  V +  +P      GF FV F +  DA+AA 
Sbjct: 1  GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 64 DSMNDQDLMGSKLRVEISR 82
            +N ++L G  ++VE ++
Sbjct: 61 RDLNGKELEGRVIKVEKAK 79

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

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 62.8 bits (152), Expect = 2e-13
 Identities = 37/76 (48%), Positives = 47/76 (61%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +VYVG L     K +LE  F  +G L SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct: 6  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 65

Query: 71 LMGSKLRVEISRGRGR 86
          L G ++RVE+S G  R
Sbjct: 66 LCGCRVRVELSNGEKR 81

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

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

 Score = 61.4 bits (150), Expect = 5e-13
 Identities = 30/69 (43%), Positives = 39/69 (56%), Gaps = 3/69 (4%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMND 68
          +YV  L  +V +EDL   F  +GK+  V +  N   P GFAFVEF++  DAEAA   +N 
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 69 QDLMGSKLR 77
            L G  LR
Sbjct: 61 LVLDGRTLR 69

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

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

 Score = 59.5 bits (145), Expect = 3e-12
 Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          +YVGGL E V ++ L   F  FG +  + +  +       GFAFVEF    DA AA D+M
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 67 NDQDLMGSKLRV 78
          N+ +L G  +RV
Sbjct: 61 NESELFGRTIRV 72

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

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

 Score = 57.5 bits (140), Expect = 8e-12
 Identities = 21/53 (39%), Positives = 27/53 (50%)

Query: 29 EFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS 81
           F  FG +  + +    PGFAFVEFS +  AE A   +N     G  LRV+ S
Sbjct: 4  LFSPFGNVEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 56.6 bits (136), Expect = 4e-11
 Identities = 36/76 (47%), Positives = 49/76 (64%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +VYVG L     K +LE  F  +G L +VW+A NPPGFAFVEF +  DAE A   ++ + 
Sbjct: 1  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 60

Query: 71 LMGSKLRVEISRGRGR 86
          + GS++RVE+S G  R
Sbjct: 61 ICGSRVRVELSTGMPR 76

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 56.7 bits (137), Expect = 4e-11
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
          +++V GL  +V KE+LE  F+K G + SV +  N    P G A+VE+ N+  A  A   M
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 67 NDQDLMGSKLRVEIS 81
          +  ++    + V IS
Sbjct: 64 DGTEIKEKTISVAIS 78

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

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

 Score = 55.7 bits (135), Expect = 8e-11
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
          +YV  L  +  +E L   F ++G++  V        +AFV F  + DA  A + MN ++L
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERV---KKIKDYAFVHFEERDDAVKAMEEMNGKEL 60

Query: 72 MGSKLRV 78
           GS + V
Sbjct: 61 EGSPIEV 67

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

>gnl|CDD|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 = 52.4 bits (126), Expect = 1e-09
 Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 20 TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
          T ++ED+E  FE FG L    +      FAFVEF +  DA  A ++++   + GS L VE
Sbjct: 11 TTREEDIEKLFEPFGPLVRCDIRKT---FAFVEFEDSEDATKALEALHGSRIDGSVLTVE 67

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

 Score = 52.6 bits (127), Expect = 1e-09
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
           +YVG L   V +EDL+  F +FG++ S  V  +       GF FVE     +A AA + 
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 66 MNDQDLMGSKLRVEISR 82
          +N  D  G  L V  +R
Sbjct: 61 LNGTDFGGRTLTVNEAR 77

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

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

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          ++VG L+  +  E L   F  FG+++   V  +       G+ FV F  + DAE A  SM
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 67 NDQDLMGSKLR 77
          N Q L G  +R
Sbjct: 62 NGQWLGGRAIR 72

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

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

 Score = 51.6 bits (124), Expect = 3e-09
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP---PGFAFVEFSNQIDAEAACDSMND 68
          ++VG L+  V KE+L   F + GK+  V +         FAF++F  +  A  A +S N 
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65

Query: 69 QDLMGSKLRVE 79
            L    + V+
Sbjct: 66 SMLKNKTMHVQ 76

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

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

 Score = 50.6 bits (122), Expect = 6e-09
 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN 67
          YVG L   V +  L   F   G + S+ V  +       G+A+V F N  DAE A D++N
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 68 DQDLMGSKLRV 78
             + G  +R+
Sbjct: 63 FDVIKGKPIRI 73

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

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

 Score = 50.3 bits (121), Expect = 7e-09
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +++VG L +    E+L   FEK+G +    V  N   + FV    + DAE A  ++N  +
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN---YGFVHMEEEEDAEDAIKALNGYE 57

Query: 71 LMGSKLRVE 79
           MG ++ VE
Sbjct: 58 FMGKRINVE 66

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

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 50.2 bits (120), Expect = 8e-09
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF--NPPGFAFVEFSNQIDAEAACDSMND 68
           VYVG L   +++ ++E  F K+G +  + +     PPG+AF+EF +  DAE A    + 
Sbjct: 1  TVYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 69 QDLMGSKLRVEI 80
           D  G +LRVE+
Sbjct: 61 YDFDGQRLRVEL 72

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 50.1 bits (120), Expect = 9e-09
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-PGFAFVEFSNQIDAEAACDSMNDQ 69
           VY G    +    D++  FE  G +  V +        AF+ F N   A+ A +++N  
Sbjct: 1  TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQPHAFITFENLEAAQLAIETLNGA 60

Query: 70 DLMGSKLRVE 79
           + G+ ++V+
Sbjct: 61 SVDGNCIKVQ 70

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

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 29/67 (43%), Positives = 41/67 (61%), Gaps = 4/67 (5%)

Query: 11 RVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          RV+VG L T+ V KEDLE  F K+GK+  + +     G+ FV+F N+ DA AA    N +
Sbjct: 2  RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLH---KGYGFVQFDNEEDARAAVAGENGR 58

Query: 70 DLMGSKL 76
          ++ G KL
Sbjct: 59 EIAGQKL 65

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

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

 Score = 50.1 bits (120), Expect = 1e-08
 Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 15/69 (21%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF----------NPPGFAFVEFSNQIDAEA 61
          VYV  L +    E L+  F K+G      V +          +  GFAF+EF    +A+ 
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGT-----VVYVSLPRYKHTGDIKGFAFIEFETPEEAQK 56

Query: 62 ACDSMNDQD 70
          AC  +N+  
Sbjct: 57 ACKHLNNPP 65

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

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

 Score = 48.9 bits (117), Expect = 2e-08
 Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 3/73 (4%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          RVY+G L    ++ D+E  F+ +G++  + +     GF FVEF +  DA+ A   +N ++
Sbjct: 1  RVYIGRLPYRARERDVERFFKGYGRIREINLKN---GFGFVEFEDPRDADDAVYELNGKE 57

Query: 71 LMGSKLRVEISRG 83
          L G ++ VE +RG
Sbjct: 58 LCGERVIVEHARG 70

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

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

 Score = 49.2 bits (118), Expect = 2e-08
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          ++V  L      E LE  F + G +   +V  +       GF +V F+ + DA+ A +  
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 67 NDQDLMGSKLRVEISRGR 84
                G K+ VE ++ +
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          T VYVG L   + +E+L+  F  FG +  V V F   G+AFV F     A  A  ++N  
Sbjct: 1  TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV-FKDKGYAFVRFDTHEAAATAIVAVNGT 59

Query: 70 DLMGSKLRV 78
           + G  ++ 
Sbjct: 60 SINGQTVKC 68

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

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

 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSV--WVAFNPPGFAFVEFSNQIDAEAACDSMND 68
          R+YVG L   +++ D+E  F K+G + ++        P FAFVEF +  DAE A    + 
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGRDG 60

Query: 69 QDLMGSKLRVE 79
           D  G +LRVE
Sbjct: 61 YDFDGYRLRVE 71

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

 Score = 48.0 bits (115), Expect = 5e-08
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
           R+YV  +   + ++D++  FE FGK+ S  +A +P      G+ F+E+ N   A+ A  
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 65 SMNDQDLMGSKLRV 78
          SMN  DL G +LRV
Sbjct: 61 SMNLFDLGGQQLRV 74

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

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

 Score = 48.0 bits (115), Expect = 6e-08
 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 15/80 (18%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----------GFAFVEFSNQIDAE 60
          +YV  L   + ++DL   F KFG++ S+ +   P            GFAFV F +   AE
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVESIRI---PKKQDEKQGRLNNGFAFVTFKDASSAE 59

Query: 61 AACDSMNDQDLMGSKLRVEI 80
           A   +N  +L G K+ V +
Sbjct: 60 NAL-QLNGTELGGRKISVSL 78

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

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

 Score = 47.7 bits (114), Expect = 7e-08
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 5/75 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          VYV  L  ++   DL   F K+GK+  V +  +       G AF+ F ++ DA     ++
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 67 NDQDLMGSKLRVEIS 81
          N+++L G  L+  I+
Sbjct: 64 NNKELFGRTLKCSIA 78

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

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

 Score = 47.4 bits (113), Expect = 9e-08
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDS 65
          R++V  L  + K++DLE  F KFG+L+ V VA         GFA+V F +  DA  A   
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 66 MNDQDLMGSKLRV 78
          ++ +   G  + +
Sbjct: 64 LDGKVFQGRLIHI 76

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

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

 Score = 47.5 bits (114), Expect = 1e-07
 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 1/46 (2%)

Query: 23 KEDLELEFEKFGKLNSVWV-AFNPPGFAFVEFSNQIDAEAACDSMN 67
          KED+  E  KFG +  + V   +P G  +V+F     A+    ++N
Sbjct: 25 KEDVLEECSKFGPVEHIKVDKNSPEGVVYVKFKTVEAAQKCIQALN 70

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

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

 Score = 47.1 bits (113), Expect = 1e-07
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
           + V  L+E   ++DL   F  FG ++ V++A +       GFAFV F  + DAE A + 
Sbjct: 1  TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 66 MNDQDLMGSKLRVEISR 82
          +N        L VE ++
Sbjct: 61 LNGFGYDNLILSVEWAK 77

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

 Score = 50.6 bits (121), Expect = 1e-07
 Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 7   ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAA 62
           ++ T +YV  L  +V ++ L   F KFG++ S  V  +      GFAFV F    DA  A
Sbjct: 176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKA 235

Query: 63  CDSMNDQDLMGSKLRVEISRGRGRGR 88
            + MN + +  +K   ++  GR + R
Sbjct: 236 VEEMNGKKIGLAKEGKKLYVGRAQKR 261

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

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

 Score = 46.5 bits (111), Expect = 2e-07
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
          R++V  L  T  +E+L   FE FG+++ V +  +       GFAFV F     A  A   
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 66 MNDQDLMGSKLRV 78
          ++     G  L V
Sbjct: 61 LDGSIFQGRLLHV 73

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

>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 46.1 bits (110), Expect = 3e-07
 Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 8/77 (10%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWV--------AFNPPGFAFVEFSNQIDAEA 61
          T +YVG L   V +E L  EF +FG L SV +                FV F N+ DAE 
Sbjct: 2  TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 62 ACDSMNDQDLMGSKLRV 78
          A D ++ +D+MG +L++
Sbjct: 62 ALDELDGKDVMGYELKL 78

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 46.0 bits (110), Expect = 3e-07
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDS 65
          T VYV  L E +  E L+  F K+GK+ S  V  +  G    F FV F N   A+ A + 
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 66 MNDQDLMGSKLRV 78
          +N +++ G KL V
Sbjct: 62 LNGKEVNGKKLYV 74

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

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

 Score = 45.9 bits (109), Expect = 3e-07
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDSM 66
          +Y+G L     +++L+  F +FG + +V VA      N   + F++F N   A  A  SM
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 67 NDQDLMGSKLRVEI 80
          N+  LMG  L+V +
Sbjct: 62 NNYLLMGKVLQVHV 75

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

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

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 10/78 (12%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-------GFAFVEFSNQIDAEAAC 63
          R+ V  L     + DL+  F  FG    VW    P        GFAFV+F+++ DAE A 
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGF---VWEVTIPRKPDGKKKGFAFVQFTSKADAEKAI 57

Query: 64 DSMNDQDLMGSKLRVEIS 81
            +N + + G  + V+ +
Sbjct: 58 KGVNGKKIKGRPVAVDWA 75

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

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

 Score = 45.5 bits (108), Expect = 4e-07
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          R+YV        +  +   F  +G +  V +  N   FAFVEF +   A  A DS++ + 
Sbjct: 1  RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISN---FAFVEFESLESAIRAKDSVHGKV 57

Query: 71 LMGSKLRV 78
          L  + L V
Sbjct: 58 LNNNPLYV 65

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

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

 Score = 49.3 bits (117), Expect = 4e-07
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 11  RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
           R+YV  +   + + D++  FE FG++    +A  P      G+ F+E++N      A  S
Sbjct: 206 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS 265

Query: 66  MNDQDLMGSKLRV 78
           MN  DL G  LRV
Sbjct: 266 MNLFDLGGQYLRV 278

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

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

 Score = 45.7 bits (109), Expect = 4e-07
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMN 67
          YVG L   + ++DL   FE FG++  V +  +P      G+ F++F++  DA+ A + +N
Sbjct: 2  YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 68 DQDLMGSKLRV 78
            +L G  ++V
Sbjct: 62 GFELAGRPIKV 72

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

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

 Score = 45.5 bits (108), Expect = 5e-07
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
           ++VG L+ +V  E L+ EFEKFG +    V  +       GF +V+F +  DA+ A ++
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 66 MNDQDLMGSKLRVEIS 81
          M+ ++L G  + V+ S
Sbjct: 61 MDGKELDGRPINVDFS 76

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 48.6 bits (116), Expect = 5e-07
 Identities = 36/62 (58%), Positives = 36/62 (58%), Gaps = 10/62 (16%)

Query: 100 RGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGG 159
            GG GG RGGG G GGGG R GG R GG G GRG       RG GG  GGR   GGG GG
Sbjct: 3   GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRG-------RGRGGGGGGR---GGGGGG 52

Query: 160 GG 161
           G 
Sbjct: 53  GP 54

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 48.2 bits (115), Expect = 6e-07
 Identities = 35/64 (54%), Positives = 35/64 (54%), Gaps = 9/64 (14%)

Query: 87  GRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGY 146
           G GGG  GGR   RGG GG   GGGG GGG          GGGRGRG GG  G RGGGG 
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGG---------RGGGRGRGRGGGGGGRGGGGG 51

Query: 147 RGGR 150
            G  
Sbjct: 52  GGPG 55

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 48.2 bits (115), Expect = 6e-07
 Identities = 28/52 (53%), Positives = 29/52 (55%)

Query: 81  SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGR 132
             G GRG G GG GG     GGRGG RGGG G G GG   G    GGGG G+
Sbjct: 5   GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56

Length = 293

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

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDS 65
          TR+ V  L   V +EDLE  F + G++  V + ++      G A V F  + DAE A   
Sbjct: 1  TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQ 60

Query: 66 MNDQDLMGSKLRVEI 80
           N   L G  ++VE+
Sbjct: 61 FNGVLLDGQPMQVEL 75

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

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 45.2 bits (107), Expect = 6e-07
 Identities = 22/58 (37%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 22 KKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE 79
          +  DLE  FE +GKL +V +  N   FAFV++  Q DA  A +S N   ++   + VE
Sbjct: 13 RTRDLERHFEPYGKLVNVRIRRN---FAFVQYETQEDATKALESTNMSKVLDRVISVE 67

This subgroup corresponds to the RRM2 in a family that represents 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 RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 48.7 bits (117), Expect = 6e-07
 Identities = 30/114 (26%), Positives = 33/114 (28%), Gaps = 3/114 (2%)

Query: 82  RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
             R        R  R D    +     G  G      RDG DR     R +GD   R   
Sbjct: 161 AERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGD---RREE 217

Query: 142 GGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSR 195
            G    G R      R     RG  +         D   G GG RG   R R R
Sbjct: 218 RGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDR 271

Length = 672

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

 Score = 44.9 bits (107), Expect = 9e-07
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDS 65
          +R+ V  L + V ++ L   FE  G++  V V     G    F FV F ++ DA+ A   
Sbjct: 1  SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 66 MNDQDLMGSKLRVEI 80
           N   +  SK+ VE+
Sbjct: 61 FNKTFIDTSKISVEL 75

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

>gnl|CDD|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 44.6 bits (106), Expect = 9e-07
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
           +V+VG LTE + +EDL   F +FG++  V++      FAFV F++   A++ C    D 
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPFRAFAFVTFADPEVAQSLCG--EDH 58

Query: 70 DLMGSKLRVEISR 82
           + G  + V  + 
Sbjct: 59 IIKGVSVHVSNAE 71

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

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

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          ++VG LT  V K+ L+  F  +G +  V +  +       G+A+VEF +  DAE A   M
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 67 NDQDLMGSKLRVE 79
          +   + G ++ VE
Sbjct: 61 DGGQIDGQEVTVE 73

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

>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 44.5 bits (106), Expect = 1e-06
 Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 29 EFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
           F KFG + ++ V +NP   A V+FS   +A+ A  S
Sbjct: 22 HFSKFGTIVNIQVNYNPES-ALVQFSTSEEAKKAYRS 57

This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. . Length = 72

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

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 5/79 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
          T +YV  + +  + +DL   F K+G +  V++  +     P GFA+V+F +  DAE A  
Sbjct: 1  TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 65 SMNDQDLMGSKLRVEISRG 83
           ++    +G ++ ++ ++G
Sbjct: 61 YLDRTRFLGREIEIQFAQG 79

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 44.2 bits (105), Expect = 1e-06
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF--------NPPGFAFVEFSNQIDAEAA 62
          R+++G L   + +  L   F K+GK+      F         P G+ FV F  + +AE A
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 63 CDSMNDQDLMGSKLRV 78
            S+N +  +G KL V
Sbjct: 61 LKSLNGKTALGKKLVV 76

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

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

 Score = 47.1 bits (112), Expect = 2e-06
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 5   MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAE 60
           M  +G  +YV  L +TV  E L   F + G++ S  V  +      GF FV FSN  +A 
Sbjct: 281 MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEAN 340

Query: 61  AACDSMNDQDLMGSKLRVEISRGR 84
            A   M+ + L G  L V +++ +
Sbjct: 341 RAVTEMHGRMLGGKPLYVALAQRK 364

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

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

 Score = 47.0 bits (111), Expect = 2e-06
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 5/73 (6%)

Query: 11  RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
           RVYVG ++  ++++ +   F+ FG + S+ ++++P      GFAFVE+     A+ A + 
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 66  MNDQDLMGSKLRV 78
           MN Q L G  ++V
Sbjct: 169 MNGQMLGGRNIKV 181

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

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

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVA-FNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          R+YVG L   ++ +D+E  F K+G +  + +     P FAFVEF +  DAE A    +  
Sbjct: 1  RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPPFAFVEFEDPRDAEDAVYGRDGY 60

Query: 70 DLMGSKLRVEISR 82
          D  G +LRVE  R
Sbjct: 61 DYDGYRLRVEFPR 73

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

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

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 29/73 (39%), Positives = 38/73 (52%), Gaps = 7/73 (9%)

Query: 12 VYVGGLTETVKKEDL-ELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEAACDS 65
          VYVG L E V +E L EL F + G + +V      V     G+ FVEF ++ DA+ A   
Sbjct: 1  VYVGNLDEKVTEELLWEL-FIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59

Query: 66 MNDQDLMGSKLRV 78
          MN   L G  +RV
Sbjct: 60 MNMIKLYGKPIRV 72

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

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 12 VYVGGLTETVKKEDLELE-FEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMND 68
          +YVG L  TV  EDL  E F + G + S  +        +AFVE+ +   A AA  +MN 
Sbjct: 1  LYVGNLDRTVT-EDLLAELFSQIGPIKSCKLIREHGNDPYAFVEYYDHRSAAAALQTMNG 59

Query: 69 QDLMGSKLRV 78
          + ++G +++V
Sbjct: 60 RLILGQEIKV 69

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

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVA----FNPP-GFAFVEFSNQIDAEAACDS 65
          R++VGGL+ +V + DLE  F +FG ++ V +       P  GFA+++          C S
Sbjct: 1  RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKS 60

Query: 66 -MNDQDLMGSKLRVE 79
           +N     GS L++E
Sbjct: 61 TLNGTKWKGSVLKIE 75

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 43.8 bits (104), Expect = 2e-06
 Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSV-----WVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +V  L      EDLE+ F +FGK+ S          +   +AF+EF  + D E A   M+
Sbjct: 7  FVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 66

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 46.8 bits (112), Expect = 3e-06
 Identities = 28/110 (25%), Positives = 29/110 (26%), Gaps = 10/110 (9%)

Query: 82  RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
                 RG     GR      R   R  G      G RDGGDR G   R           
Sbjct: 184 EAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDN 243

Query: 142 GGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
                    D+  G  G  G R     R           G  GG GG  R
Sbjct: 244 REDRGDRDGDDGEGRGGRRGRRFRDRDR----------RGRRGGDGGNER 283

Length = 672

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

 Score = 43.4 bits (102), Expect = 3e-06
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 6/69 (8%)

Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQD 70
          V  L+ +  ++ L+   E F K  S+ +  N   P G+AFVEF +  DA+ A +S N+ +
Sbjct: 6  VNNLSYSASEDSLQ---EVFEKATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 71 LMGSKLRVE 79
          + G  +R+E
Sbjct: 63 IEGRSIRLE 71

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

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

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDS 65
          +R+ V  L + +K++ L   FE FG +  V + +   G    F FV +  + +A+ A   
Sbjct: 1  SRLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKH 60

Query: 66 MNDQDLMGSKLRVEI 80
           N+  +  SK+ VEI
Sbjct: 61 FNNSFIDTSKITVEI 75

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

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 21 VKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAAC---DSMNDQDLM 72
            +E+L+  F +FG++    +  +       G AFV+F  +  A+      D+  D  L 
Sbjct: 12 ATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLS 71

Query: 73 --GSKLRVEIS 81
            G +L V ++
Sbjct: 72 LDGRRLIVTLA 82

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

>gnl|CDD|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMN 67
          T V+VGGL   V +++L   F  FG++  V +   PPG    FV+F ++  AEAA   + 
Sbjct: 2  TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKI---PPGKGCGFVQFVHRAAAEAAIQQLQ 58

Query: 68 DQDLMGSKLR 77
             + GS++R
Sbjct: 59 GTIIGGSRIR 68

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

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

 Score = 43.3 bits (103), Expect = 4e-06
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%)

Query: 23 KEDLELEFEKFGKLNSVWVAFNPP--------GFAFVEFSNQIDAEAACDSMN 67
           ED++ E  K+GK+ SV +             G  FVEF++  DA+ A  ++ 
Sbjct: 25 LEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

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

 Score = 42.9 bits (101), Expect = 4e-06
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 4/71 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWV--AFNPP--GFAFVEFSNQIDAEAACDS 65
          T++ V  L     K+D+   F  +G+L SV V   F+    GFAFVEFS   +A  A ++
Sbjct: 1  TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 66 MNDQDLMGSKL 76
          + D  L+G +L
Sbjct: 61 LKDTHLLGRRL 71

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 42.9 bits (101), Expect = 5e-06
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
          +  +++VGGL        L   F ++GKL    V  +P      GF F+ FS+  +A+ A
Sbjct: 1  QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 63 CDSM 66
           ++ 
Sbjct: 61 MEAQ 64

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

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

 Score = 42.6 bits (101), Expect = 5e-06
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 5/70 (7%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
          T VY+ GL      EDLE   + FGK+ S     +       G+ FV+F +   A  A +
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 65 SMNDQDLMGS 74
           +N + +   
Sbjct: 61 GLNGRGVQAQ 70

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

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

 Score = 42.3 bits (100), Expect = 7e-06
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 5/70 (7%)

Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSMND 68
          V  LT     +DL   FEK+G++  V++  +       GFAFV F ++ DAE A D+M+ 
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 69 QDLMGSKLRV 78
          ++L G +LRV
Sbjct: 63 KELDGRELRV 72

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

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

 Score = 42.2 bits (100), Expect = 7e-06
 Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 5/74 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-PGFAFVEFSNQIDAEAACDSMNDQD 70
          ++VGGL       +LE EF++FG +  +   ++P   +A++E+ +   A+AA +++    
Sbjct: 1  LWVGGLGPWTSLAELEREFDRFGAIRRI--DYDPGRNYAYIEYESIEAAQAAKEALRGFP 58

Query: 71 L--MGSKLRVEISR 82
          L   G +LRV+ + 
Sbjct: 59 LGGPGRRLRVDFAD 72

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

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

 Score = 42.0 bits (99), Expect = 8e-06
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
          RVYVG ++  + ++ +   F  FG + S+ ++++P      GFAFVE+     A+ A + 
Sbjct: 2  RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 66 MNDQDLMGSKLRV 78
          MN   L G  ++V
Sbjct: 62 MNGVMLGGRNIKV 74

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

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN 67
          +V  L     +  L  EFE++G +  + +  +     P G+AF+EF ++ D +AA    +
Sbjct: 5  FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 68 DQDLMGSKLRVEISRGR 84
           + + G ++ V++ RGR
Sbjct: 65 GKKIDGRRVLVDVERGR 81

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

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

 Score = 42.1 bits (100), Expect = 9e-06
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 8/77 (10%)

Query: 13 YVGGLTETVKKED----LELEFEKFGKLNSVWVAFNPP---GFAFVEFSNQIDAEAACDS 65
          Y+  L E +KK++    L   F +FG +  + VA       G AFV F +   A  A  +
Sbjct: 3  YINNLNEKIKKDELKRSLYALFSQFGPVLDI-VASKTLKMRGQAFVVFKDVESATNALRA 61

Query: 66 MNDQDLMGSKLRVEISR 82
          +         +R++ ++
Sbjct: 62 LQGFPFYDKPMRIQYAK 78

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

 Score = 42.2 bits (100), Expect = 9e-06
 Identities = 18/72 (25%), Positives = 44/72 (61%), Gaps = 5/72 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSM 66
          ++V G+ E  ++ED+  +F +FG++ ++ +  +       G+A +E+  + +A+AA + +
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 67 NDQDLMGSKLRV 78
          N ++L+G  + V
Sbjct: 69 NGKELLGQTISV 80

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

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

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAE-AACDSMND 68
          T +YVGGL E V ++DL   F +FG++ S+ V       AFV F+ +  AE AA    N 
Sbjct: 2  TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-QQCAFVTFTTREAAEKAAERLFNK 60

Query: 69 QDLMGSKLRV 78
            + G +L++
Sbjct: 61 LIINGRRLKL 70

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

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

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAA 62
          R  +++VGGL   V + DL   F +FG +  V V ++     P GF F+ F ++   +  
Sbjct: 1  RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 63 CDSMNDQDLMGSKLRVEISR 82
            + +  D+ G K  VE+ R
Sbjct: 61 V-NEHFHDINGKK--VEVKR 77

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 29/64 (45%), Positives = 30/64 (46%), Gaps = 8/64 (12%)

Query: 101 GGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGG 160
           G  GG+ GG GG  GGG        GGGGRG G  G     G G  RGG     GG GGG
Sbjct: 1   GMGGGFGGGRGGGRGGG--------GGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGG 52

Query: 161 GYRG 164
           G   
Sbjct: 53  GPGK 56

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.0 bits (104), Expect = 2e-05
 Identities = 25/55 (45%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 82  RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGG 136
            G   G  GGGRGG      G GG  GG GG  G G   GG   G GG G G  G
Sbjct: 3   GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRG--RGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA-----FNPPGFAFVEFSNQIDAEAACDSM 66
          VY+G L     + +L   F +FG +  + ++         G+AFVEF +   A+   ++M
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 67 NDQDLMGSKLRVE 79
          N+  L    L+ +
Sbjct: 62 NNYLLFERLLKCK 74

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

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 41.2 bits (96), Expect = 2e-05
 Identities = 22/79 (27%), Positives = 46/79 (58%), Gaps = 5/79 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
          T ++V  + +  + EDL  EF ++G +  V+V  +     P GFA+++F +  DAE A  
Sbjct: 1  TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 65 SMNDQDLMGSKLRVEISRG 83
          ++N + + G ++ ++ ++G
Sbjct: 61 NLNRKWVCGRQIEIQFAQG 79

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 40.8 bits (95), Expect = 2e-05
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
          +++VGGL+     ED++  FE+FGK++   + F+       GF FV F ++   E  C+
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 43.7 bits (104), Expect = 3e-05
 Identities = 24/116 (20%), Positives = 30/116 (25%), Gaps = 1/116 (0%)

Query: 81  SRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGS 140
           +  R           R + R              G   R       G  R R D   +G 
Sbjct: 154 TEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGD 213

Query: 141 RGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGG-GGRFRSR 195
           R     R    +  G R     R  R     +       + G G  G  G RFR R
Sbjct: 214 RREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDR 269

Length = 672

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMND 68
          V GL+    + DL   F ++G +  V V ++       GF FV F +  DA+ A + +N 
Sbjct: 4  VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 69 QDLMGSKLRVEIS 81
           ++ G ++RV+ S
Sbjct: 64 MEIDGRRIRVDYS 76

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
          ++V  L  TV +E LE  F +FGKL  V        +AFV F  +  A  A D MN +++
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKLERVK---KLKDYAFVHFEERDAAVRAMDEMNGKEI 60

Query: 72 MGSKLRVEISR 82
           G ++ + +++
Sbjct: 61 EGEEIEIVLAK 71

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACDSM 66
          ++VG +      E+L+  F+  G +N + +        P GFA++EF ++   E A   +
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60

Query: 67 NDQDLMGSKLRV 78
          N+ +  G +++V
Sbjct: 61 NESEFRGRQIKV 72

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

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

 Score = 40.4 bits (95), Expect = 3e-05
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPG--FAFVEFSNQIDAEAACDSM 66
          ++V GL+ T K  DL+  F K+GK+    +  N   P    F FV  ++  +A      +
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 67 NDQDLMGSKLRVE 79
          +  +L G  + VE
Sbjct: 62 HRTELHGRVISVE 74

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

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

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 16/59 (27%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACD 64
          +++VGGL+    ++D++  F +FGK+    + F+       GF FV F ++   +  C+
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE 59

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

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 40.7 bits (95), Expect = 3e-05
 Identities = 21/79 (26%), Positives = 46/79 (58%), Gaps = 5/79 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
          + ++V  + +  + EDL  EF ++G +  V+V  +     P GFA+V+F +  DAE A  
Sbjct: 1  SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 65 SMNDQDLMGSKLRVEISRG 83
          +++ + + G ++ ++ ++G
Sbjct: 61 NLDRKWICGRQIEIQFAQG 79

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKF-GKLNSVWVAFNPPG----FAFVEFSNQIDAEAACD 64
          +R+ V  L  ++ + +L+  F K  G++  V +     G     AF+ +  + +A+ A D
Sbjct: 1  SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 65 SMNDQDLMGSKLRVE 79
            N+  +  SK+ VE
Sbjct: 61 YFNNTYINTSKISVE 75

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

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

 Score = 40.3 bits (95), Expect = 4e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          V+VG +     +E L   F + G + S  +  +     P G+ F EF +   A +A  ++
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 67 NDQDLMGSKLRVE 79
          N  +  G  LRV+
Sbjct: 61 NGYEFNGRALRVD 73

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

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 40.0 bits (93), Expect = 4e-05
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 4/73 (5%)

Query: 10 TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
          +RV++G L T  VKK D+E  F K+GK+    V     GFAFV++ N+ +A AA    + 
Sbjct: 2  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDG 58

Query: 69 QDLMGSKLRVEIS 81
          + + G  L + ++
Sbjct: 59 RMIAGQVLDINLA 71

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.4 bits (100), Expect = 5e-05
 Identities = 35/63 (55%), Positives = 35/63 (55%), Gaps = 9/63 (14%)

Query: 129 GRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGG 188
           G G G GG RG   GGG  GGR   GGGRGGG  RGG   RG  GG      GG GG GG
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRG--GGGRGGG--RGGGRGRGRGGGG-----GGRGGGGG 51

Query: 189 GGR 191
           GG 
Sbjct: 52  GGP 54

Length = 293

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 43.0 bits (102), Expect = 5e-05
 Identities = 28/91 (30%), Positives = 29/91 (31%), Gaps = 3/91 (3%)

Query: 82  RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGR-GRGDGGFRGS 140
           RGR               R    G R GG   G    RD  D  G   R  RGD      
Sbjct: 196 RGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDG 255

Query: 141 RGGGGYRGGRDEYG--GGRGGGGYRGGRDSR 169
            G GG RG R       GR GG     R+  
Sbjct: 256 EGRGGRRGRRFRDRDRRGRRGGDGGNEREPE 286

Length = 672

>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          TR+ V  L  +V ++D+   F   G L    +    PG A V +  + DA  A D  N++
Sbjct: 1  TRLVVSNLHPSVTEDDIVELFSAIGALKRARL--VRPGVAEVVYVRKDDALTAIDKYNNR 58

Query: 70 DLMGSKLRVEI 80
          +L G  ++ ++
Sbjct: 59 ELDGQPMKCKL 69

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

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

 Score = 39.5 bits (93), Expect = 6e-05
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 4/65 (6%)

Query: 16 GLTETVKKEDLELEFEKFGKLNSV-WVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-G 73
           L E   KE LE+ F +F     V  V     G AFVEF  +  A  A  ++    +  G
Sbjct: 9  NLPEETTKEMLEMLFNQFPGFKEVRLVP--RRGIAFVEFETEEQATVALQALQGFKITPG 66

Query: 74 SKLRV 78
            +++
Sbjct: 67 HAMKI 71

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 7/67 (10%)

Query: 21 VKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQIDAEAACDSMNDQDL--MG 73
          V ++DL   F  FG++  +WV          G A+V+F+    A  A + MN + L    
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCLGGDT 73

Query: 74 SKLRVEI 80
            L+V I
Sbjct: 74 KPLKVLI 80

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

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 39.7 bits (93), Expect = 6e-05
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM 72
          Y+G L+  V + DL   FE+  K+    V     G+AFV+  +Q  A+ A + +N + L 
Sbjct: 2  YIGNLSSDVNESDLRQLFEE-HKIPVSSVLVKKGGYAFVDCPDQSWADKAIEKLNGKILQ 60

Query: 73 GSKLRVEIS 81
          G  + VE S
Sbjct: 61 GKVIEVEHS 69

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 39.6 bits (93), Expect = 6e-05
 Identities = 22/78 (28%), Positives = 47/78 (60%), Gaps = 5/78 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
           ++VG L+ + +++DLE  F++ G++  V +A +      GF  VEF+ +  A+ A    
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKAL-EK 59

Query: 67 NDQDLMGSKLRVEISRGR 84
          + ++L+G ++RV+++  R
Sbjct: 60 SGEELLGREIRVDLATER 77

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

>gnl|CDD|240694 cd12248, RRM_RBM44, RNA recognition motif in RNA-binding protein 44 (RBM44) and similar proteins

 Score = 39.5 bits (92), Expect = 6e-05
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV-AFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          V+VGGL+ +V + DL   F+K+ +++ + +   +   +A + F    DA  A   MN   
Sbjct: 2  VHVGGLSPSVSEGDLRSHFQKY-QVSVISLCKLSNYRYASLHFDRASDALLAVKKMNGGV 60

Query: 71 LMGSKLRV 78
          L G  ++V
Sbjct: 61 LSGLSIKV 68

This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells. Length = 74

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 42.0 bits (99), Expect = 8e-05
 Identities = 28/55 (50%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 121 GGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGK 175
            G  FGGG  G   GG  G RGGGG  GGR   G GRG GG  GGR   G  G  
Sbjct: 2   MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGG-GRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 10/80 (12%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA----------FNPPGFAFVEFSNQIDAEA 61
          ++V  L     +E L+  FEK G + SV +A              G+ FVEF ++  A+ 
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 62 ACDSMNDQDLMGSKLRVEIS 81
          A   +    L G  L +++S
Sbjct: 63 ALKRLQGTVLDGHALELKLS 82

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

>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 23 KEDLELEFEKFGKLNSVWV-AFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS 81
          ++DL  E EKFG++  V V   +P G A V+F    +A+   +++N +   G +L  E  
Sbjct: 26 RDDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQLEAERW 85

Query: 82 RGR 84
           G+
Sbjct: 86 DGK 88

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

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

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          +YVG L   V +  L   F+ FG + SV V  +       G+ +V F N  DAE A ++M
Sbjct: 3  LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 67 NDQDLMGSKLRV 78
          N + L G  +R+
Sbjct: 63 NFKRLGGKPIRI 74

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

>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 5/57 (8%)

Query: 30 FEKFGKLNSVWVAFNP-PGF-AFVEFSNQIDAEAACDSMNDQD-LMGS-KLRVEISR 82
          F  +G +  + + F    G  A V+F +   AE A  ++N ++   G   L ++ SR
Sbjct: 22 FSPYGAVEKI-LIFEKNTGVQALVQFDSVESAENAKKALNGRNIYDGCCTLDIQFSR 77

This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. . Length = 85

>gnl|CDD|240973 cd12529, RRM2_MEI2_like, RNA recognition motif 2 in plant Mei2-like proteins

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +GT V V  L  +V  +DL   F  +G++  +    N     F+EF +   AEAA  ++N
Sbjct: 1  QGTLV-VFNLDPSVSNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALN 59

Query: 68 DQDLMGSKLRVE 79
            ++ G ++++E
Sbjct: 60 RSEIAGKRIKLE 71

This subgroup corresponds to the RRM2 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 is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 71

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 5/50 (10%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSN 55
          +++VGGL E V +EDL   F ++G + SV +  +       GFAFV F +
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD 50

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

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 23/61 (37%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 98  DSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFR-GSRGGGGYRGGRDEYGGG 156
           D++   GG R GGG   GG  R+GG  F G  R  G G  R  S      R  R +   G
Sbjct: 562 DAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTG 621

Query: 157 R 157
           R
Sbjct: 622 R 622

Length = 629

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 22/65 (33%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 141 RGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGRFRSRSPVQR 200
             GG  RGG   +GG R  GG     + R   GG+ D     G  R G    R  S  +R
Sbjct: 566 HTGGERRGGGRGFGGERREGGRNFSGERRE--GGRGDGRRFSGERREGRAPRRDDSTGRR 623

Query: 201 RYNVD 205
           R+  D
Sbjct: 624 RFGGD 628

Length = 629

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

 Score = 38.4 bits (90), Expect = 1e-04
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          R++VG L   + +E+ +  F K+G+++ V++     GF F+    + +AE A   ++   
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGEVSEVFLN-KEKGFGFIRLDTRTNAEKAKAELDGIM 61

Query: 71 LMGSKLRV 78
            G +LRV
Sbjct: 62 RKGRQLRV 69

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

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          ++VG L+  V    L   F  F   +   V ++       G+ FV F +Q DAE A + M
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 67 NDQDLMGSKLRV 78
          N + L    +R 
Sbjct: 62 NGKWLGSRPIRC 73

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 5/78 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          ++V  L  +V +EDL   F     +    V  +P      G+ FV F+   DA+ A   +
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 67 NDQDLMGSKLRVEISRGR 84
           ++ L G  LR++I+  R
Sbjct: 62 KNKKLHGRILRLDIAERR 79

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

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 16/66 (24%)

Query: 17 LTETVKKEDLELEFEKFG--KLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQD 70
          L + ++K      F KFG  K+  +++  +      G+AFVEF+   +A+ A  ++N   
Sbjct: 20 LKKVLRKI-----FSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALN--- 71

Query: 71 LMGSKL 76
            G KL
Sbjct: 72 --GYKL 75

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

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSV-----WVAFNPPGFAFVEFSNQIDAEAACDSM 66
          ++VG L+    +E L   F ++G +  +      V     G+AFVE+ ++ DA  A    
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 67 NDQDLMGSKLRVEISRGR 84
          +   + GS++ V+  R R
Sbjct: 66 HKLVIDGSEIFVDFERER 83

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

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          +R++VG L   + +E++   FEK+GK   +++     GF F+    +  AE A   +++ 
Sbjct: 2  SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIH-KDKGFGFIRLETRTLAEIAKAELDNM 60

Query: 70 DLMGSKLRV 78
           L G +LRV
Sbjct: 61 PLRGKQLRV 69

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.5 bits (95), Expect = 2e-04
 Identities = 30/60 (50%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 132 RGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGRDSRGFDGGKPDYYNGGGGGRGGGGR 191
              GGF G RGGG   GG    GGGRGGGG  GGR   G   G+     G GGG GGG  
Sbjct: 1   GMGGGFGGGRGGGRGGGG----GGGRGGGGRGGGRG-GGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFNPPGFA-FVEFSNQIDAEAACDSMN 67
           ++ +  +   V+ EDL+     +G + +   V          V + +   A+ A + +N
Sbjct: 1  RKIQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVNKLN 60

Query: 68 DQDLMGSKLRVE 79
            +  GSKL+V 
Sbjct: 61 GHEYEGSKLKVS 72

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

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

 Score = 41.5 bits (97), Expect = 2e-04
 Identities = 50/183 (27%), Positives = 70/183 (38%), Gaps = 26/183 (14%)

Query: 12  VYVGGLTETVKKEDLELEFEKF--GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
           +YV  L  T  +E +E  F +F  GK+  V    +   +AFV F ++ DA  A D +N +
Sbjct: 236 LYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD---YAFVHFEDREDAVKAMDELNGK 292

Query: 70  DLMGSKLRVEISR----------GRGRGRGGGGRGGRFDSRGGRGG----YRGGGGGYGG 115
           +L GS++ V +++           RG G  G  R     S G               Y  
Sbjct: 293 ELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYH 352

Query: 116 GGYRDGGDRFGG----GGRGRGDGGFR--GSRGGGGYRGGRDEYGGGRGGGGYRGGRDSR 169
             Y              GRGRG    R  G RG   Y G    YG   G   YRG  + +
Sbjct: 353 PPYAPSLHFPRMPGPIRGRGRGGAPSRAAGGRGYPPY-GYEAYYGDYYGYHDYRGKYEDK 411

Query: 170 GFD 172
            + 
Sbjct: 412 YYG 414

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

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACD 64
          G  +YV  L +++  E L  EF  FG + S  V  +      GF FV FS+  +A  A  
Sbjct: 1  GVNLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVT 60

Query: 65 SMNDQDLMGSK 75
           MN + ++G K
Sbjct: 61 EMNGR-IIGGK 70

This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 79

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

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 5/73 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFG-----KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          ++VG L   + +++L+  F++FG     ++NS       P F FV F +    +    + 
Sbjct: 6  LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 67 NDQDLMGSKLRVE 79
                  +L VE
Sbjct: 66 PIYFRGDHRLNVE 78

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

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMND 68
          R+YVG L   V+++DLE  F K+G++  + +        FAFV F +  DAE A    N 
Sbjct: 1  RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVPFAFVRFEDPRDAEDAVFGRNG 60

Query: 69 QDLMGSKLRVE 79
           D    +LRVE
Sbjct: 61 YDFGQCRLRVE 71

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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 5/62 (8%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAA 62
          R  +++VGGL+     ED++  FE+FGK+    + F+       GF FV F N+   E  
Sbjct: 2  RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61

Query: 63 CD 64
          C+
Sbjct: 62 CE 63

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 5/59 (8%)

Query: 15 GGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQDL 71
          GGL   V +E+L   FEK+G +  + +   PPG  + FV +S+  DA AA D++N ++L
Sbjct: 9  GGLGNGVSREELLRVFEKYGTVEDLVM---PPGKPYCFVSYSSIEDAAAAYDALNGKEL 64

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

>gnl|CDD|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 = 38.0 bits (89), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 24 EDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
          +DL   F  FG + S  V  +        F FV + N   A+AA  +MN   + G +L+V
Sbjct: 13 QDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGKRLKV 72

Query: 79 E 79
          +
Sbjct: 73 Q 73

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

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 12 VYVGGLTETVKKEDL-ELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAACDSM 66
          ++VG L   V +E L EL F + G L  V +  +P G    FAFV F +++    A   +
Sbjct: 4  LFVGNLDARVTEEILYEL-FLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 67 NDQDLMGSKLRVE 79
          N   L G +LR++
Sbjct: 63 NGIRLFGRELRIK 75

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

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

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 4/53 (7%)

Query: 30 FEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
          F + GK     +A  P     GFAFVE++   DAE A  ++N   L GS +RV
Sbjct: 24 FSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALNGHSLQGSPIRV 76

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

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 3/73 (4%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          RVY+G L+  V+++D++  F  +GKL  + +     G+ FVEF +  DA+ A   +N +D
Sbjct: 1  RVYIGRLSYHVREKDIQRFFGGYGKLLEIDLK---NGYGFVEFEDSRDADDAVYELNGKD 57

Query: 71 LMGSKLRVEISRG 83
          L G ++ VE +RG
Sbjct: 58 LCGERVIVEHARG 70

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 16/55 (29%), Positives = 33/55 (60%), Gaps = 5/55 (9%)

Query: 26 LELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
          LE  F +FG L  V++    PG  + + +++++  AE A  +++ +++ G KL+V
Sbjct: 16 LEDVFCRFGGLIDVYLV---PGKNYGYAKYADRESAERAITTLHGKEVNGVKLKV 67

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

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

 Score = 37.8 bits (88), Expect = 3e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMN 67
          R++V  +    +  DL   F +FG +  V + FN     GF FV F+N  DA+ A + ++
Sbjct: 2  RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLH 61

Query: 68 DQDLMGSKLRV 78
             + G K+ V
Sbjct: 62 GTVVEGRKIEV 72

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

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

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 3/77 (3%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-GFAFVEFSNQIDAEAACDSMND 68
          T +++G L++ V +EDL+  FE++G++ S+     PP G A+V    + DA  A   + +
Sbjct: 3  TTLWIGHLSKKVTEEDLKNLFEEYGEIQSI--DMIPPRGCAYVCMETRQDAHRALQKLRN 60

Query: 69 QDLMGSKLRVEISRGRG 85
            L G K++V  +  +G
Sbjct: 61 VKLAGKKIKVAWAPNKG 77

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

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

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
           +++VG ++ T   ++L   FE+FG++           +AFV    + +A AA +++N +
Sbjct: 1  WKIFVGNVSATCTSDELRGLFEEFGRVVECDKV---KDYAFVHMEREEEALAAIEALNGK 57

Query: 70 DLMGSKLRVEI 80
          ++ G ++ VE+
Sbjct: 58 EVKGRRINVEL 68

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

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

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 6/73 (8%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSM 66
          V+VG L   +++E+L   FE  G + +V +  +       GF +V F  +     A   +
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 67 NDQDLMGSKLRVE 79
          N   L G K+RV+
Sbjct: 61 NGIKLKGRKIRVK 73

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

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

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 27/124 (21%), Positives = 51/124 (41%), Gaps = 23/124 (18%)

Query: 11  RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
           ++YVG L   + +++L   FE FG +  V +  +P      GF F++F +  +A+ A + 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 66  MNDQDLMGSKLRV-----------------EISRGRGRGRGGGGRG-GRFDSRGGRGGYR 107
           MN  +L G  ++V                 +I + +  G+        +   +  R    
Sbjct: 248 MNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGD 307

Query: 108 GGGG 111
           GG  
Sbjct: 308 GGLL 311

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

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
          ++V  L  TV +E LE  F +FGKL  V        +AF+ F  +  A  A + MN ++L
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKLERVK---KLKDYAFIHFDERDGAVKAMEEMNGKEL 60

Query: 72 MGSKLRVEISR 82
           G  + +  ++
Sbjct: 61 EGENIEIVFAK 71

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 37.5 bits (88), Expect = 4e-04
 Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 5/77 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          +YVG L+    +E +   F + G +  + +  +     P GF FVE+  + DAE A   +
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 67 NDQDLMGSKLRVEISRG 83
          N   L    +RV+   G
Sbjct: 61 NGTKLDDRIIRVDWDAG 77

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

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

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
          R+++  L  T  +EDLE  F K+G L+ V +  +     P GFAFV +     A  A   
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 66 MNDQDLMGSKLRV 78
          ++     G  L +
Sbjct: 64 LDGTVFQGRLLHL 76

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

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG--FAFVEFSNQIDAEAACDSMNDQ 69
          +YVG +     + +L   F+ FG++  + + F   G  + FV +    DA  A +  ND 
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDNYGFVTYRYACDAFRAIEHGNDD 64

Query: 70 D 70
           
Sbjct: 65 P 65

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)

Query: 30 FEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK 75
          F + G++ SV +  N       G+ FVEF+    AE A  S+N + +  ++
Sbjct: 20 FAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQ 70

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

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

 Score = 37.0 bits (85), Expect = 6e-04
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 12 VYVGGLTETVKKEDLELE-FEKFGKLNSVWV----AFNPPGFAFVEFSNQIDAEAACDSM 66
          +YVG L+  V  E L L+ F + G   S  +      N P + FVEF    DA AA  +M
Sbjct: 2  LYVGNLSRDVT-EVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAM 59

Query: 67 NDQDLMGSKLRV 78
          N + ++G +++V
Sbjct: 60 NGRKILGKEVKV 71

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

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMN 67
          +++  L +++  + L   F  FG + S  VA +      G+ FV F  +  A  A + +N
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

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

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

 Score = 36.8 bits (86), Expect = 7e-04
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 5/59 (8%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAAC 63
          T+++VGGL      + L   F +FG++    V  +       G+ FV F ++  AE AC
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERAC 59

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

>gnl|CDD|240706 cd12260, RRM2_SREK1, RNA recognition motif 2 in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAF---NPPGFAFVEFSNQIDAEAACDSMND 68
          +YVG L  T   + L   F + G++  V +A     P  +AFVEF+ Q     A   +N 
Sbjct: 7  IYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINAL-KLNG 65

Query: 69 QDLMGSKLRVEISR 82
              G  L+V  S 
Sbjct: 66 AMFGGRPLKVNHSN 79

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS 65
          ++++GGL+    ++ LE  F K+G+++ V V  +       GF FV F N  DA+ A  +
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 66 MNDQDLMGSKLRVE 79
          MN + + G ++RV+
Sbjct: 62 MNGKSVDGRQIRVD 75

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 36.6 bits (85), Expect = 8e-04
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 13/83 (15%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLN--------SVWVAFN-----PPGFAFVEFSNQID 58
          V+V  L     ++DL   F   G +          +W+  +     P G A V + +   
Sbjct: 1  VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 59 AEAACDSMNDQDLMGSKLRVEIS 81
          A AA +  N++D MG+ ++V ++
Sbjct: 61 ASAAIEWFNNKDFMGNTIKVSLA 83

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241049 cd12605, RRM_RALYL, RNA recognition motif in vertebrate RNA-binding Raly-like protein (RALYL)

 Score = 36.5 bits (84), Expect = 8e-04
 Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 10 TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
          +RV++G L T  VKK D+E  F K+GK+    V     G+AFV++ ++  A AA    N 
Sbjct: 2  SRVFIGNLNTAIVKKADIEAIFAKYGKIVGCSVH---KGYAFVQYISERHARAAVAGENA 58

Query: 69 QDLMGSKLRV 78
          + + G  L +
Sbjct: 59 RIIAGQPLDI 68

This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. . Length = 69

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

 Score = 36.6 bits (85), Expect = 9e-04
 Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 5/73 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSM 66
          ++VG L+    ++ +   F ++G+++SV +  +P      GF +VEFS+Q  A+AA D++
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 67 NDQDLMGSKLRVE 79
             DL+G  +R++
Sbjct: 61 GGTDLLGRPVRLD 73

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

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 36.6 bits (84), Expect = 9e-04
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 4/73 (5%)

Query: 10 TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
          +RV++G L T  VKK D+E  F K+G++    V     G+AFV++SN+  A  A    N 
Sbjct: 2  SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSVH---KGYAFVQYSNERHARGAVIGENG 58

Query: 69 QDLMGSKLRVEIS 81
          + L G  L + ++
Sbjct: 59 RVLAGQTLDINMA 71

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

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

 Score = 36.5 bits (85), Expect = 9e-04
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSM 66
          R++VGG+     +E+L   F +FG +  V +  +      G+ FV F  Q DAE     M
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILA-M 62

Query: 67 NDQDLMGSKLRV 78
           + +  G KL +
Sbjct: 63 GNLNFRGKKLNI 74

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

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDA 59
          VY+G L E+  +E+L  + EKFG ++ + +       AFV F +  +A
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIKI-VKEKNIAFVHFLSIANA 52

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

>gnl|CDD|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 7/60 (11%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGK-LNSVWVAFNPP------GFAFVEFSNQIDAEAA 62
           R++VGG+ +T  KE++  EF K  + +  V V  +P       GFAFVE+ +   A  A
Sbjct: 2  CRLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMA 61

This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 40/118 (33%), Positives = 56/118 (47%), Gaps = 14/118 (11%)

Query: 10  TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
           T++++GGL+       L   F  FG +    V  +       GF FV F+++  A AA  
Sbjct: 35  TKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAIS 94

Query: 65  SMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGG 122
            M+ ++L G  +RV  +  R              + GG GGY GGGGGYGGGG   GG
Sbjct: 95  EMDGKELNGRHIRVNPANDRPSAP---------RAYGGGGGYSGGGGGYGGGGDGGGG 143

Length = 144

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

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 3/76 (3%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          RVY+G L+   ++ D+E  F+ +GK+  V +     G+ FVEF +  DA+ A   +N +D
Sbjct: 1  RVYIGRLSYQARERDVERFFKGYGKILEVDLK---NGYGFVEFDDLRDADDAVYELNGKD 57

Query: 71 LMGSKLRVEISRGRGR 86
          L G ++ VE +RG  R
Sbjct: 58 LCGERVIVEHARGPRR 73

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

>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]

 Score = 38.1 bits (89), Expect = 0.001
 Identities = 16/35 (45%), Positives = 17/35 (48%)

Query: 83  GRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGG 117
           GR R   G G  G        GG+ GGGG  GGGG
Sbjct: 232 GRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGG 266

Length = 271

>gnl|CDD|240942 cd12498, RRM3_ACF, RNA recognition motif 3 in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
          +YV  L  +  +E +E EF    K  +V        +AFV FSN+ DA  A +++N + +
Sbjct: 11 LYVRNLMLSTTEETIEKEFNSI-KPGAVERVKKIRDYAFVHFSNREDAVDAMNALNGKVI 69

Query: 72 MGSKLRVEISR 82
           GS + V +++
Sbjct: 70 DGSPIEVTLAK 80

This subgroup corresponds to the RRM3 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. ACF 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 = 83

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +++VG + E   +E+L   FE +G + S  V      FAFV    +  A+ A + +N ++
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ---FAFVHLRGEAAADRAIEELNGRE 58

Query: 71 LMGSKLRVEIS 81
          L G KL VE S
Sbjct: 59 LHGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 10/78 (12%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF----------AFVEFSNQIDAE 60
          RVY+  L+ +  +EDLE   + F  ++ +  +    GF          A+ EFS+   AE
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAE 60

Query: 61 AACDSMNDQDLMGSKLRV 78
               +N +     KL V
Sbjct: 61 KVVKDLNGKVFKNRKLFV 78

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

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMND 68
          V GL+    + DL   F K+G +  V + ++       GFAFV F N  DA+ A +  N 
Sbjct: 14 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 69 QDLMGSKLRVEIS 81
           +L G ++RV+ S
Sbjct: 74 MELDGRRIRVDFS 86

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

>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of calcineurin (RCANs) and similar proteins

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 23 KEDLELEFEKFGKLNSVWVAFNP-PGF--AFVEFSNQIDAEAACDSMNDQDLMGSKLRV 78
          K  LE  F  +G++      F   P F  A V FS+  +A  A   ++     GS LRV
Sbjct: 17 KAALESLFSSYGEI----ATFVYLPSFRRARVVFSSPEEAALARIELHGTVFEGSVLRV 71

This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic subunit. Overexpressed RCANs may bind and inhibit calcineurin. In contrast, low levels of phosphorylated RCANs may stimulate the calcineurin signaling. RCANs are characterized by harboring a central short, unique serine-proline motif containing FLIISPPxSPP box, which is strongly conserved from yeast to human but is absent in bacteria. They consist of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. . Length = 75

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          V+VG L+  +  ED++  F  FGK++   V  +       G+ FV F N++DAE A   M
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 67 NDQDLMGSKLR 77
            Q L G ++R
Sbjct: 64 GGQWLGGRQIR 74

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

>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 35/87 (40%), Positives = 38/87 (43%), Gaps = 19/87 (21%)

Query: 88  RGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYR 147
            GGG  G RFD  GG GG+  GG G       +  D F   GRG G        GG G  
Sbjct: 79  AGGGFGGRRFDGGGGFGGFGTGGDGAE----FNLNDLFDAAGRGGG--------GGIG-- 124

Query: 148 GGRDEYGG--GRGGGGYRGGRDSRGFD 172
              D +GG   RGGG  R  R  RG D
Sbjct: 125 ---DLFGGLFNRGGGSARPSRPRRGND 148

Length = 392

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 16/66 (24%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACDSM 66
          +++VG L +   ++++E  F  +G++  +++  +      G AFV++S++  A+AA  ++
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 67 NDQDLM 72
          N    M
Sbjct: 61 NGVYTM 66

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVW-------VAFNPPGFAFVEFSNQIDAEAAC 63
          +V+VGGL   + ++++   F +FG L   W         F P G+AF+ F  +   +A  
Sbjct: 2  KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 61

Query: 64 DS 65
          D+
Sbjct: 62 DA 63

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

>gnl|CDD|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 35.5 bits (82), Expect = 0.002
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWV----AFNPPGFAFVEFSNQIDAEAACDSMN 67
          +YV G     +  DL  EFE++G+L    +     F    FAFVE+ +  DAE A + M+
Sbjct: 2  LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPRTFQSRPFAFVEYESHRDAEDAYEEMH 61

Query: 68 DQDLMGSK--LRVEISR 82
           +    +   L V+ ++
Sbjct: 62 GRRFPDTGDTLHVQWAK 78

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but 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. Some family members also contain another RRM domain. Length = 78

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

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 5/74 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-----NPPGFAFVEFSNQIDAEAACD 64
          T + V  L + + +E+L   FE  G + S  +          G+ FV++ ++ DA+ A +
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 65 SMNDQDLMGSKLRV 78
          ++N  ++   +L+V
Sbjct: 61 TLNGFEIRNKRLKV 74

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 15/41 (36%), Positives = 25/41 (60%)

Query: 23 KEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAAC 63
          +++L   F K+G ++ V V+    G A VEF+++  AEAA 
Sbjct: 18 EDELRKIFSKYGDVSDVVVSSKKKGSAIVEFASKKAAEAAV 58

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 22/51 (43%), Positives = 24/51 (47%)

Query: 80  ISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGR 130
           +  GR   R   G  GR     G GG  G GGG  GGG+  GG   GGGG 
Sbjct: 217 LYLGRQPDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGA 267

Length = 271

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

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          VYVG +      E+LE  F   G +N V +  +     P GFA++EFS++     A   +
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALA-L 60

Query: 67 NDQDLMGSKLRVEISR 82
          ++    G +++V   R
Sbjct: 61 DESLFRGRQIKVMPKR 76

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

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 5/71 (7%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSMN 67
           VG L      E        FG +   ++ ++       G+ FVE++++  A  A + ++
Sbjct: 3  CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 68 DQDLMGSKLRV 78
           + + G KL+V
Sbjct: 63 GKQIGGRKLQV 73

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

>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 28/61 (45%), Positives = 31/61 (50%)

Query: 107 RGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSRGGGGYRGGRDEYGGGRGGGGYRGGR 166
           RGGGGG GGGG+  GG   GGGG G G GG  G  G        D +      GG+ GG 
Sbjct: 122 RGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGD 181

Query: 167 D 167
           D
Sbjct: 182 D 182

Length = 186

>gnl|CDD|240940 cd12496, RRM3_RBM46, RNA recognition motif 3 in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
          +YV  L  +  +E ++ EF KF K   V        +AFV F N+ DA AA   MN + +
Sbjct: 4  LYVRNLMISTTEETIKAEFNKF-KPGVVERVKKLRDYAFVHFFNREDAVAAMSVMNGKCI 62

Query: 72 MGSKLRVEISR 82
           G+ + V +++
Sbjct: 63 DGASIEVTLAK 73

This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDSM 66
          +YV GL +T+ +++LE  F  +G++ +  +  +       G  F+ F  +I+AE A  ++
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 67 NDQDLMGS 74
          N     G+
Sbjct: 63 NGTIPPGA 70

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

>gnl|CDD|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 5/64 (7%)

Query: 12 VYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +YVGG+      + +E      F ++G +  + V     G AFV +  +  AE A ++M 
Sbjct: 4  LYVGGIKAGSALKQIEEILRRHFGEWGDIEDIRV-LPSKGIAFVRYKYRASAEFAKEAMA 62

Query: 68 DQDL 71
          DQ L
Sbjct: 63 DQSL 66

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

>gnl|CDD|240750 cd12304, RRM_Set1, RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)

Query: 16 GLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDSMNDQD 70
           L + + +  L+   +K+G++  V + F+P      G A V F +   A+   + +N   
Sbjct: 9  NLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCVEKLNQTS 68

Query: 71 LMGSKLRVEI 80
          +MG  ++V +
Sbjct: 69 VMGKIIKVFL 78

This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. . Length = 93

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 34.5 bits (80), Expect = 0.004
 Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 19 ETVKKEDLELEFEKFGKLNSVWVAFNPP----GFAFVEFSNQIDAEAACDSMNDQDLMGS 74
          E  KKE  EL F  FG++ SV +         GFAFVEF  + +A+ A +++    L G 
Sbjct: 11 EATKKELREL-FSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGR 69

Query: 75 KLRVE 79
           L +E
Sbjct: 70 HLVLE 74

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 11 RVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          R+++G L T+ V KEDL   F  +G+L  + +      + FV+F +      A +    +
Sbjct: 1  RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKNA---YGFVQFDSPESCANAINCEQGK 57

Query: 70 DLMGSKLRVEISR 82
           + G KL +E+S+
Sbjct: 58 MIRGRKLHLEVSK 70

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

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

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF----NPPGFAFVEFSNQIDAEAACD 64
          G  +++G L   + +++L    EK GK+  + +      N  G+AFV FSN+ +A+ A  
Sbjct: 1  GCEIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIK 60

Query: 65 SMNDQDLMGSKL 76
           +N+ ++   +L
Sbjct: 61 QLNNYEIRNGRL 72

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|217469 pfam03276, Gag_spuma, Spumavirus gag protein

 Score = 37.2 bits (86), Expect = 0.004
 Identities = 34/124 (27%), Positives = 44/124 (35%), Gaps = 16/124 (12%)

Query: 82  RGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGYGGGGYRDGGDRFGGGGRGRGDGGFRGSR 141
           R   RGRG G RG R   +  R     G         R   +R     + +  G  +G R
Sbjct: 445 RPVSRGRGRGQRGPRSQPQNQRRQQNRGRQSSQPP--RQQQNRSNQNNQRQSQGPNQGPR 502

Query: 142 GGGGYRGGRD-----EYGGGRGGGG----YR-----GGRDSRGFDGGKPDYYNGGGGGRG 187
           G GGY           YGGG+G       YR       +  +     + +     G GRG
Sbjct: 503 GQGGYNLRPRTYQPQRYGGGQGRRWNPNPYRQSGQGRSQQQQPQPEARGNQSRTPGPGRG 562

Query: 188 GGGR 191
            GGR
Sbjct: 563 QGGR 566

Length = 582

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	207
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.88
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
KOG0107|consensus	195		99.76
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.75
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.74
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
KOG0125|consensus	376		99.71
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.7
PLN03120	260	nucleic acid binding protein; Provisional	99.66
KOG0122|consensus	270		99.65
KOG0149|consensus	247		99.65
KOG0148|consensus	321		99.65
KOG0121|consensus	153		99.64
KOG0117|consensus	506		99.63
KOG0105|consensus	241		99.63
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.6
PLN03121	243	nucleic acid binding protein; Provisional	99.59
KOG0113|consensus	335		99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
KOG4207|consensus	256		99.59
smart00362	72	RRM_2 RNA recognition motif.	99.59
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.58
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.57
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.57
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.57
KOG0130|consensus	170		99.56
PLN03213	759	repressor of silencing 3; Provisional	99.56
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.55
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.55
KOG0117|consensus	506		99.54
KOG0144|consensus	510		99.53
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.53
KOG0109|consensus	346		99.52
smart00360	71	RRM RNA recognition motif.	99.52
KOG0111|consensus	298		99.52
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.51
KOG0131|consensus	203		99.5
KOG0114|consensus	124		99.48
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.48
KOG0148|consensus	321		99.48
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
KOG4212|consensus	608		99.46
KOG0144|consensus	510		99.46
KOG0109|consensus	346		99.41
KOG0145|consensus	360		99.41
KOG0146|consensus	371		99.41
KOG0415|consensus	479		99.4
KOG0127|consensus	678		99.4
KOG0108|consensus	435		99.39
KOG0116|consensus	419		99.39
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.37
KOG0145|consensus	360		99.37
KOG0126|consensus	219		99.33
KOG0127|consensus	678		99.32
KOG0123|consensus	369		99.31
KOG0132|consensus	894		99.31
KOG4206|consensus	221		99.29
smart00361	70	RRM_1 RNA recognition motif.	99.28
KOG0153|consensus	377		99.27
KOG0131|consensus	203		99.24
KOG4205|consensus	311		99.23
KOG4205|consensus	311		99.23
KOG4212|consensus	608		99.23
KOG0147|consensus	549		99.19
KOG0146|consensus	371		99.19
KOG0124|consensus	544		99.17
KOG0110|consensus	725		99.14
KOG4661|consensus	940		99.14
KOG1457|consensus	284		99.12
KOG0533|consensus	243		99.06
KOG4454|consensus	267		99.06
KOG4211|consensus	510		99.02
KOG4208|consensus	214		99.01
KOG0110|consensus	725		99.01
KOG0106|consensus	216		98.95
KOG0123|consensus	369		98.94
KOG0124|consensus	544		98.89
KOG1548|consensus	382		98.88
KOG4660|consensus	549		98.86
KOG4209|consensus	231		98.85
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.81
KOG1995|consensus	351		98.7
KOG0151|consensus	877		98.65
KOG1190|consensus	492		98.65
KOG4206|consensus	221		98.6
KOG4211|consensus	510		98.59
KOG0106|consensus	216		98.58
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.53
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.51
KOG1457|consensus	284		98.51
KOG0120|consensus	500		98.42
KOG0226|consensus	290		98.42
KOG1855|consensus	484		98.34
KOG1456|consensus	494		98.32
KOG1456|consensus	494		98.3
KOG1190|consensus	492		98.25
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.23
KOG0105|consensus	241		98.21
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	98.17
KOG2202|consensus	260		98.13
KOG1548|consensus	382		98.1
KOG4307|consensus	944		98.08
KOG0147|consensus	549		98.06
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	98.01
KOG4210|consensus	285		98.01
KOG0129|consensus	520		97.99
KOG0129|consensus	520		97.96
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.94
KOG4849|consensus	498		97.85
KOG0120|consensus	500		97.81
KOG1365|consensus	508		97.8
KOG2314|consensus	698		97.72
KOG3152|consensus	278		97.71
KOG2416|consensus	718		97.62
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.61
KOG4676|consensus	479		97.44
KOG0128|consensus	881		97.33
KOG1996|consensus	378		97.33
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.27
KOG2591|consensus	684		97.23
KOG0112|consensus	975		97.22
KOG0921|consensus	1282		97.19
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	97.18
KOG2193|consensus	584		97.09
KOG4307|consensus	944		97.08
KOG1365|consensus	508		97.02
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.99
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.79
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.76
KOG2135|consensus	526		96.67
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.66
KOG0115|consensus	275		96.61
KOG4285|consensus	350		96.52
KOG0112|consensus	975		96.48
KOG0128|consensus	881		96.34
KOG2068|consensus	327		96.19
KOG4574|consensus	1007		96.16
KOG0804|consensus	493		96.12
KOG2253|consensus	668		95.99
KOG4660|consensus	549		95.7
KOG2318|consensus	650		95.28
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	95.19
KOG3973|consensus	465		94.97
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.7
KOG4210|consensus	285		94.54
KOG2193|consensus	584		92.97
KOG4019|consensus	193		92.69
KOG3973|consensus	465		92.06
KOG4676|consensus	479		91.24
KOG3262|consensus	215		90.58
KOG4410|consensus	396		90.46
KOG4483|consensus	528		90.26
KOG2295|consensus	648		89.54
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	89.28
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	88.49
PF00403	62	HMA: Heavy-metal-associated domain; InterPro: IPR0	85.64
cd06405	79	PB1_Mekk2_3 The PB1 domain is present in the two m	84.97
PF02714	325	DUF221: Domain of unknown function DUF221; InterPr	83.06
COG0724	306	RNA-binding proteins (RRM domain) [General functio	82.65
PF14893	331	PNMA: PNMA	82.64
PRK10629	127	EnvZ/OmpR regulon moderator; Provisional	82.05
KOG2891|consensus	445		81.59

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

Probab=99.88  E-value=1.8e-21  Score=149.87  Aligned_cols=84  Identities=27%  Similarity=0.486  Sum_probs=77.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ....+++|||.|||+++||++|+++|++|++|++|+|++|     +++||||+|+++++|++||+.||+++|++++|+|+
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999987     68999999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q psy2347          80 ISRGRGRGR   88 (207)
Q Consensus        80 ~a~~k~~~~   88 (207)
                      ++++++...
T Consensus       110 ~a~~~~~~~  118 (144)
T PLN03134        110 PANDRPSAP  118 (144)
T ss_pred             eCCcCCCCC
Confidence            998776543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=1.1e-17  Score=145.67  Aligned_cols=81  Identities=27%  Similarity=0.525  Sum_probs=73.0

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVEI   80 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~~   80 (207)
                      +.++|||.|||+++||++|+++|++|++|+.|+|+.|     +++||||+|+++++|++||++||+++|.+  ++|+|++
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            4678999999999999999999999999999999987     56899999999999999999999998876  6899999


Q ss_pred             eecCCCCC
Q psy2347          81 SRGRGRGR   88 (207)
Q Consensus        81 a~~k~~~~   88 (207)
                      ++++.+.+
T Consensus       272 a~~~~~~~  279 (346)
T TIGR01659       272 AEEHGKAK  279 (346)
T ss_pred             CCcccccc
Confidence            88765443

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).

>KOG0107|consensus

Probab=99.76  E-value=6.2e-18  Score=130.94  Aligned_cols=85  Identities=52%  Similarity=0.885  Sum_probs=78.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGR   86 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~   86 (207)
                      +-.++|||+||+..+++.||+.+|..|++|..|.|...+.+||||||+++.+|++|+..|++++|++..|+|++++-+++
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~r   87 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRPR   87 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCcc
Confidence            45789999999999999999999999999999999988999999999999999999999999999999999999988776


Q ss_pred             CCCCC
Q psy2347          87 GRGGG   91 (207)
Q Consensus        87 ~~~~g   91 (207)
                      ...++
T Consensus        88 ~~r~g   92 (195)
T KOG0107|consen   88 GSRRG   92 (195)
T ss_pred             ccccC
Confidence            54433

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.75  E-value=6.3e-18  Score=147.10  Aligned_cols=80  Identities=24%  Similarity=0.428  Sum_probs=74.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      .....++|||++||+++||++|+++|++|++|++|+|++|     +++||||+|+++++|++||++||+++|.+++|+|+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            3456789999999999999999999999999999999987     67999999999999999999999999999999999


Q ss_pred             EeecC
Q psy2347          80 ISRGR   84 (207)
Q Consensus        80 ~a~~k   84 (207)
                      ++++.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            98763

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.74  E-value=2e-17  Score=143.71  Aligned_cols=78  Identities=24%  Similarity=0.314  Sum_probs=74.2

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+|||.|||+++++++|+++|++||.|++|+|++|     +++||||+|++.++|++||++||+.+|.+++|+|.++.+
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            447999999999999999999999999999999987     699999999999999999999999999999999999998


Q ss_pred             CCC
Q psy2347          84 RGR   86 (207)
Q Consensus        84 k~~   86 (207)
                      |+.
T Consensus       349 ~~~  351 (352)
T TIGR01661       349 KAY  351 (352)
T ss_pred             CCC
Confidence            865

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=3.8e-17  Score=141.87  Aligned_cols=80  Identities=26%  Similarity=0.427  Sum_probs=74.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++.++|||+|||.++||++|+++|++||+|++|+|++|     +++||||+|+++++|++||+.||+..|.+++|+|+++
T Consensus         1 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a   80 (352)
T TIGR01661         1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA   80 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee
Confidence            35789999999999999999999999999999999987     6799999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy2347          82 RGRGR   86 (207)
Q Consensus        82 ~~k~~   86 (207)
                      +++..
T Consensus        81 ~~~~~   85 (352)
T TIGR01661        81 RPSSD   85 (352)
T ss_pred             ccccc
Confidence            87653

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

>KOG0125|consensus

Probab=99.71  E-value=2.2e-17  Score=138.68  Aligned_cols=83  Identities=30%  Similarity=0.457  Sum_probs=77.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ..+..++|+|+|||+...|.||+.+|++||+|.+|+|+.+   +|+|+||+|++.++|++|-++||+..|++|+|+|..|
T Consensus        92 s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   92 SKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            3455689999999999999999999999999999999988   9999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++-..
T Consensus       172 TarV~n  177 (376)
T KOG0125|consen  172 TARVHN  177 (376)
T ss_pred             chhhcc
Confidence            876443

>PF00076 RRM_1: RNA recognition motif

Probab=99.71  E-value=4e-17  Score=109.05  Aligned_cols=66  Identities=42%  Similarity=0.712  Sum_probs=63.0

Q ss_pred             EEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347          12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus        12 lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      |||+|||+++|+++|+++|++|++|+.++++.+    ++++|||+|+++++|++|++.|+++.|.+++|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999985    679999999999999999999999999999885

(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 ....

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

Probab=99.70  E-value=7.5e-16  Score=141.22  Aligned_cols=79  Identities=32%  Similarity=0.503  Sum_probs=73.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhC--CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKF--GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~--G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +.+.++|||+||++++||++|+++|++|  ++|++|++++   .||||+|+++++|++||++||+++|.+++|+|++++|
T Consensus       230 ~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r---gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp  306 (578)
T TIGR01648       230 MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR---DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKP  306 (578)
T ss_pred             cccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec---CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            4556899999999999999999999999  9999998875   4999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      +...
T Consensus       307 ~~~~  310 (578)
T TIGR01648       307 VDKK  310 (578)
T ss_pred             CCcc
Confidence            7554

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.66  E-value=6.9e-16  Score=127.83  Aligned_cols=74  Identities=16%  Similarity=0.218  Sum_probs=70.2

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+.+||++|+++|+.||+|++|+|+.+  +++||||+|+++++|++||. |++..|.++.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            579999999999999999999999999999999988  67999999999999999996 899999999999999864

>KOG0122|consensus

Probab=99.65  E-value=6.4e-16  Score=125.37  Aligned_cols=79  Identities=34%  Similarity=0.505  Sum_probs=75.2

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +..++|-|.||+++++|++|+++|.+|+.|..|.|..|     +|+||||+|++.++|++||+.||++-++...|+|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            45678999999999999999999999999999999998     8999999999999999999999999999999999999


Q ss_pred             ecCC
Q psy2347          82 RGRG   85 (207)
Q Consensus        82 ~~k~   85 (207)
                      +|+.
T Consensus       267 kP~~  270 (270)
T KOG0122|consen  267 KPSN  270 (270)
T ss_pred             CCCC
Confidence            9863

>KOG0149|consensus

Probab=99.65  E-value=2.7e-16  Score=126.93  Aligned_cols=75  Identities=29%  Similarity=0.491  Sum_probs=69.7

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .-+||||++|+|+++.++|+++|++||+|++..|++|     +|+|+||+|.|.|+|++||+. ..-.|++|+..|.+|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            5679999999999999999999999999999999999     899999999999999999987 5678999999999875


Q ss_pred             c
Q psy2347          83 G   83 (207)
Q Consensus        83 ~   83 (207)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            3

>KOG0148|consensus

Probab=99.65  E-value=6.1e-16  Score=127.18  Aligned_cols=83  Identities=27%  Similarity=0.448  Sum_probs=77.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +.++.+++|||+||+..+||++|+++|++||+|.+|+|.++ ++||||.|+++|+|.+||..||+.+|.++.|+|.|-+.
T Consensus       159 Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  159 QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKE  237 (321)
T ss_pred             cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-cceEEEEecchhhHHHHHHHhcCceeCceEEEEecccc
Confidence            45678899999999999999999999999999999999999 99999999999999999999999999999999999877


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      ....
T Consensus       238 ~~~~  241 (321)
T KOG0148|consen  238 GDDG  241 (321)
T ss_pred             CCCC
Confidence            5443

>KOG0121|consensus

Probab=99.64  E-value=3.8e-16  Score=115.46  Aligned_cols=78  Identities=27%  Similarity=0.480  Sum_probs=72.7

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      +..++++|||+||+..++|++|.++|+++|+|..|.+-.|     +.+||||+|.+.++|+.||+-|++..|+.++|+|.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            4567899999999999999999999999999999987666     78999999999999999999999999999999999


Q ss_pred             Eee
Q psy2347          80 ISR   82 (207)
Q Consensus        80 ~a~   82 (207)
                      |.-
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            874

>KOG0117|consensus

Probab=99.63  E-value=5e-16  Score=134.97  Aligned_cols=81  Identities=30%  Similarity=0.472  Sum_probs=76.0

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +.+.+.+.|||.||+.+|||+.|+++|++|+.|++|+.++|   ||||.|.+.++|.+||+.||+++|++..|+|.+|+|
T Consensus       254 d~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD---YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  254 DTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD---YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             hhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc---eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            46678899999999999999999999999999999999877   999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      ..+.
T Consensus       331 ~~k~  334 (506)
T KOG0117|consen  331 VDKK  334 (506)
T ss_pred             hhhh
Confidence            6544

>KOG0105|consensus

Probab=99.63  E-value=1.8e-15  Score=118.42  Aligned_cols=77  Identities=38%  Similarity=0.670  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+++|||+|||.++.|.||+++|.+|+.|.+|+|...  +..||||+|+++.+|+.||..-++..+++..|+|+++..
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            45789999999999999999999999999999998766  678999999999999999999999999999999999854

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=3.1e-15  Score=100.55  Aligned_cols=66  Identities=41%  Similarity=0.672  Sum_probs=60.4

Q ss_pred             EEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347          12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus        12 lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      |||.|||+++++++|+++|+.++.|+.|+++.+    .+++|||+|.++++|++|++.+++++|++++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999987    369999999999999999999988999999885

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 ....

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

Probab=99.60  E-value=7.9e-15  Score=133.08  Aligned_cols=78  Identities=27%  Similarity=0.351  Sum_probs=73.7

Q ss_pred             CCCcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           7 ERGTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         7 ~~~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      +++++|||.|||+ .+|+++|+++|++||+|++|+|++++++||||+|+++++|++||+.||++.|.+++|+|++++.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            4678999999998 69999999999999999999999988899999999999999999999999999999999998664

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).

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.59  E-value=9.1e-15  Score=119.57  Aligned_cols=76  Identities=16%  Similarity=0.188  Sum_probs=70.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .+...+|||.||++.+||++|+++|+.||+|++|+|+.|  .++||||+|+++++|+.||. |++.+|.+++|.|..+.
T Consensus         2 ~~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          2 YPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            345689999999999999999999999999999999998  56899999999999999995 89999999999998754

>KOG0113|consensus

Probab=99.59  E-value=7.5e-15  Score=122.14  Aligned_cols=80  Identities=25%  Similarity=0.525  Sum_probs=75.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      .-++-+||||.-|+.+++|.+|+..|++||+|+.|.|+.|     +++||||+|+++.++++|.+..++++|+++.|.|.
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            4467899999999999999999999999999999999998     89999999999999999999999999999999999


Q ss_pred             EeecC
Q psy2347          80 ISRGR   84 (207)
Q Consensus        80 ~a~~k   84 (207)
                      +...+
T Consensus       177 vERgR  181 (335)
T KOG0113|consen  177 VERGR  181 (335)
T ss_pred             ecccc
Confidence            87643

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

Probab=99.59  E-value=4.7e-15  Score=136.70  Aligned_cols=81  Identities=32%  Similarity=0.507  Sum_probs=75.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ....++|||.||++++|+++|+++|++||+|++|+|+.|    +++||||+|+++++|++||+.||++.|.+++|.|.+|
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            345678999999999999999999999999999999987    6899999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy2347          82 RGRGR   86 (207)
Q Consensus        82 ~~k~~   86 (207)
                      +.+..
T Consensus       362 ~~k~~  366 (562)
T TIGR01628       362 QRKEQ  366 (562)
T ss_pred             cCcHH
Confidence            87653

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

>KOG4207|consensus

Probab=99.59  E-value=5.5e-15  Score=117.46  Aligned_cols=78  Identities=38%  Similarity=0.598  Sum_probs=73.4

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ++-..+|.|-||...||.++|+.+|++||.|.+|.|+.|     +++||||.|.+..+|++||++|++.+|+++.|.|++
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            344578999999999999999999999999999999998     899999999999999999999999999999999999


Q ss_pred             eec
Q psy2347          81 SRG   83 (207)
Q Consensus        81 a~~   83 (207)
                      |+-
T Consensus        90 ary   92 (256)
T KOG4207|consen   90 ARY   92 (256)
T ss_pred             hhc
Confidence            874

>smart00362 RRM_2 RNA recognition motif

Probab=99.59  E-value=1.3e-14  Score=95.94  Aligned_cols=69  Identities=45%  Similarity=0.707  Sum_probs=64.4

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      +|||.+||.++++++|+++|++|++|+.+.++.+   ++++|||+|.++++|++|++.|++..|.+++|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            5899999999999999999999999999999877   36999999999999999999999999999998874

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

Probab=99.58  E-value=9e-15  Score=134.57  Aligned_cols=80  Identities=29%  Similarity=0.417  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ..++|||+|||+++++++|+++|++||+|++|+|++|     +++||||+|+++++|++||+.||+.+|.++.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            4579999999999999999999999999999999987     68999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      +++..
T Consensus       283 ~pP~~  287 (612)
T TIGR01645       283 TPPDA  287 (612)
T ss_pred             CCccc
Confidence            75543

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

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

Probab=99.58  E-value=7.5e-15  Score=134.69  Aligned_cols=75  Identities=29%  Similarity=0.511  Sum_probs=67.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l~V~~   80 (207)
                      .+..++|||+|||++++|++|+++|++|++|.+|+|++|    +++||||+|+++|+|++||+.||+.+|. ++.|.|.+
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            345689999999999999999999999999999999987    7899999999999999999999998885 56655543

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=99.57  E-value=2.2e-14  Score=130.49  Aligned_cols=78  Identities=23%  Similarity=0.425  Sum_probs=72.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++.++|||+|||+.+|+++|+++|++||.|+.|.|+++     +++||||+|+++++|++||+.||++.|.+++|.|+++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45679999999999999999999999999999999886     6899999999999999999999999999999999998


Q ss_pred             ecC
Q psy2347          82 RGR   84 (207)
Q Consensus        82 ~~k   84 (207)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            653

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

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

Probab=99.57  E-value=1.1e-14  Score=134.12  Aligned_cols=78  Identities=29%  Similarity=0.531  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      .....++|||+|||++++|++|+++|++||+|++|+|+.|     +++||||+|+++++|++||+.||++.|.+++|+|.
T Consensus       103 a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~  182 (612)
T TIGR01645       103 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  182 (612)
T ss_pred             hhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeec
Confidence            3456789999999999999999999999999999999887     78999999999999999999999999999999998


Q ss_pred             Eee
Q psy2347          80 ISR   82 (207)
Q Consensus        80 ~a~   82 (207)
                      +..
T Consensus       183 rp~  185 (612)
T TIGR01645       183 RPS  185 (612)
T ss_pred             ccc
Confidence            654

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.

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

Probab=99.57  E-value=1.4e-14  Score=131.48  Aligned_cols=76  Identities=22%  Similarity=0.208  Sum_probs=70.6

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc--CCceeCCcEEEEEEeecC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM--NDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l--~g~~i~g~~l~V~~a~~k   84 (207)
                      ++++|||+|||+++||++|+++|++||+|++|.|+++ +++|||+|+++++|++||+.|  +...|.+++|.|++++.+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~   78 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQ   78 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCc
Confidence            5789999999999999999999999999999999986 899999999999999999864  678999999999998754

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0130|consensus

Probab=99.56  E-value=9.7e-15  Score=108.97  Aligned_cols=79  Identities=27%  Similarity=0.578  Sum_probs=74.0

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ....|||.++.+++||++|.+.|..||+|++|++..|     .|+||+|+|++.++|++||++||+.+|.+++|.|.|+-
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEE
Confidence            4568999999999999999999999999999999998     78999999999999999999999999999999999987


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      .+.+
T Consensus       151 v~gp  154 (170)
T KOG0130|consen  151 VKGP  154 (170)
T ss_pred             ecCC
Confidence            6544

>PLN03213 repressor of silencing 3; Provisional

Probab=99.56  E-value=1.4e-14  Score=127.56  Aligned_cols=79  Identities=28%  Similarity=0.414  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCH--HHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQ--IDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~--e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ......+|||+||++++|+++|+++|.+||.|+.|+|++. -|+||||+|.+.  +++++||+.||+.+++++.|+|..|
T Consensus         6 s~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          6 SGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             cCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            3445689999999999999999999999999999999977 789999999987  7899999999999999999999999


Q ss_pred             ec
Q psy2347          82 RG   83 (207)
Q Consensus        82 ~~   83 (207)
                      +|
T Consensus        86 KP   87 (759)
T PLN03213         86 KE   87 (759)
T ss_pred             cH
Confidence            76

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

Probab=99.55  E-value=2.2e-14  Score=132.31  Aligned_cols=75  Identities=35%  Similarity=0.512  Sum_probs=70.3

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .+|||+|||+++||++|+++|++||+|++|+|++|     +++||||+|.++++|++||+.||...|.++.|+|.|+...
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            37999999999999999999999999999999987     5689999999999999999999999999999999998643

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

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

Probab=99.55  E-value=3.5e-14  Score=127.64  Aligned_cols=76  Identities=28%  Similarity=0.540  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ..++|||.|||.++|+++|+++|++|+.|+.|.|+.+     +++||||+|.++++|++||+.||+.+|.+++|+|.+++
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            3589999999999999999999999999999999976     57899999999999999999999999999999999986


Q ss_pred             c
Q psy2347          83 G   83 (207)
Q Consensus        83 ~   83 (207)
                      .
T Consensus       265 ~  265 (457)
T TIGR01622       265 D  265 (457)
T ss_pred             C
Confidence            4

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.

>KOG0117|consensus

Probab=99.54  E-value=4e-14  Score=123.28  Aligned_cols=78  Identities=31%  Similarity=0.517  Sum_probs=72.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCcee-CCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDL-MGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i-~g~~l~V   78 (207)
                      ..+..+.|||+.||.++.|+||..+|++.|+|-+++||.|     +|+||||+|.++++|++||+.||+++| .++.|.|
T Consensus        79 ~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   79 PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             CCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence            3466899999999999999999999999999999999998     899999999999999999999999998 4788888


Q ss_pred             EEee
Q psy2347          79 EISR   82 (207)
Q Consensus        79 ~~a~   82 (207)
                      +++.
T Consensus       159 c~Sv  162 (506)
T KOG0117|consen  159 CVSV  162 (506)
T ss_pred             EEee
Confidence            7764

>KOG0144|consensus

Probab=99.53  E-value=9.3e-15  Score=126.71  Aligned_cols=81  Identities=22%  Similarity=0.426  Sum_probs=73.8

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCce-e--CCcEEEEEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQD-L--MGSKLRVEI   80 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~-i--~g~~l~V~~   80 (207)
                      ..++|||+.|+..+||+||+++|++||.|++|.|++|    +|+||||+|+++|.|..||+.||+.. +  +..+|.|+|
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            4789999999999999999999999999999999998    89999999999999999999999864 4  457899999


Q ss_pred             eecCCCCC
Q psy2347          81 SRGRGRGR   88 (207)
Q Consensus        81 a~~k~~~~   88 (207)
                      |.++.++.
T Consensus       203 ADtqkdk~  210 (510)
T KOG0144|consen  203 ADTQKDKD  210 (510)
T ss_pred             cccCCCch
Confidence            99876653

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

Probab=99.53  E-value=5.9e-14  Score=126.13  Aligned_cols=78  Identities=27%  Similarity=0.334  Sum_probs=71.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+.++|||.|||.++|+++|+++|++|++|+.|+|++|     +++||||+|.++++|++||+ |++..|.+++|.|+.
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            345789999999999999999999999999999999987     68999999999999999997 899999999999988


Q ss_pred             eecC
Q psy2347          81 SRGR   84 (207)
Q Consensus        81 a~~k   84 (207)
                      +..+
T Consensus       165 ~~~~  168 (457)
T TIGR01622       165 SQAE  168 (457)
T ss_pred             cchh
Confidence            7543

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.

>KOG0109|consensus

Probab=99.52  E-value=1.5e-14  Score=120.12  Aligned_cols=73  Identities=25%  Similarity=0.508  Sum_probs=69.7

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      .+|||+|||.++++.+|+.+|++|++|++|+|+++   |+||..+++++|+.||..||+.+|++..|+|+.++.|.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN---YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN---YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc---cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            48999999999999999999999999999999976   99999999999999999999999999999999998773

>smart00360 RRM RNA recognition motif

Probab=99.52  E-value=9.2e-14  Score=91.35  Aligned_cols=66  Identities=44%  Similarity=0.710  Sum_probs=61.2

Q ss_pred             EcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347          14 VGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus        14 V~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      |.+||.++++++|+++|++|+.|+.|.|+.+     ++++|||+|.+.++|++|++.|++..+.+++|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            5799999999999999999999999999886     36899999999999999999999999999998874

>KOG0111|consensus

Probab=99.52  E-value=1e-14  Score=116.95  Aligned_cols=82  Identities=34%  Similarity=0.661  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .+....++|||+.|..++||..|...|-+||.|+.|+|+.|     .++|+||||+..|+|.+||..||..+|.++.|+|
T Consensus         5 ~~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirV   84 (298)
T KOG0111|consen    5 QMANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRV   84 (298)
T ss_pred             cccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEE
Confidence            34556789999999999999999999999999999999998     7899999999999999999999999999999999


Q ss_pred             EEeecCC
Q psy2347          79 EISRGRG   85 (207)
Q Consensus        79 ~~a~~k~   85 (207)
                      .+|+|..
T Consensus        85 N~AkP~k   91 (298)
T KOG0111|consen   85 NLAKPEK   91 (298)
T ss_pred             eecCCcc
Confidence            9998743

>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=99.51  E-value=1.5e-13  Score=91.13  Aligned_cols=70  Identities=46%  Similarity=0.737  Sum_probs=65.5

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCC----CcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~----rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      +|+|.+||+.+++++|+++|+.+++|..+.++.+.    +++|||+|.++++|+.|++.++...+.+++|+|++
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            58999999999999999999999999999999873    78999999999999999999999999999999864

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).

>KOG0131|consensus

Probab=99.50  E-value=4.7e-14  Score=110.09  Aligned_cols=80  Identities=28%  Similarity=0.377  Sum_probs=75.2

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ....+...+|||+||++.++++.|.++|-+.++|++|+|++|     .++||||||.++|+|+-||+.||...|.+++|+
T Consensus         3 ~~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIr   82 (203)
T KOG0131|consen    3 IIERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIR   82 (203)
T ss_pred             ccccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeE
Confidence            345677889999999999999999999999999999999988     789999999999999999999999999999999


Q ss_pred             EEEee
Q psy2347          78 VEISR   82 (207)
Q Consensus        78 V~~a~   82 (207)
                      |..+.
T Consensus        83 v~kas   87 (203)
T KOG0131|consen   83 VNKAS   87 (203)
T ss_pred             EEecc
Confidence            99987

>KOG0114|consensus

Probab=99.48  E-value=2.1e-13  Score=97.48  Aligned_cols=77  Identities=23%  Similarity=0.392  Sum_probs=71.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +.++.|||.|||.++|.+++.++|.+|+.|..|+|-.+  .++.|||.|++..+|++|++.|++..++++.|.|-+-.+
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            45678999999999999999999999999999999766  789999999999999999999999999999999987654

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

Probab=99.48  E-value=2.9e-13  Score=110.72  Aligned_cols=74  Identities=38%  Similarity=0.634  Sum_probs=70.6

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .++|||+|||+++|+++|+++|.+|+.|..|.|+.+     +++||||+|+++++|++|++.|++..|.+++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            589999999999999999999999999999998877     78999999999999999999999999999999999965

>KOG0148|consensus

Probab=99.48  E-value=9.3e-14  Score=114.38  Aligned_cols=78  Identities=31%  Similarity=0.476  Sum_probs=74.3

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      -..|||+.|..+++.++|++.|.+||+|.+++|++|     +|+|+||.|.++++|+.||..||+++|..|.|+-.||+.
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            457999999999999999999999999999999999     899999999999999999999999999999999999988


Q ss_pred             CCC
Q psy2347          84 RGR   86 (207)
Q Consensus        84 k~~   86 (207)
                      |+.
T Consensus       142 Kp~  144 (321)
T KOG0148|consen  142 KPS  144 (321)
T ss_pred             Ccc
Confidence            773

>PF13893 RRM_5: RNA recognition motif

Probab=99.47  E-value=3.1e-13  Score=87.21  Aligned_cols=56  Identities=34%  Similarity=0.557  Sum_probs=51.8

Q ss_pred             HHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          26 LELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        26 L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      |+++|++||+|++|.+..+.+.+|||+|++.++|++|++.||+..+.+++|+|++|
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            78999999999999998875599999999999999999999999999999999986

(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 ....

>KOG4212|consensus

Probab=99.46  E-value=3.3e-13  Score=117.45  Aligned_cols=79  Identities=22%  Similarity=0.365  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHh-CCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEK-FGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~-~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ....+.+||.|||+++.|++||++|.+ .++|+.|+++.|    +++||.|||+++|.++||++.||.+++++++|+|+.
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            345567999999999999999999974 899999999998    899999999999999999999999999999999987


Q ss_pred             eecC
Q psy2347          81 SRGR   84 (207)
Q Consensus        81 a~~k   84 (207)
                      ....
T Consensus       121 d~d~  124 (608)
T KOG4212|consen  121 DHDE  124 (608)
T ss_pred             cCch
Confidence            7553

>KOG0144|consensus

Probab=99.46  E-value=1.2e-13  Score=119.82  Aligned_cols=81  Identities=23%  Similarity=0.468  Sum_probs=71.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCce-e--CCcEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQD-L--MGSKL   76 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~-i--~g~~l   76 (207)
                      ...+.-+|||+-||..++|+||+++|++|+.|.+|.|++|     +++||||+|.+.++|.+|+.+||+++ |  ...+|
T Consensus        30 ~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pv  109 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPV  109 (510)
T ss_pred             CCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcce
Confidence            3345679999999999999999999999999999999999     89999999999999999999999865 4  35778


Q ss_pred             EEEEeecCC
Q psy2347          77 RVEISRGRG   85 (207)
Q Consensus        77 ~V~~a~~k~   85 (207)
                      .|++|....
T Consensus       110 qvk~Ad~E~  118 (510)
T KOG0144|consen  110 QVKYADGER  118 (510)
T ss_pred             eecccchhh
Confidence            888886543

>KOG0109|consensus

Probab=99.41  E-value=3.3e-13  Score=112.15  Aligned_cols=82  Identities=27%  Similarity=0.505  Sum_probs=76.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ...+++|+|+||.+.++.+||++.|++|++|.+|+|++|   ++||.|+-.++|..|++.|++.++.+++|+|++++++-
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd---y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD---YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc---eeEEEEeeccchHHHHhcccccccccceeeeeeecccc
Confidence            456789999999999999999999999999999999977   99999999999999999999999999999999999877


Q ss_pred             CCCCC
Q psy2347          86 RGRGG   90 (207)
Q Consensus        86 ~~~~~   90 (207)
                      +....
T Consensus       152 rtapg  156 (346)
T KOG0109|consen  152 RTAPG  156 (346)
T ss_pred             ccCCC
Confidence            65443

>KOG0145|consensus

Probab=99.41  E-value=8.3e-13  Score=108.44  Aligned_cols=82  Identities=23%  Similarity=0.392  Sum_probs=75.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .+..+.|.|--||..+|++||+.+|...|+|++|++++|     +.+|.||.|.++++|++||..||+..|..+.|+|++
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            344567888889999999999999999999999999999     779999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      |+|....
T Consensus       118 ARPSs~~  124 (360)
T KOG0145|consen  118 ARPSSDS  124 (360)
T ss_pred             ccCChhh
Confidence            9986543

>KOG0146|consensus

Probab=99.41  E-value=2.3e-13  Score=112.11  Aligned_cols=82  Identities=27%  Similarity=0.423  Sum_probs=77.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++.|.|||-.||.+..+.||..+|..||.|++.+|..|     +|+|.||.|+++.+|++||.+||+..|.-|+|+|.+.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            57899999999999999999999999999999999888     8999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy2347          82 RGRGRGR   88 (207)
Q Consensus        82 ~~k~~~~   88 (207)
                      +||...+
T Consensus       363 RPkdanR  369 (371)
T KOG0146|consen  363 RPKDANR  369 (371)
T ss_pred             CccccCC
Confidence            9987653

>KOG0415|consensus

Probab=99.40  E-value=3.8e-13  Score=114.41  Aligned_cols=80  Identities=28%  Similarity=0.424  Sum_probs=75.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .+.+|...|||..|.+-+|+++|+-+|+.||+|+.|+|+.|     +..||||+|++++++++|.-+|++..|+.++|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            45678899999999999999999999999999999999998     6689999999999999999999999999999999


Q ss_pred             EEeec
Q psy2347          79 EISRG   83 (207)
Q Consensus        79 ~~a~~   83 (207)
                      .++.+
T Consensus       314 DFSQS  318 (479)
T KOG0415|consen  314 DFSQS  318 (479)
T ss_pred             ehhhh
Confidence            98764

>KOG0127|consensus

Probab=99.40  E-value=1e-12  Score=117.05  Aligned_cols=79  Identities=29%  Similarity=0.416  Sum_probs=73.8

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .+-.+|.|.|||+.|.+++|+.+|+.||.|.+|.|++.    .++||||+|.+..+|.+||+.+|.++|.+++|.|.||-
T Consensus       115 ~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  115 LPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             CccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            34679999999999999999999999999999999976    56999999999999999999999999999999999998


Q ss_pred             cCC
Q psy2347          83 GRG   85 (207)
Q Consensus        83 ~k~   85 (207)
                      ++.
T Consensus       195 ~Kd  197 (678)
T KOG0127|consen  195 DKD  197 (678)
T ss_pred             ccc
Confidence            764

>KOG0108|consensus

Probab=99.39  E-value=9.3e-13  Score=117.04  Aligned_cols=77  Identities=31%  Similarity=0.541  Sum_probs=73.6

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ++|||+|||++++|++|.++|+..+.|..++++.|     +++|+|++|.++++|++|++.||+.++.+++|+|.++...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            89999999999999999999999999999999999     8999999999999999999999999999999999998765


Q ss_pred             CC
Q psy2347          85 GR   86 (207)
Q Consensus        85 ~~   86 (207)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG0116|consensus

Probab=99.39  E-value=3.6e-12  Score=112.75  Aligned_cols=79  Identities=30%  Similarity=0.489  Sum_probs=68.8

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ...+|||.|||.++++++|+++|.+||+|++..|...     ..+|+||+|++.++++.||++ +...|.+++|.|+..+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKR  365 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecc
Confidence            3456999999999999999999999999998877653     238999999999999999997 6888999999999887


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      +..+.
T Consensus       366 ~~~~g  370 (419)
T KOG0116|consen  366 PGFRG  370 (419)
T ss_pred             ccccc
Confidence            75544

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

Probab=99.37  E-value=2.2e-12  Score=117.41  Aligned_cols=76  Identities=22%  Similarity=0.334  Sum_probs=63.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhC------------CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKF------------GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM   72 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~------------G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~   72 (207)
                      +....++|||+|||+++|+++|+++|.++            ..|..+.+..+ ++||||+|.+.++|++||+ |+++.|.
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~-kg~afVeF~~~e~A~~Al~-l~g~~~~  248 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKE-KNFAFLEFRTVEEATFAMA-LDSIIYS  248 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCC-CCEEEEEeCCHHHHhhhhc-CCCeEee
Confidence            34457899999999999999999999975            23455555544 8999999999999999995 9999999


Q ss_pred             CcEEEEEEee
Q psy2347          73 GSKLRVEISR   82 (207)
Q Consensus        73 g~~l~V~~a~   82 (207)
                      ++.|+|...+
T Consensus       249 g~~l~v~r~~  258 (509)
T TIGR01642       249 NVFLKIRRPH  258 (509)
T ss_pred             CceeEecCcc
Confidence            9999987543

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

>KOG0145|consensus

Probab=99.37  E-value=2.8e-12  Score=105.36  Aligned_cols=77  Identities=27%  Similarity=0.337  Sum_probs=73.4

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ...|||-||.++++|..|+++|.+||.|+.|+|++|     .|+|+||++.+.++|..||..||+..|.++.|.|.+.+.
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            578999999999999999999999999999999999     789999999999999999999999999999999999877


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      |.
T Consensus       358 k~  359 (360)
T KOG0145|consen  358 KA  359 (360)
T ss_pred             CC
Confidence            64

>KOG0126|consensus

Probab=99.33  E-value=1.7e-13  Score=107.07  Aligned_cols=76  Identities=24%  Similarity=0.512  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ..+.-|||++||.++||.||..+|++||+|++|.+++|     +++|||+.|++..+...|+..||+..|.++.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            45678999999999999999999999999999999999     8999999999999999999999999999999999865


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      .
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

>KOG0127|consensus

Probab=99.32  E-value=6.9e-12  Score=111.81  Aligned_cols=78  Identities=29%  Similarity=0.466  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcC-----C-ceeCCcEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN-----D-QDLMGSKL   76 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~-----g-~~i~g~~l   76 (207)
                      ...+|||.|||+++||++|.++|++||+|..+.|+.+     ++++|||.|.+..+|++||+...     + ..|.++.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~L  370 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLL  370 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEE
Confidence            4589999999999999999999999999999999887     89999999999999999998752     2 56899999


Q ss_pred             EEEEeecCC
Q psy2347          77 RVEISRGRG   85 (207)
Q Consensus        77 ~V~~a~~k~   85 (207)
                      .|.+|-++.
T Consensus       371 kv~~Av~Rk  379 (678)
T KOG0127|consen  371 KVTLAVTRK  379 (678)
T ss_pred             eeeeccchH
Confidence            999987653

>KOG0123|consensus

Probab=99.31  E-value=6.1e-12  Score=110.45  Aligned_cols=76  Identities=28%  Similarity=0.459  Sum_probs=71.7

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCCC
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRG   87 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~~   87 (207)
                      .|||.||+++++.++|.++|+.||+|++|+|+++   ++++ ||+|+++++|++|++.||+..+.+++|.|.+..++..+
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            3999999999999999999999999999999999   8999 99999999999999999999999999999988776554

>KOG0132|consensus

Probab=99.31  E-value=5.2e-12  Score=116.26  Aligned_cols=80  Identities=25%  Similarity=0.512  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ++--++||||+.|+..++|.||..+|+.||+|++|.++.. ++||||++...++|++||.+|+.+.+..+.|+|.|+..+
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC-CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            3445789999999999999999999999999999988876 999999999999999999999999999999999999755


Q ss_pred             C
Q psy2347          85 G   85 (207)
Q Consensus        85 ~   85 (207)
                      .
T Consensus       496 G  496 (894)
T KOG0132|consen  496 G  496 (894)
T ss_pred             C
Confidence            3

>KOG4206|consensus

Probab=99.29  E-value=1.3e-11  Score=99.41  Aligned_cols=82  Identities=24%  Similarity=0.410  Sum_probs=74.5

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHH----HHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLEL----EFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~----~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ..+++..||||.||++.+..++|++    +|++||.|..|.+.+.  .++-|||.|.+.++|..|+.+|++..+.++.|+
T Consensus         4 ~~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    4 MSVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             cccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            4456667999999999999999888    9999999999988766  789999999999999999999999999999999


Q ss_pred             EEEeecCC
Q psy2347          78 VEISRGRG   85 (207)
Q Consensus        78 V~~a~~k~   85 (207)
                      |++|+.+.
T Consensus        84 iqyA~s~s   91 (221)
T KOG4206|consen   84 IQYAKSDS   91 (221)
T ss_pred             eecccCcc
Confidence            99997654

>smart00361 RRM_1 RNA recognition motif

Probab=99.28  E-value=1.7e-11  Score=82.78  Aligned_cols=57  Identities=26%  Similarity=0.476  Sum_probs=50.3

Q ss_pred             HHHHHHHHH----hCCCeeEEE-EeeC-------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347          23 KEDLELEFE----KFGKLNSVW-VAFN-------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus        23 e~~L~~~F~----~~G~V~~v~-i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      +++|+++|+    +||+|.+|. |+.+       +++|+||+|+++++|++|++.||+..+.+++|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            678888888    999999985 4443       58999999999999999999999999999999863

>KOG0153|consensus

Probab=99.27  E-value=1.8e-11  Score=103.97  Aligned_cols=76  Identities=28%  Similarity=0.507  Sum_probs=68.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc-CCceeCCcEEEEEEeec
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM-NDQDLMGSKLRVEISRG   83 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l-~g~~i~g~~l~V~~a~~   83 (207)
                      ...++|||++|...++|.+|+++|.+||+|+.|.|+.. +.+|||+|.+.++|++|.+++ +...|++++|+|.|.++
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            34679999999999999999999999999999999887 779999999999999998864 44568999999999988

>KOG0131|consensus

Probab=99.24  E-value=2.2e-11  Score=95.25  Aligned_cols=85  Identities=27%  Similarity=0.407  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .++...+|||+||.++++|..|.++|+.||.|.. -+|+.+     +++|+||.|++.|++.+|++.||++.++.++|+|
T Consensus        92 nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv  171 (203)
T KOG0131|consen   92 NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITV  171 (203)
T ss_pred             cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEE
Confidence            3455689999999999999999999999999765 366666     7889999999999999999999999999999999


Q ss_pred             EEeecCCCCCC
Q psy2347          79 EISRGRGRGRG   89 (207)
Q Consensus        79 ~~a~~k~~~~~   89 (207)
                      +++..+..+..
T Consensus       172 ~ya~k~~~kg~  182 (203)
T KOG0131|consen  172 SYAFKKDTKGE  182 (203)
T ss_pred             EEEEecCCCcc
Confidence            99988766543

>KOG4205|consensus

Probab=99.23  E-value=1.1e-11  Score=106.02  Aligned_cols=82  Identities=28%  Similarity=0.525  Sum_probs=75.1

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ..++|||+.||.++++++|+++|++|+.|..+.|+.|     +++|+||+|++++++++++.+ +-++|++++|+|+.|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~-~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ-KFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc-ceeeecCceeeEeecc
Confidence            3569999999999999999999999999999999988     789999999999999999975 8899999999999999


Q ss_pred             cCCCCCCC
Q psy2347          83 GRGRGRGG   90 (207)
Q Consensus        83 ~k~~~~~~   90 (207)
                      ||+.....
T Consensus       175 pk~~~~~~  182 (311)
T KOG4205|consen  175 PKEVMQST  182 (311)
T ss_pred             chhhcccc
Confidence            98766543

>KOG4205|consensus

Probab=99.23  E-value=8.6e-12  Score=106.66  Aligned_cols=79  Identities=23%  Similarity=0.440  Sum_probs=73.2

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||+.|+|+++|+.|+++|.+|++|.+|.||+|     +++|.||+|++++.+.++|.. ..++|+++.|.++.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            7899999999999999999999999999999999998     789999999999999999875 6789999999999998


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      ++...
T Consensus        84 ~r~~~   88 (311)
T KOG4205|consen   84 SREDQ   88 (311)
T ss_pred             Ccccc
Confidence            87644

>KOG4212|consensus

Probab=99.23  E-value=2.2e-11  Score=106.22  Aligned_cols=78  Identities=23%  Similarity=0.290  Sum_probs=70.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+..+.|+|||.|||.++||+.|++-|.+|+.|+.++||..-+....|.|.++++|+.||..|++..|+++.|+|.+.
T Consensus       531 gaarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  531 GAARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            456788999999999999999999999999999999997773444589999999999999999999999999999863

>KOG0147|consensus

Probab=99.19  E-value=3e-11  Score=107.73  Aligned_cols=77  Identities=32%  Similarity=0.558  Sum_probs=71.5

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .+|||+||..++||++|+.+|+.|+.|+.|.+++|     +++|+||+|.+.++|++|+++||+.+|.++.|+|...+.+
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            34999999999999999999999999999999998     7999999999999999999999999999999999887655


Q ss_pred             CC
Q psy2347          85 GR   86 (207)
Q Consensus        85 ~~   86 (207)
                      ..
T Consensus       359 ~~  360 (549)
T KOG0147|consen  359 VD  360 (549)
T ss_pred             cc
Confidence            43

>KOG0146|consensus

Probab=99.19  E-value=2.6e-11  Score=100.06  Aligned_cols=80  Identities=25%  Similarity=0.431  Sum_probs=71.0

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCcee---CCcEEEEEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDL---MGSKLRVEI   80 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i---~g~~l~V~~   80 (207)
                      +.++|||+-|....+|||++.+|..||+|++|.|+..    +|+||||.|.+..+|+.||..||+...   ....|.|++
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            5789999999999999999999999999999999876    899999999999999999999998653   246799999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      +...+++
T Consensus        98 ADTdkER  104 (371)
T KOG0146|consen   98 ADTDKER  104 (371)
T ss_pred             ccchHHH
Confidence            8765443

>KOG0124|consensus

Probab=99.17  E-value=2.1e-11  Score=104.39  Aligned_cols=73  Identities=32%  Similarity=0.569  Sum_probs=69.2

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      -|+|||+.|.+++.|+.|+..|..||+|++|.+.+|     .|+||||||+-+|.|+.|++.||+..+.++.|+|...
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            478999999999999999999999999999999888     7899999999999999999999999999999998743

>KOG0110|consensus

Probab=99.14  E-value=1.3e-10  Score=106.26  Aligned_cols=73  Identities=36%  Similarity=0.482  Sum_probs=68.3

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++|||.||++++|.++|+.+|.+.+.|..|.|.+.        +.+|+||+|.++++|++|+++|+++.|+++.|.|+++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            34999999999999999999999999999988765        3499999999999999999999999999999999999


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            7

>KOG4661|consensus

Probab=99.14  E-value=1e-10  Score=105.02  Aligned_cols=76  Identities=28%  Similarity=0.490  Sum_probs=71.3

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      -.+.|||..|+..+...+|+.||++|++|+-.+|+++     .++|.||++.+.++|.+||+.||..+|.++.|.|+.++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            3578999999999999999999999999999999988     68999999999999999999999999999999999886


Q ss_pred             c
Q psy2347          83 G   83 (207)
Q Consensus        83 ~   83 (207)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            4

>KOG1457|consensus

Probab=99.12  E-value=3.7e-10  Score=91.13  Aligned_cols=85  Identities=21%  Similarity=0.344  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeC---CcEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLM---GSKL   76 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~---g~~l   76 (207)
                      ....++|||.+||.++...||..+|..|---+.+.|...      .+.++||+|.+..+|++|+++||+..|+   ...|
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            345789999999999999999999999876666655443      3579999999999999999999999985   6789


Q ss_pred             EEEEeecCCCCCCC
Q psy2347          77 RVEISRGRGRGRGG   90 (207)
Q Consensus        77 ~V~~a~~k~~~~~~   90 (207)
                      +|++|+...+.+++
T Consensus       111 hiElAKSNtK~kr~  124 (284)
T KOG1457|consen  111 HIELAKSNTKRKRR  124 (284)
T ss_pred             EeeehhcCcccccC
Confidence            99999887766554

>KOG0533|consensus

Probab=99.06  E-value=8.5e-10  Score=91.21  Aligned_cols=80  Identities=34%  Similarity=0.449  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ...++|.|.|||..|++++|+++|++|++++.+.|..+    +.+.|-|+|+..++|++||+.+|+..|+++.|++.+..
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            44578999999999999999999999999988888877    77999999999999999999999999999999998876


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      +...
T Consensus       161 ~~~~  164 (243)
T KOG0533|consen  161 SPSQ  164 (243)
T ss_pred             Cccc
Confidence            5443

>KOG4454|consensus

Probab=99.06  E-value=6.3e-11  Score=95.23  Aligned_cols=81  Identities=22%  Similarity=0.229  Sum_probs=72.9

Q ss_pred             CCCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           1 MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         1 ms~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      |-..+.+...+|||.||...++|+.|.++|-+.|+|.+|.|..+   ...||||+|+++.++.-|++.||+..|.+..|+
T Consensus         1 mgaaaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q   80 (267)
T KOG4454|consen    1 MGAAAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQ   80 (267)
T ss_pred             CCCCCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhh
Confidence            45667788899999999999999999999999999999999876   333999999999999999999999999998888


Q ss_pred             EEEe
Q psy2347          78 VEIS   81 (207)
Q Consensus        78 V~~a   81 (207)
                      |++.
T Consensus        81 ~~~r   84 (267)
T KOG4454|consen   81 RTLR   84 (267)
T ss_pred             cccc
Confidence            8764

>KOG4211|consensus

Probab=99.02  E-value=1.1e-09  Score=96.79  Aligned_cols=79  Identities=19%  Similarity=0.273  Sum_probs=68.5

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      +...+....|-+..|||++|++||++||+.+ .|+++++.+.   +.+.|||||+++|++++||++ +...+..+-|+|-
T Consensus         4 ~~e~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf   81 (510)
T KOG4211|consen    4 ENEGSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVF   81 (510)
T ss_pred             ccCCCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEeccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEE
Confidence            3456667788889999999999999999999 4888888776   789999999999999999996 8888999999998


Q ss_pred             Eeec
Q psy2347          80 ISRG   83 (207)
Q Consensus        80 ~a~~   83 (207)
                      .+.+
T Consensus        82 ~~~~   85 (510)
T KOG4211|consen   82 TAGG   85 (510)
T ss_pred             ccCC
Confidence            7754

>KOG4208|consensus

Probab=99.01  E-value=1.4e-09  Score=86.72  Aligned_cols=78  Identities=27%  Similarity=0.388  Sum_probs=69.0

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhC-CCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKF-GKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~-G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .....++|..||.-+.+.+|..+|.+| +.|..+++.++     +++||||+|+++|.|+-|.+.||+..|.++.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            345678899999999999999999998 67777777565     899999999999999999999999999999999998


Q ss_pred             eecC
Q psy2347          81 SRGR   84 (207)
Q Consensus        81 a~~k   84 (207)
                      ..|.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7654

>KOG0110|consensus

Probab=99.01  E-value=3.1e-10  Score=103.97  Aligned_cols=75  Identities=29%  Similarity=0.528  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|+|.|||+.++..+|+++|..||.|..|+|++.     .++||||+|-++++|.+|+++|....|.++.|.++||+.
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            469999999999999999999999999999999876     689999999999999999999999999999999999975

>KOG0106|consensus

Probab=98.95  E-value=9.9e-10  Score=89.13  Aligned_cols=73  Identities=36%  Similarity=0.660  Sum_probs=67.1

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      .+|||++||+.+.+.+|++||..|+.|.+|.+.   .+|+||+|++..+|+.||..||+.+|.+.+|.|++++.+.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk---~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK---NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee---cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            479999999999999999999999999999886   4699999999999999999999999999998888887643

>KOG0123|consensus

Probab=98.94  E-value=1e-09  Score=96.49  Aligned_cols=82  Identities=33%  Similarity=0.528  Sum_probs=75.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ......+|||.||+..++++.|+++|+.+++|+.++|+.+    +++|+||+|++.++|++|+..+|+..|.++.|.|.+
T Consensus       266 ~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav  345 (369)
T KOG0123|consen  266 VSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAV  345 (369)
T ss_pred             ccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhH
Confidence            3556789999999999999999999999999999999987    889999999999999999999999999999999998


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      +..+..
T Consensus       346 ~qr~~~  351 (369)
T KOG0123|consen  346 AQRKED  351 (369)
T ss_pred             Hhhhcc
Confidence            875443

>KOG0124|consensus

Probab=98.89  E-value=3.9e-09  Score=90.62  Aligned_cols=77  Identities=30%  Similarity=0.439  Sum_probs=71.2

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +-.+|||..+.++++|+||+.+|+.||+|++|++.++     .|+|.||||++..+...||..||-..|.+.-|+|-.+-
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            4579999999999999999999999999999999887     78999999999999999999999999999999997765


Q ss_pred             cC
Q psy2347          83 GR   84 (207)
Q Consensus        83 ~k   84 (207)
                      ..
T Consensus       289 TP  290 (544)
T KOG0124|consen  289 TP  290 (544)
T ss_pred             CC
Confidence            43

>KOG1548|consensus

Probab=98.88  E-value=8e-09  Score=87.99  Aligned_cols=76  Identities=26%  Similarity=0.370  Sum_probs=68.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCee--------EEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLN--------SVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~--------~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      ..+++|||.+||.++|.+++.++|++|+.|.        .|+|..+    .|+=|+|+|...|+++.||+.|+..+|.++
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            4567899999999999999999999999875        3666666    789999999999999999999999999999


Q ss_pred             EEEEEEee
Q psy2347          75 KLRVEISR   82 (207)
Q Consensus        75 ~l~V~~a~   82 (207)
                      +|+|+.|+
T Consensus       212 ~~rVerAk  219 (382)
T KOG1548|consen  212 KLRVERAK  219 (382)
T ss_pred             EEEEehhh
Confidence            99999885

>KOG4660|consensus

Probab=98.86  E-value=1.9e-09  Score=96.56  Aligned_cols=71  Identities=25%  Similarity=0.426  Sum_probs=66.2

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      .+..+|+|-|||..|++++|+.+|+.||+|+.|+.....++.+||+|.|..+|++|+++|+..+|.++.|+
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            35679999999999999999999999999999877666889999999999999999999999999999887

>KOG4209|consensus

Probab=98.85  E-value=5.6e-09  Score=86.22  Aligned_cols=82  Identities=30%  Similarity=0.457  Sum_probs=73.9

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ....+.+.|||+|+...+|.++|+.+|+.|+.|..|.|++|     +|+|+||+|.+.+.+++|+. |+...|.++.|+|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~v  174 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEV  174 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccccee
Confidence            34456789999999999999999999999999998888887     68999999999999999999 8999999999999


Q ss_pred             EEeecCCC
Q psy2347          79 EISRGRGR   86 (207)
Q Consensus        79 ~~a~~k~~   86 (207)
                      .+.+.+..
T Consensus       175 t~~r~~~p  182 (231)
T KOG4209|consen  175 TLKRTNVP  182 (231)
T ss_pred             eeeeeecC
Confidence            98877633

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

Probab=98.81  E-value=3.2e-08  Score=70.89  Aligned_cols=75  Identities=19%  Similarity=0.302  Sum_probs=63.1

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhC--CCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeC----CcEEEE
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKF--GKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLM----GSKLRV   78 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~--G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~----g~~l~V   78 (207)
                      +||.|.|||...|.++|.+++.+.  +....+.++.|     +.+||||.|.++++|.+..+.++++.+.    .+.++|
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            689999999999999999998763  44556666666     6899999999999999999999998874    577888


Q ss_pred             EEeecC
Q psy2347          79 EISRGR   84 (207)
Q Consensus        79 ~~a~~k   84 (207)
                      .+|+-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            888643

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

>KOG1995|consensus

Probab=98.70  E-value=4.7e-08  Score=83.72  Aligned_cols=81  Identities=21%  Similarity=0.339  Sum_probs=71.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCee--------EEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLN--------SVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLM   72 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~--------~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~   72 (207)
                      .....+|||..||..+++++|.++|.+++.|+        +|+|-+|     +|+-|.|+|++..+|++||+.++.+.+.
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            45567999999999999999999999999875        2444444     8899999999999999999999999999


Q ss_pred             CcEEEEEEeecCCC
Q psy2347          73 GSKLRVEISRGRGR   86 (207)
Q Consensus        73 g~~l~V~~a~~k~~   86 (207)
                      +.+|+|.+|+.+..
T Consensus       143 gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  143 GNTIKVSLAERRTG  156 (351)
T ss_pred             CCCchhhhhhhccC
Confidence            99999999987663

>KOG0151|consensus

Probab=98.65  E-value=5.6e-08  Score=89.40  Aligned_cols=78  Identities=28%  Similarity=0.429  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      .+..+.|||.||++.++|+.|...|..|++|..|+||..        .+.|+||.|-+..+|++|++.|+++.+....|+
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            456789999999999999999999999999999999876        568999999999999999999999999999999


Q ss_pred             EEEeec
Q psy2347          78 VEISRG   83 (207)
Q Consensus        78 V~~a~~   83 (207)
                      +-|+++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            998854

>KOG1190|consensus

Probab=98.65  E-value=1.2e-07  Score=82.62  Aligned_cols=75  Identities=27%  Similarity=0.423  Sum_probs=69.8

Q ss_pred             CcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ++.|.|.||.+ .+|.+.|..+|.-||+|.+|+|+.+++--|+|.|.+...|+-|++.|+++.|.+++|+|.+++-
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            57899999955 5899999999999999999999999888999999999999999999999999999999999874

>KOG4206|consensus

Probab=98.60  E-value=2.2e-07  Score=75.14  Aligned_cols=80  Identities=19%  Similarity=0.324  Sum_probs=70.8

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEEEEEEe
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKLRVEIS   81 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l~V~~a   81 (207)
                      +.+.++...||+.|||.+++.+.|..+|++|.-.++|+++...+..|||+|.+...|..|...|++..|. ..+|+|.++
T Consensus       140 ~~~~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  140 AQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             ccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhhhHHHhhhhccceeccCceEEeccc
Confidence            3456788899999999999999999999999999999998877889999999999999999999988876 777877766


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      +
T Consensus       220 ~  220 (221)
T KOG4206|consen  220 K  220 (221)
T ss_pred             C
Confidence            4

>KOG4211|consensus

Probab=98.59  E-value=1e-07  Score=84.63  Aligned_cols=74  Identities=24%  Similarity=0.311  Sum_probs=62.6

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ....|-|..||+.||++||.+||+-.-.|.. |.++.+    +.+.|||.|++.|+|++||.. |...|..+-|+|..+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehhH
Confidence            5678999999999999999999998865555 444555    779999999999999999987 7888888989987664

>KOG0106|consensus

Probab=98.58  E-value=3.4e-08  Score=80.22  Aligned_cols=72  Identities=33%  Similarity=0.450  Sum_probs=63.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ...+.|+|.+|+..+.+.+|+++|+++++++...++   +.++||+|+++++|++||+.|++.+|.++.|+|...
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~---~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR---RNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCCCchhhhh---ccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            456789999999999999999999999999665553   569999999999999999999999999999999443

>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=98.53  E-value=1.5e-07  Score=68.54  Aligned_cols=71  Identities=21%  Similarity=0.386  Sum_probs=46.2

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCc-----eeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ-----DLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~-----~i~g~~l~V~~a   81 (207)
                      +.|+|.+++..++.++|+++|++|++|..|.+... .-.|+|.|.++++|++|++++...     .|.+..+++++-
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL   77 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL   77 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT--SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence            57899999999999999999999999999998876 458999999999999999876544     566777776654

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

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

Probab=98.51  E-value=4.5e-07  Score=62.74  Aligned_cols=68  Identities=31%  Similarity=0.417  Sum_probs=47.3

Q ss_pred             cEEEEcCCCcCCcHHHH----HHHHHhCC-CeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          10 TRVYVGGLTETVKKEDL----ELEFEKFG-KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L----~~~F~~~G-~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.|+|.|||.+.+...|    +.++..+| .|..|     ....|+|.|.++|.|++|++.|++..+-+.+|.|++..
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v-----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~~   75 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV-----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFSP   75 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS-
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE-----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEcC
Confidence            47999999998887654    55666675 35554     25799999999999999999999999999999999874

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

>KOG1457|consensus

Probab=98.51  E-value=1.1e-07  Score=77.03  Aligned_cols=63  Identities=13%  Similarity=0.261  Sum_probs=54.9

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCcee
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDL   71 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i   71 (207)
                      ..+|||.||..++||++|+.+|+.|--...++|... -..+|||+|++.+.|..||..|++..|
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            468999999999999999999999988777777654 456899999999999999999887665

>KOG0120|consensus

Probab=98.42  E-value=2.4e-07  Score=83.55  Aligned_cols=80  Identities=23%  Similarity=0.412  Sum_probs=73.7

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..+....+|||++||..++++++++++..|++++..+++.|     +++|||.+|.+......|++.||++.+.+++|.|
T Consensus       284 ~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvv  363 (500)
T KOG0120|consen  284 DVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVV  363 (500)
T ss_pred             CcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEe
Confidence            34556789999999999999999999999999999988887     7999999999999999999999999999999999


Q ss_pred             EEeec
Q psy2347          79 EISRG   83 (207)
Q Consensus        79 ~~a~~   83 (207)
                      ..|.+
T Consensus       364 q~A~~  368 (500)
T KOG0120|consen  364 QRAIV  368 (500)
T ss_pred             ehhhc
Confidence            98754

>KOG0226|consensus

Probab=98.42  E-value=2e-07  Score=76.71  Aligned_cols=79  Identities=24%  Similarity=0.388  Sum_probs=71.4

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +...+||.+.|..+++++.|...|.+|-.....++++|     +++|.||.|.+.+++..|++.|+++.+..+.|++..+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            45679999999999999999999999988888888888     7899999999999999999999999999999988766


Q ss_pred             ecCC
Q psy2347          82 RGRG   85 (207)
Q Consensus        82 ~~k~   85 (207)
                      ..++
T Consensus       268 ~wke  271 (290)
T KOG0226|consen  268 EWKE  271 (290)
T ss_pred             hHHh
Confidence            5544

>KOG1855|consensus

Probab=98.34  E-value=3.6e-07  Score=79.94  Aligned_cols=64  Identities=19%  Similarity=0.226  Sum_probs=57.2

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------------------CCcEEEEEEcCHHHHHHHHHhcCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------------------PPGFAFVEFSNQIDAEAACDSMND   68 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------------------~rG~afV~F~~~e~A~~Al~~l~g   68 (207)
                      .++++|.+.|||.+-.-+.|.+||..+|.|+.|+|++.                  .+-||+|||+..++|.+|.+.|+.
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            47899999999999999999999999999999999765                  267999999999999999998865


Q ss_pred             ce
Q psy2347          69 QD   70 (207)
Q Consensus        69 ~~   70 (207)
                      ..
T Consensus       309 e~  310 (484)
T KOG1855|consen  309 EQ  310 (484)
T ss_pred             hh
Confidence            43

>KOG1456|consensus

Probab=98.32  E-value=3.9e-06  Score=72.61  Aligned_cols=79  Identities=28%  Similarity=0.359  Sum_probs=71.5

Q ss_pred             CCCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           6 MERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      -.+.+.++|-.|... +..+.|..+|..||.|++|++|+.+.+.|.||+-|+.++++||..||+..+-+.+|.|.+++..
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeecccc
Confidence            356789999999764 6678899999999999999999998899999999999999999999999999999999988753

>KOG1456|consensus

Probab=98.30  E-value=3.2e-06  Score=73.07  Aligned_cols=81  Identities=17%  Similarity=0.133  Sum_probs=66.5

Q ss_pred             CCCCCCcEEEEcCC--CcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEE
Q psy2347           4 GMMERGTRVYVGGL--TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVE   79 (207)
Q Consensus         4 ~~~~~~~~lfV~nL--p~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~   79 (207)
                      +...+++.|.+.=|  -..+|.+.|..+....|+|..|.|++..---|.|||++.+.|++|.++||+..|..  .+|+|+
T Consensus       115 es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIe  194 (494)
T KOG1456|consen  115 ESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIE  194 (494)
T ss_pred             CCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHHHHHHHhhcccccccccceeEEEE
Confidence            34455666666544  45689999999999999999999998755679999999999999999999999854  678888


Q ss_pred             EeecC
Q psy2347          80 ISRGR   84 (207)
Q Consensus        80 ~a~~k   84 (207)
                      +|+|.
T Consensus       195 yAkP~  199 (494)
T KOG1456|consen  195 YAKPT  199 (494)
T ss_pred             ecCcc
Confidence            88874

>KOG1190|consensus

Probab=98.25  E-value=2.7e-06  Score=74.26  Aligned_cols=78  Identities=18%  Similarity=0.195  Sum_probs=65.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEE-EEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC-cEEEEEEeec
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG-SKLRVEISRG   83 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v-~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g-~~l~V~~a~~   83 (207)
                      .+++.+|++.|||.+++||+|+++|.+-+-+++. +.....+.+|++.+++.|+|..|+..|+.+.+.. ..|+|++++.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            4678899999999999999999999998876554 3333246799999999999999999999999865 5899999875

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

Probab=98.23  E-value=3.7e-06  Score=53.66  Aligned_cols=52  Identities=25%  Similarity=0.501  Sum_probs=43.3

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHH
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAAC   63 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al   63 (207)
                      +.|-|.+.+++..+..| ++|.+||+|+++.+... ..+.+|+|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~vl-~~F~~fGeI~~~~~~~~-~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVL-EHFASFGEIVDIYVPES-TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHH-HHHHhcCCEEEEEcCCC-CcEEEEEECCHHHHHhhC
Confidence            56888899887775555 58889999999988743 679999999999999985

>KOG0105|consensus

Probab=98.21  E-value=1.7e-05  Score=62.79  Aligned_cols=64  Identities=25%  Similarity=0.306  Sum_probs=58.5

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ...+|.|..||+..++++||++..+.++|...++.+|  ++..|+|..+|+++-||.+|+.+++..
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD--g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD--GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc--cceeeeeeehhhHHHHHHhhccccccC
Confidence            4568999999999999999999999999999999987  689999999999999999999877643

>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=98.17  E-value=1.1e-05  Score=58.26  Aligned_cols=74  Identities=19%  Similarity=0.249  Sum_probs=52.6

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEE------------EeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVW------------VAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~------------i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      ..+.|.|-+.|+..+ ..|.++|++||+|++..            -......+..|+|+++.+|++||.+ |+..|.+..
T Consensus         5 ~~~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCE
T ss_pred             CCeEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcE
Confidence            456788889998854 56667899999998875            1222467999999999999999986 999998854


Q ss_pred             -EEEEEeec
Q psy2347          76 -LRVEISRG   83 (207)
Q Consensus        76 -l~V~~a~~   83 (207)
                       |-|.++++
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence             55776644

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.

>KOG2202|consensus

Probab=98.13  E-value=7e-07  Score=73.56  Aligned_cols=58  Identities=33%  Similarity=0.489  Sum_probs=49.6

Q ss_pred             HHHHHHH-hCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          25 DLELEFE-KFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        25 ~L~~~F~-~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +|...|+ +|++|++++|..+    .++-++|.|..+|+|++|++.||+..+.+++|.+++..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3333444 8999999987766    67899999999999999999999999999999998864

>KOG1548|consensus

Probab=98.10  E-value=2.2e-05  Score=67.31  Aligned_cols=78  Identities=31%  Similarity=0.426  Sum_probs=63.2

Q ss_pred             CCCCcEEEEcCC--Cc--CCc-------HHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           6 MERGTRVYVGGL--TE--TVK-------KEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         6 ~~~~~~lfV~nL--p~--~~t-------e~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      +...++|.|.||  |.  ..+       +++|++-.++||.|.+|.|... +.+.+-|.|.+.++|+.||+.|++..+.+
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdg  341 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEEADQCIQTMDGRWFDG  341 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHHHHHHHHHhcCeeecc
Confidence            345678889987  22  222       3456666889999999987754 88999999999999999999999999999


Q ss_pred             cEEEEEEeec
Q psy2347          74 SKLRVEISRG   83 (207)
Q Consensus        74 ~~l~V~~a~~   83 (207)
                      ++|..++..-
T Consensus       342 Rql~A~i~DG  351 (382)
T KOG1548|consen  342 RQLTASIWDG  351 (382)
T ss_pred             eEEEEEEeCC
Confidence            9999987644

>KOG4307|consensus

Probab=98.08  E-value=9.2e-06  Score=75.07  Aligned_cols=74  Identities=22%  Similarity=0.296  Sum_probs=62.7

Q ss_pred             CCCc-EEEEcCCCcCCcHHHHHHHHHhCCCee-EEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           7 ERGT-RVYVGGLTETVKKEDLELEFEKFGKLN-SVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         7 ~~~~-~lfV~nLp~~~te~~L~~~F~~~G~V~-~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .+.+ .|-+.|+|++++-+||.+||..|-.+. +|.|..+    ..+.|.|.|++.|+|.+|...|+++.|..++|+|.+
T Consensus       864 ~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  864 SPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3445 777899999999999999999997654 3444333    789999999999999999999999999999999875

>KOG0147|consensus

Probab=98.06  E-value=8.5e-06  Score=73.39  Aligned_cols=59  Identities=22%  Similarity=0.315  Sum_probs=53.2

Q ss_pred             HHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          24 EDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        24 ~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ++|++...+|+.|..|.|.+++.++.||.|.+.++|.+|+++||+.+|.++.|++.+-.
T Consensus       468 edV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  468 EDVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             HHHHHHHHhcCCeeEEEEccCCCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            45666678999999999988877999999999999999999999999999999998764

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

Probab=98.01  E-value=3.4e-05  Score=59.01  Aligned_cols=76  Identities=17%  Similarity=0.252  Sum_probs=54.1

Q ss_pred             CCCCCcEEEEcCCC------cCCcH---HHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           5 MMERGTRVYVGGLT------ETVKK---EDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         5 ~~~~~~~lfV~nLp------~~~te---~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      +-++..+|.|.-+.      ....+   ++|.+.|.+||+|.-|+++.+   .-+|+|.+-++|.+|+. |++.+|+++.
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~---~mwVTF~dg~sALaals-~dg~~v~g~~   98 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD---TMWVTFRDGQSALAALS-LDGIQVNGRT   98 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT---CEEEEESSCHHHHHHHH-GCCSEETTEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC---eEEEEECccHHHHHHHc-cCCcEECCEE
Confidence            34566778776554      12332   367788899999998888865   78999999999999998 6999999999


Q ss_pred             EEEEEeecC
Q psy2347          76 LRVEISRGR   84 (207)
Q Consensus        76 l~V~~a~~k   84 (207)
                      |+|++.+|.
T Consensus        99 l~i~LKtpd  107 (146)
T PF08952_consen   99 LKIRLKTPD  107 (146)
T ss_dssp             EEEEE----
T ss_pred             EEEEeCCcc
Confidence            999998764

; PDB: 1UFW_A 2DNR_A.

>KOG4210|consensus

Probab=98.01  E-value=3.3e-06  Score=71.96  Aligned_cols=79  Identities=27%  Similarity=0.479  Sum_probs=70.1

Q ss_pred             CCcEEE-EcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           8 RGTRVY-VGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         8 ~~~~lf-V~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +..++| |.+|+..+++++|+++|..++.|+.++++.+     +++|++|+|.+...+++++.. +...|.+++|.|...
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            344555 9999999999999999999999999999887     789999999999999999987 788899999999988


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      ++++..
T Consensus       262 ~~~~~~  267 (285)
T KOG4210|consen  262 EPRPKS  267 (285)
T ss_pred             CCCccc
Confidence            887654

>KOG0129|consensus

Probab=97.99  E-value=2.7e-05  Score=69.86  Aligned_cols=63  Identities=30%  Similarity=0.430  Sum_probs=57.7

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHH-hCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHh
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFE-KFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDS   65 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~-~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~   65 (207)
                      +..+++.+||||+.||.-++.+||..+|+ .||.|+.+-|-+|     +++-+=|+|++..+-.+||++
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            45678899999999999999999999999 5999999988887     789999999999999999985

>KOG0129|consensus

Probab=97.96  E-value=2.8e-05  Score=69.72  Aligned_cols=59  Identities=22%  Similarity=0.485  Sum_probs=48.1

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCc---EEEEEEcCHHHHHHHHHhc
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPG---FAFVEFSNQIDAEAACDSM   66 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG---~afV~F~~~e~A~~Al~~l   66 (207)
                      .-+++|||+.||++++|++|.+.|..||.|. |+....        +++   |+|+.|+++.++++.|.++
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            3468999999999999999999999999864 333211        677   9999999999998877654

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.94  E-value=2.2e-05  Score=67.26  Aligned_cols=73  Identities=25%  Similarity=0.408  Sum_probs=60.1

Q ss_pred             cEEEEcCCCcCCcHHH----H--HHHHHhCCCeeEEEEeeC------CCcEE--EEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347          10 TRVYVGGLTETVKKED----L--ELEFEKFGKLNSVWVAFN------PPGFA--FVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~----L--~~~F~~~G~V~~v~i~~d------~rG~a--fV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      .-|||-.||+.+..++    |  .++|.+||.|++|.|.+.      ....+  ||+|.+.|+|.+||.++++..++++.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            4678888988876665    3  378999999999988765      12233  99999999999999999999999999


Q ss_pred             EEEEEee
Q psy2347          76 LRVEISR   82 (207)
Q Consensus        76 l~V~~a~   82 (207)
                      |++.+-+
T Consensus       195 lkatYGT  201 (480)
T COG5175         195 LKATYGT  201 (480)
T ss_pred             EeeecCc
Confidence            9988754

>KOG4849|consensus

Probab=97.85  E-value=1.4e-05  Score=68.72  Aligned_cols=71  Identities=17%  Similarity=0.232  Sum_probs=58.4

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCC--eeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGK--LNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~--V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+||+||-|.+|++||.+.+...|.  |.++++..+     +|+||+|...+..++++.++.|..++|.++.-+|-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            357899999999999999998877653  444444443     89999999999999999999999999988765554

>KOG0120|consensus

Probab=97.81  E-value=5.7e-05  Score=68.43  Aligned_cols=57  Identities=23%  Similarity=0.363  Sum_probs=48.9

Q ss_pred             HHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          26 LELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        26 L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      |+.-+.+|+.|..|+|..+        ..+..||+|.+.+++++|+++|++.++.+++|.+.+-.
T Consensus       426 vr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  426 VRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            3344568899999999876        45789999999999999999999999999999888754

>KOG1365|consensus

Probab=97.80  E-value=3.1e-05  Score=67.36  Aligned_cols=75  Identities=23%  Similarity=0.251  Sum_probs=63.9

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCC-eeE--EEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGK-LNS--VWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~-V~~--v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ..+|-+.+||.+.+.++|.+||..|-. |..  |+++.+    +.+.|||+|.++|+|.+|+.+.+.+..+.+-|+|..+
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            557889999999999999999999865 333  666666    7899999999999999999988888888999998876


Q ss_pred             ec
Q psy2347          82 RG   83 (207)
Q Consensus        82 ~~   83 (207)
                      ..
T Consensus       360 S~  361 (508)
T KOG1365|consen  360 SV  361 (508)
T ss_pred             cH
Confidence            53

>KOG2314|consensus

Probab=97.72  E-value=8.6e-05  Score=67.38  Aligned_cols=74  Identities=27%  Similarity=0.376  Sum_probs=60.4

Q ss_pred             CCcEEEEcCCCcCCc------HHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEE
Q psy2347           8 RGTRVYVGGLTETVK------KEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKL   76 (207)
Q Consensus         8 ~~~~lfV~nLp~~~t------e~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l   76 (207)
                      -...|+|-++|.--.      ...|.++|+++++|+.+.++.+    .++++|++|.+..+|++|++.||++.|+ .+++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            356889999985321      2356789999999999999876    7899999999999999999999999874 6777


Q ss_pred             EEEEe
Q psy2347          77 RVEIS   81 (207)
Q Consensus        77 ~V~~a   81 (207)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77653

>KOG3152|consensus

Probab=97.71  E-value=2.5e-05  Score=64.52  Aligned_cols=68  Identities=18%  Similarity=0.313  Sum_probs=59.1

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--C---------------CcEEEEEEcCHHHHHHHHHhcCCce
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--P---------------PGFAFVEFSNQIDAEAACDSMNDQD   70 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~---------------rG~afV~F~~~e~A~~Al~~l~g~~   70 (207)
                      ..-.|||++||+.+....|+++|+.||+|-.|.|...  +               --.++|||.+...|+++.+.||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4568999999999999999999999999999988654  1               1236799999999999999999999


Q ss_pred             eCCcE
Q psy2347          71 LMGSK   75 (207)
Q Consensus        71 i~g~~   75 (207)
                      |.+++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98765

>KOG2416|consensus

Probab=97.62  E-value=5.8e-05  Score=68.82  Aligned_cols=77  Identities=13%  Similarity=0.172  Sum_probs=63.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHh-CCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCcee---CCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEK-FGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL---MGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~-~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i---~g~~l~V~~a   81 (207)
                      ...+..|+|.||-..+|.-+|++++.. .+.|+++ +|..-|..|||.|.+.++|.+.+++||+..+   +.+.|.|.++
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf~  519 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADFV  519 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHH-HHHHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeeec
Confidence            346789999999999999999999995 5666666 3333477999999999999999999999876   6688888887


Q ss_pred             ec
Q psy2347          82 RG   83 (207)
Q Consensus        82 ~~   83 (207)
                      ..
T Consensus       520 ~~  521 (718)
T KOG2416|consen  520 RA  521 (718)
T ss_pred             ch
Confidence            53

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

Probab=97.61  E-value=0.00041  Score=45.54  Aligned_cols=56  Identities=16%  Similarity=0.178  Sum_probs=45.8

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhC---CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKF---GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM   66 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~---G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l   66 (207)
                      ...+|+|.+|. +++.++|+.+|..|   .....|+.+.|  --|-|.|.+++.|.+||.+|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdD--tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDD--TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecC--CcEEEEECCHHHHHHHHHcC
Confidence            34589999985 58889999999998   23567888887  35789999999999999865

>KOG4676|consensus

Probab=97.44  E-value=0.00022  Score=62.19  Aligned_cols=70  Identities=16%  Similarity=0.267  Sum_probs=58.2

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..|.|.||.+.+|.++++.||.-.|+|.++.|+..        ..-.|||.|.+.+.+..|.. |.+.++-++.|.|..
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEEe
Confidence            38999999999999999999999999999988764        34689999999999998887 566666666555543

>KOG0128|consensus

Probab=97.33  E-value=7.7e-05  Score=70.43  Aligned_cols=76  Identities=22%  Similarity=0.234  Sum_probs=68.2

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ..+|||.++|+..|.++|+.++.+++.++++.+++.    +++.|+|.|.++.++.+++..++...+.-..+.|.++.|.
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~  815 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPE  815 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCc
Confidence            468999999999999999999999999999887766    7899999999999999999988888888888888887663

>KOG1996|consensus

Probab=97.33  E-value=0.00071  Score=57.17  Aligned_cols=60  Identities=23%  Similarity=0.242  Sum_probs=51.1

Q ss_pred             HHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          23 KEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        23 e~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      |+++++..++|+.|.+|.|..+      ..--.||+|+..++|.+|+..||+..|.++.+...+-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            4578888999999999988766      23457999999999999999999999999999877653

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

Probab=97.27  E-value=0.00086  Score=46.49  Aligned_cols=59  Identities=20%  Similarity=0.262  Sum_probs=42.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND   68 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g   68 (207)
                      .......+|. +|.++...||.++|+.||.|. |..+.|  --|||...+.+.|+.|+..++-
T Consensus         6 P~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d--TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    6 PSRDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND--TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             -SGCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT--TEEEEEECCCHHHHHHHHHHTT
T ss_pred             CCcceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC--CcEEEEeecHHHHHHHHHHhcc
Confidence            3445566666 999999999999999999875 444443  4899999999999999988753

; 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.

>KOG2591|consensus

Probab=97.23  E-value=0.00041  Score=63.01  Aligned_cols=74  Identities=20%  Similarity=0.242  Sum_probs=57.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHh--CCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC--ceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEK--FGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND--QDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~--~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g--~~i~g~~l~V~~   80 (207)
                      +..+.|.|.|..||+.+.+|+||.||+.  +-++++|++..+  .-=||+|++.++|++|.+.|..  ++|.+|.|...+
T Consensus       171 p~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N--~nWyITfesd~DAQqAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  171 PNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHN--DNWYITFESDTDAQQAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             cCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeec--CceEEEeecchhHHHHHHHHHHHHHhhcCcchhhhh
Confidence            3456788889999999999999999975  667888877654  2358999999999999887653  356677665544

>KOG0112|consensus

Probab=97.22  E-value=0.00044  Score=65.85  Aligned_cols=79  Identities=25%  Similarity=0.410  Sum_probs=69.9

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~~a~   82 (207)
                      ...+.+.|+|+.|..++....|...|..||.|..|.+-.. ..||+|.+++...|+.|++.|.+..|.+  +.|.|.+|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLAS  529 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-CcceeeecccCccchhhHHHHhcCcCCCCCccccccccc
Confidence            3457789999999999999999999999999999988765 6799999999999999999999988864  679999987


Q ss_pred             cC
Q psy2347          83 GR   84 (207)
Q Consensus        83 ~k   84 (207)
                      +.
T Consensus       530 ~~  531 (975)
T KOG0112|consen  530 PP  531 (975)
T ss_pred             CC
Confidence            53

>KOG0921|consensus

Probab=97.19  E-value=0.0072  Score=58.30  Aligned_cols=13  Identities=62%  Similarity=1.071  Sum_probs=5.5

Q ss_pred             CCCCCCCCCCCCC
Q psy2347         183 GGGRGGGGRFRSR  195 (207)
Q Consensus       183 ~g~~~~g~~~~~~  195 (207)
                      +|+++++...+.|
T Consensus      1267 gGgfg~G~~Gg~~ 1279 (1282)
T KOG0921|consen 1267 GGGFGGGGRGGNA 1279 (1282)
T ss_pred             CCCCCCCCccccc
Confidence            4444444444333

>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=97.18  E-value=0.0027  Score=43.10  Aligned_cols=67  Identities=24%  Similarity=0.387  Sum_probs=41.6

Q ss_pred             EEEEc-CCCcCCcHHHHHHHHHhCCC-----eeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          11 RVYVG-GLTETVKKEDLELEFEKFGK-----LNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        11 ~lfV~-nLp~~~te~~L~~~F~~~G~-----V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +|||. +-...++..+|..++.....     |-.|+|..+   |+||+-.. +.|++++++|+...+.+++|+|+.|
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~---~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN---FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS----EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee---EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45662 12456889999999988754     557777755   99999887 5788999999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG2193|consensus

Probab=97.09  E-value=0.00039  Score=61.31  Aligned_cols=76  Identities=28%  Similarity=0.406  Sum_probs=60.4

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCc-eeCCcEEEEEEeecCCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ-DLMGSKLRVEISRGRGR   86 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~-~i~g~~l~V~~a~~k~~   86 (207)
                      .+|||.||.+.++.++|+.+|...-.-..-.++. ..+++||.+.+..-|.+|++.++++ ++.++++.|+.+-++..
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kkq   78 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKKQ   78 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHHH
Confidence            4799999999999999999997652211212222 3689999999999999999999875 58999999998876643

>KOG4307|consensus

Probab=97.08  E-value=0.00029  Score=65.46  Aligned_cols=75  Identities=16%  Similarity=0.030  Sum_probs=60.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .....|||..||..+++.++.++|+..-.|++ |.|...    .+..|||+|..++++.+|+..-+.+.+..+.|+|.-.
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            34679999999999999999999998777777 555433    6789999999988888888766667777888888754

>KOG1365|consensus

Probab=97.02  E-value=0.00056  Score=59.67  Aligned_cols=70  Identities=23%  Similarity=0.166  Sum_probs=51.9

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCC----eeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGK----LNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~----V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      -.|-+.+||+++|+.++.+||.+.-.    ++.|.+++.    ..+-|||.|..+++|++||.+ |...|.-+-|+|..
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElFR  239 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELFR  239 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHHH
Confidence            35667899999999999999964322    334444433    679999999999999999987 66666655555543

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

Probab=96.99  E-value=0.0061  Score=44.71  Aligned_cols=68  Identities=12%  Similarity=0.158  Sum_probs=49.3

Q ss_pred             CCCCcEEEEcCCCc-CCcHHHHHHHHHhCCC-eeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           6 MERGTRVYVGGLTE-TVKKEDLELEFEKFGK-LNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         6 ~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~-V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ....++|.|--+|+ .++.++|..+.+.+-+ |+.++|++|   ++-.++|+|.+.++|++..+.+|++.++.
T Consensus         9 ~~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen    9 DERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CCCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33445555544444 4555667666666544 778899998   55678999999999999999999988753

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

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

Probab=96.79  E-value=0.0013  Score=52.28  Aligned_cols=75  Identities=17%  Similarity=0.221  Sum_probs=48.2

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHh-CCCe---eEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCceeCCc-
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEK-FGKL---NSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQDLMGS-   74 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~-~G~V---~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~-   74 (207)
                      ....+|.|.+||+.+||+++++.++. +...   ..+.-...       ...-|||.|.+.+++...+..++++.+.+. 
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34569999999999999999986665 4444   23321122       235699999999999999999999887432 


Q ss_pred             ----EEEEEEe
Q psy2347          75 ----KLRVEIS   81 (207)
Q Consensus        75 ----~l~V~~a   81 (207)
                          ...|++|
T Consensus        85 g~~~~~~VE~A   95 (176)
T PF03467_consen   85 GNEYPAVVEFA   95 (176)
T ss_dssp             S-EEEEEEEE-
T ss_pred             CCCcceeEEEc
Confidence                3455555

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.76  E-value=0.011  Score=45.18  Aligned_cols=74  Identities=16%  Similarity=0.161  Sum_probs=54.5

Q ss_pred             CCCCcEEEEcCCCcCC----cHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETV----KKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~----te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .++-.+|.|.=|..++    +.+.|...++.||+|++|.++-  +--|.|+|+|..+|=+|+.+++. ..-+..+.+.|-
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsWq  159 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG--RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSWQ  159 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC--CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeecc
Confidence            3455677776555544    3344556678899999997763  56899999999999999998765 556777777765


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      .
T Consensus       160 q  160 (166)
T PF15023_consen  160 Q  160 (166)
T ss_pred             c
Confidence            3

>KOG2135|consensus

Probab=96.67  E-value=0.001  Score=59.39  Aligned_cols=75  Identities=16%  Similarity=0.213  Sum_probs=59.7

Q ss_pred             CCcEEEEcCCCcCC-cHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           8 RGTRVYVGGLTETV-KKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         8 ~~~~lfV~nLp~~~-te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ..+.|-|.-+|..+ |.++|..+|.+||+|+.|.|-.. .-.|.|+|.+..+|-+|.. .+...|+++.|+|.|-++.
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc-hhhheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            34445555556554 56899999999999999988654 4589999999999977765 4889999999999998873

>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=96.66  E-value=0.0084  Score=47.95  Aligned_cols=62  Identities=18%  Similarity=0.133  Sum_probs=46.7

Q ss_pred             cHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcC--CceeCCcEEEEEEeecC
Q psy2347          22 KKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN--DQDLMGSKLRVEISRGR   84 (207)
Q Consensus        22 te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~--g~~i~g~~l~V~~a~~k   84 (207)
                      ..+.|+++|.++..+..+.+++. -.-..|.|.+.++|++|...|+  ...+.+..|+|.++.+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45789999999999988877776 3468899999999999999999  88999999999988543

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.

>KOG0115|consensus

Probab=96.61  E-value=0.002  Score=53.46  Aligned_cols=72  Identities=24%  Similarity=0.367  Sum_probs=58.0

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCc----eeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQ----DLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~----~i~g~~l~V~~a   81 (207)
                      ..|+|.||+.-++.+.|++.|+.|++|+...++.|    ...-.+|+|..+..|.+|+..++-.    ++..+.+-|...
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            68999999999999999999999999998777666    5678899999999999999876433    234455555433

>KOG4285|consensus

Probab=96.52  E-value=0.015  Score=49.44  Aligned_cols=71  Identities=17%  Similarity=0.168  Sum_probs=52.3

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE-EEEEEeec
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK-LRVEISRG   83 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~-l~V~~a~~   83 (207)
                      .=|-|-.+|+..+ ..|..+|++||+|++.... ..-.|-+|.|.+..+|+|||.+ |++.|++.. |-|+.+..
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~-~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP-SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC-CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCC
Confidence            3455556766543 4566789999999887655 3467999999999999999987 888887654 45555443

>KOG0112|consensus

Probab=96.48  E-value=0.00056  Score=65.15  Aligned_cols=77  Identities=16%  Similarity=0.271  Sum_probs=64.9

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ...+.+||++||+..+++.+|+..|..++.|++|.|.+.    -.-++||.|.+.+.+-+|+..|....|..-.+++.+.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            345789999999999999999999999999999988655    2358999999999999999888888876656666555


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      .
T Consensus       449 ~  449 (975)
T KOG0112|consen  449 Q  449 (975)
T ss_pred             c
Confidence            3

>KOG0128|consensus

Probab=96.34  E-value=0.00012  Score=69.19  Aligned_cols=62  Identities=27%  Similarity=0.321  Sum_probs=51.5

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEe--eC---CCcEEEEEEcCHHHHHHHHHhcCCce
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVA--FN---PPGFAFVEFSNQIDAEAACDSMNDQD   70 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~--~d---~rG~afV~F~~~e~A~~Al~~l~g~~   70 (207)
                      ..++||+||+..+.+++|...|..++.|+.++|.  .+   .++.|+|+|.+++.+.+||.....+.
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~  733 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCF  733 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhh
Confidence            3689999999999999999999999988776554  11   78999999999999999998544333

>KOG2068|consensus

Probab=96.19  E-value=0.0014  Score=56.18  Aligned_cols=75  Identities=21%  Similarity=0.357  Sum_probs=57.8

Q ss_pred             cEEEEcCCCcCCcHHHH-H--HHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347          10 TRVYVGGLTETVKKEDL-E--LEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L-~--~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..+||-.|+..+.++++ +  +.|.+|+.|.+|.+..+        ...-++|+|+.+|+|..||...++..+.++.|++
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            45677778776655444 3  47888999999988775        1234899999999999999999999988888777


Q ss_pred             EEeecC
Q psy2347          79 EISRGR   84 (207)
Q Consensus        79 ~~a~~k   84 (207)
                      .+.+++
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            766544

>KOG4574|consensus

Probab=96.16  E-value=0.0045  Score=58.87  Aligned_cols=74  Identities=19%  Similarity=0.310  Sum_probs=62.1

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCcee--CCcEEEEEEeecCC
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL--MGSKLRVEISRGRG   85 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i--~g~~l~V~~a~~k~   85 (207)
                      +..+.|.+-..+...|..+|.+|++|..+..+++ -..|.|+|.+.|.|..|+++|+++++  .+.+.+|.+|++-+
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~~  375 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc-ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            4444555566778889999999999999988877 56899999999999999999999885  57889999988654

>KOG0804|consensus

Probab=96.12  E-value=0.019  Score=51.28  Aligned_cols=66  Identities=14%  Similarity=0.236  Sum_probs=57.6

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCC-CeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFG-KLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G-~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      +++.|+|--+|..+|-.||..|...+- .|..|+|++|   .+=.++|+|.+.++|....+.+|++.++.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            378899999999999999999988764 4889999998   56678999999999999999999988754

>KOG2253|consensus

Probab=95.99  E-value=0.0044  Score=57.45  Aligned_cols=74  Identities=22%  Similarity=0.238  Sum_probs=65.0

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +..++..+|||+||...+.++-++.++..+|.|..++.++    |.|.+|.++..+..|+..|+-..++++.|.+...
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~----fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK----FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh----hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            3556788999999999999999999999999998887654    9999999999999999999988898888777653

>KOG4660|consensus

Probab=95.70  E-value=0.015  Score=52.93  Aligned_cols=73  Identities=14%  Similarity=0.232  Sum_probs=44.6

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHh-CCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeC----CcEEEEE
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEK-FGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLM----GSKLRVE   79 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~-~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~----g~~l~V~   79 (207)
                      +++.|.|+|...|...|.+.-++ .+.-..+.++.|     ..+||||.|.+++++..+.++.|++.++    .+.++|.
T Consensus       389 tt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~it  468 (549)
T KOG4660|consen  389 TTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASIT  468 (549)
T ss_pred             hhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeee
Confidence            34444454444443333333221 233334445545     5799999999999999999999998653    3455666


Q ss_pred             Eee
Q psy2347          80 ISR   82 (207)
Q Consensus        80 ~a~   82 (207)
                      +|+
T Consensus       469 YAr  471 (549)
T KOG4660|consen  469 YAR  471 (549)
T ss_pred             hhh
Confidence            654

>KOG2318|consensus

Probab=95.28  E-value=0.11  Score=48.00  Aligned_cols=75  Identities=25%  Similarity=0.298  Sum_probs=59.3

Q ss_pred             CCCCcEEEEcCCCcC-CcHHHHHHHHHhC----CCeeEEEEeeC--------------C---------------------
Q psy2347           6 MERGTRVYVGGLTET-VKKEDLELEFEKF----GKLNSVWVAFN--------------P---------------------   45 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~-~te~~L~~~F~~~----G~V~~v~i~~d--------------~---------------------   45 (207)
                      -..+++|-|.||.|+ +..++|..+|..|    |.|.+|.|...              +                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456789999999987 6778999999887    35778877543              1                     


Q ss_pred             -----------------CcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347          46 -----------------PGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus        46 -----------------rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                                       -=||.|+|++.+.|.++.+.+++.++....+.+.+
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DL  302 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDL  302 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeee
Confidence                             13799999999999999999999998765544444

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=95.19  E-value=0.48  Score=44.92  Aligned_cols=69  Identities=4%  Similarity=0.100  Sum_probs=52.0

Q ss_pred             EEEEcCC--CcCCcHHHHHHHHHhCCCe-----eEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347          11 RVYVGGL--TETVKKEDLELEFEKFGKL-----NSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus        11 ~lfV~nL--p~~~te~~L~~~F~~~G~V-----~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ++|| ++  ...++..+|..++..-..|     -.|+|..+   |.||+... +.|++.++.|+...+.+++|.|+.++.
T Consensus       488 ~~~~-~~g~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~---~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        488 LYRI-EVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFAS---HSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             EEEE-ecccccCCCHHHHHHHHHhhcCCChhhCCcEEEeCC---ceEEEcCh-hhHHHHHHHhccccccCCceEEEECCC
Confidence            3555 33  4568888888888776654     45666654   99999876 558888999999999999999998854


Q ss_pred             C
Q psy2347          84 R   84 (207)
Q Consensus        84 k   84 (207)
                      .
T Consensus       563 ~  563 (629)
T PRK11634        563 A  563 (629)
T ss_pred             C
Confidence            3

>KOG3973|consensus

Probab=94.97  E-value=0.24  Score=43.11  Aligned_cols=6  Identities=0%  Similarity=0.246  Sum_probs=2.3

Q ss_pred             HHHHHH
Q psy2347          25 DLELEF   30 (207)
Q Consensus        25 ~L~~~F   30 (207)
                      +|.++|
T Consensus       244 ei~~~~  249 (465)
T KOG3973|consen  244 EIQSIL  249 (465)
T ss_pred             HHHHHH
Confidence            333333

>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=94.70  E-value=0.22  Score=33.05  Aligned_cols=56  Identities=14%  Similarity=0.299  Sum_probs=43.2

Q ss_pred             cCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347          19 ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus        19 ~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..++-++|+..+.+|.- .  +|..|..| -||.|.+.++|++|....++..+...+|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~-~--~I~~d~tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRW-D--RIRDDRTG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCc-c--eEEecCCE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            35788999999999853 3  34445344 489999999999999999988887776654

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

>KOG4210|consensus

Probab=94.54  E-value=0.021  Score=48.83  Aligned_cols=76  Identities=17%  Similarity=0.155  Sum_probs=59.3

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ..+++||+++.+.+.+.++..++.+.+.+..+.+...     +++++.|.|...+.+..||+....+.+....+...+.+
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            4789999999999999999999999987766554432     78999999999999999998654456666555555544


Q ss_pred             c
Q psy2347          83 G   83 (207)
Q Consensus        83 ~   83 (207)
                      .
T Consensus       167 ~  167 (285)
T KOG4210|consen  167 R  167 (285)
T ss_pred             c
Confidence            3

>KOG2193|consensus

Probab=92.97  E-value=0.0033  Score=55.65  Aligned_cols=76  Identities=16%  Similarity=0.252  Sum_probs=63.5

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEee-C-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF-N-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~-d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ..+++|-|.|||+...++.|..++.+|+.|+.|.++. + ..-..-|+|.+.+.++.||.+|++..|....++|.+..
T Consensus        78 qrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen   78 QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             HHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccCc
Confidence            3467788999999999999999999999999986643 3 23344578899999999999999999999999887653

>KOG4019|consensus

Probab=92.69  E-value=0.14  Score=40.59  Aligned_cols=75  Identities=16%  Similarity=0.119  Sum_probs=54.2

Q ss_pred             CcEEEEcCCCcCCcH-----HHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCc-EEEEEEee
Q psy2347           9 GTRVYVGGLTETVKK-----EDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGS-KLRVEISR   82 (207)
Q Consensus         9 ~~~lfV~nLp~~~te-----~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~-~l~V~~a~   82 (207)
                      ..+|++.+|+.++-.     ...+.+|.++-+...+++++. ....-|.|.+++.|..|..+++...|.++ .|++-++.
T Consensus        10 p~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs-frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~~k~yfaQ   88 (193)
T KOG4019|consen   10 PTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS-FRRVRINFSNPEAAADARIKLHSTSFNGKNELKLYFAQ   88 (193)
T ss_pred             cceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh-hceeEEeccChhHHHHHHHHhhhcccCCCceEEEEEcc
Confidence            456788888765422     234456666665555555443 55778999999999999999999999998 78887776


Q ss_pred             cC
Q psy2347          83 GR   84 (207)
Q Consensus        83 ~k   84 (207)
                      +-
T Consensus        89 ~~   90 (193)
T KOG4019|consen   89 PG   90 (193)
T ss_pred             CC
Confidence            53

>KOG3973|consensus

Probab=92.06  E-value=0.82  Score=39.93  Aligned_cols=12  Identities=17%  Similarity=0.219  Sum_probs=5.9

Q ss_pred             CcHHHHHHHHHh
Q psy2347          21 VKKEDLELEFEK   32 (207)
Q Consensus        21 ~te~~L~~~F~~   32 (207)
                      .++++|+++.+.
T Consensus       198 a~w~~iE~~~~~  209 (465)
T KOG3973|consen  198 ATWPEIEKQCES  209 (465)
T ss_pred             hhHHHHHHHHHH
Confidence            445555554443

>KOG4676|consensus

Probab=91.24  E-value=0.028  Score=49.46  Aligned_cols=71  Identities=17%  Similarity=0.122  Sum_probs=54.7

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+|+|.+|+..+...++.++|..+|+|...++... ..-+|.|+|....+...|+.. ++.++.-+...+.+
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~ask~~s~~c~~sf~~qts~~halr~-~gre~k~qhsr~ai  222 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTASKSRSSSCSHSFRKQTSSKHALRS-HGRERKRQHSRRAI  222 (479)
T ss_pred             HhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhccCCCcchhhhHhhhhhHHHHHHh-cchhhhhhhhhhhh
Confidence            367999999999999999999999999987766544 445777999998888888875 66666544333333

>KOG3262|consensus

Probab=90.58  E-value=0.8  Score=36.47  Aligned_cols=6  Identities=17%  Similarity=0.119  Sum_probs=2.2

Q ss_pred             EEcCHH
Q psy2347          52 EFSNQI   57 (207)
Q Consensus        52 ~F~~~e   57 (207)
                      -+++++
T Consensus        84 ylenk~   89 (215)
T KOG3262|consen   84 YLENKE   89 (215)
T ss_pred             eecchh
Confidence            333333

>KOG4410|consensus

Probab=90.46  E-value=0.93  Score=38.60  Aligned_cols=58  Identities=24%  Similarity=0.363  Sum_probs=42.4

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcC-------HHHHHHHHHhcC
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSN-------QIDAEAACDSMN   67 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~-------~e~A~~Al~~l~   67 (207)
                      .+-|+|.|||.++.-.||+..+.+.+.+ .+.|... ..+-||+.|-+       .+++.+++.++|
T Consensus       330 ~~di~~~nl~rd~rv~dlk~~lr~~~~~-pm~iswkg~~~k~flh~~~~~~~~~~~~~~~~~~~s~~  395 (396)
T KOG4410|consen  330 KTDIKLTNLSRDIRVKDLKSELRKRECT-PMSISWKGHFGKCFLHFGNRKGVPSTQDDMDKVLKSLN  395 (396)
T ss_pred             ccceeeccCccccchHHHHHHHHhcCCC-ceeEeeecCCcceeEecCCccCCCCCchHHHHHhccCC
Confidence            3569999999999999999999887643 3334433 67889999965       345566665554

>KOG4483|consensus

Probab=90.26  E-value=0.76  Score=40.82  Aligned_cols=55  Identities=20%  Similarity=0.146  Sum_probs=44.9

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCe-eEEEEeeCCCcEEEEEEcCHHHHHHHHHh
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKL-NSVWVAFNPPGFAFVEFSNQIDAEAACDS   65 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V-~~v~i~~d~rG~afV~F~~~e~A~~Al~~   65 (207)
                      .+.|-|.++|.....+||..+|+.|..- -+|++|.|  -+||..|++...|..||..
T Consensus       391 pHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDd--thalaVFss~~~AaeaLt~  446 (528)
T KOG4483|consen  391 PHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDD--THALAVFSSVNRAAEALTL  446 (528)
T ss_pred             cceeEeccCchhhccHHHHHHHHHhhcCCceeEEeec--ceeEEeecchHHHHHHhhc
Confidence            4688899999999999999999999752 34555554  5899999999999999974

>KOG2295|consensus

Probab=89.54  E-value=0.06  Score=49.30  Aligned_cols=71  Identities=13%  Similarity=0.130  Sum_probs=56.1

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      .+.++|||.||++.++-++|+.+++.+--+..+.+..+     ..-+.+|+|+-....+.|+.+||++.+....+.
T Consensus       229 hke~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~s~~~s  304 (648)
T KOG2295|consen  229 HKECSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLRSNFLS  304 (648)
T ss_pred             hHHHHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhccccccccc
Confidence            35688999999999999999999998876666655444     345788999988888888888888877655443

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

Probab=89.28  E-value=0.83  Score=33.73  Aligned_cols=52  Identities=23%  Similarity=0.316  Sum_probs=27.1

Q ss_pred             EEEEcCCCcC---------CcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcC-HHHHHHHH
Q psy2347          11 RVYVGGLTET---------VKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSN-QIDAEAAC   63 (207)
Q Consensus        11 ~lfV~nLp~~---------~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~-~e~A~~Al   63 (207)
                      ++.|-|++.+         ++.++|++.|+.|.+++ ++.+.+   ..++++|+|.+ -.-.+.|+
T Consensus        10 mgIi~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~k-v~~l~~~~gh~g~aiv~F~~~w~Gf~~A~   74 (116)
T PF03468_consen   10 MGIIVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLK-VKPLYGKQGHTGFAIVEFNKDWSGFKNAM   74 (116)
T ss_dssp             EEEEE----EE-TTS-EE---SHHHHHHHHH---SE-EEEEEETTEEEEEEEEE--SSHHHHHHHH
T ss_pred             EEEEEcCccccCCCCceeccCHHHHHHHHHhcCCce-eEECcCCCCCcEEEEEEECCChHHHHHHH
Confidence            5667787543         35678999999998875 444443   56899999985 33334443

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

>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=88.49  E-value=1  Score=38.42  Aligned_cols=75  Identities=12%  Similarity=0.229  Sum_probs=57.8

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCC------------CcEEEEEEcCHHHHHHHH----HhcC--Cc
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP------------PGFAFVEFSNQIDAEAAC----DSMN--DQ   69 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~------------rG~afV~F~~~e~A~~Al----~~l~--g~   69 (207)
                      .++.|.+.||..+++-.++...|.+|++|+.|.++.+.            .....+.|-+.+.|....    ..|+  .+
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            46788899999999999999999999999999998762            467889999988876433    2222  23


Q ss_pred             eeCCcEEEEEEee
Q psy2347          70 DLMGSKLRVEISR   82 (207)
Q Consensus        70 ~i~g~~l~V~~a~   82 (207)
                      .|+...|+|.+..
T Consensus        94 ~L~S~~L~lsFV~  106 (309)
T PF10567_consen   94 KLKSESLTLSFVS  106 (309)
T ss_pred             hcCCcceeEEEEE
Confidence            4677778877765

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.

>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures

Probab=85.64  E-value=5.8  Score=25.04  Aligned_cols=54  Identities=19%  Similarity=0.152  Sum_probs=41.6

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCH----HHHHHHHHh
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQ----IDAEAACDS   65 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~----e~A~~Al~~   65 (207)
                      +|.|.+|.-..-...|++.+.+.-.|.++.+... ...+-|+|+..    ++..++|++
T Consensus         1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~-~~~v~v~~~~~~~~~~~i~~~i~~   58 (62)
T PF00403_consen    1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLE-TKTVTVTYDPDKTSIEKIIEAIEK   58 (62)
T ss_dssp             EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETT-TTEEEEEESTTTSCHHHHHHHHHH
T ss_pred             CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECC-CCEEEEEEecCCCCHHHHHHHHHH
Confidence            4677777776677889999999988999888765 56888898743    566666665

These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....

>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development

Probab=84.97  E-value=9.8  Score=25.86  Aligned_cols=62  Identities=23%  Similarity=0.288  Sum_probs=44.8

Q ss_pred             CCCcCCcHHHHHHHH-HhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          16 GLTETVKKEDLELEF-EKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        16 nLp~~~te~~L~~~F-~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+|..+.-+||+... ..||...++..+.+   .-.|-..+.++.++|++.++. ...-+.|+|-+.
T Consensus        15 ~f~RPvkf~dl~~kv~~afGq~mdl~ytn~---eL~iPl~~Q~DLDkAie~ld~-s~~~ksLRilL~   77 (79)
T cd06405          15 QFPRPVKFKDLQQKVTTAFGQPMDLHYTNN---ELLIPLKNQEDLDRAIELLDR-SPHMKSLRILLS   77 (79)
T ss_pred             ecCCCccHHHHHHHHHHHhCCeeeEEEecc---cEEEeccCHHHHHHHHHHHcc-CccccceeEeEe
Confidence            456677767766544 46998888877765   477888999999999998766 445555666554

The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length

Probab=83.06  E-value=1.2  Score=38.17  Aligned_cols=33  Identities=27%  Similarity=0.314  Sum_probs=24.5

Q ss_pred             EEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347          49 AFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus        49 afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      |||+|+++++|+.|++.+..++  .++++|+.|.+
T Consensus         1 aFVtF~~~~~a~~~~q~~~~~~--~~~~~v~~APe   33 (325)
T PF02714_consen    1 AFVTFNSQKSAQIALQLLLSKR--PNSWRVSPAPE   33 (325)
T ss_pred             CEEEECCHHHHHHHHHHHhcCC--CCCceEeeCCC
Confidence            7999999999999998654443  35556766644

; GO: 0016020 membrane

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

Probab=82.65  E-value=1.6  Score=34.95  Aligned_cols=40  Identities=23%  Similarity=0.392  Sum_probs=34.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN   44 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d   44 (207)
                      .......+++.+++..+++.++..+|..++.+..+.+...
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         221 LLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             cccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence            4456789999999999999999999999999977766655

>PF14893 PNMA: PNMA

Probab=82.64  E-value=1.1  Score=39.08  Aligned_cols=52  Identities=19%  Similarity=0.316  Sum_probs=35.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHh-CCCeeEEEEeeC------CCcEEEEEEcCHH
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEK-FGKLNSVWVAFN------PPGFAFVEFSNQI   57 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~-~G~V~~v~i~~d------~rG~afV~F~~~e   57 (207)
                      .++-+.|.|.+||+++++++|++.+.. .-++-..+|...      ..-.|+|+|...-
T Consensus        15 ~~~~r~lLv~giP~dc~~~ei~e~l~~~l~plg~yrvl~~~f~~~~~~~aalve~~e~~   73 (331)
T PF14893_consen   15 VDPQRALLVLGIPEDCEEAEIEEALQAALSPLGRYRVLGKMFRREENAKAALVEFAEDV   73 (331)
T ss_pred             cChhhhheeecCCCCCCHHHHHHHHHHhhcccccceehhhHhhhhcccceeeeeccccc
Confidence            356678999999999999999998765 323333333222      4457888887533

>PRK10629 EnvZ/OmpR regulon moderator; Provisional

Probab=82.05  E-value=13  Score=27.83  Aligned_cols=73  Identities=8%  Similarity=0.070  Sum_probs=49.7

Q ss_pred             CCCcEEEEcCCCcC---CcHHHHHHHHHhCCC-eeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           7 ERGTRVYVGGLTET---VKKEDLELEFEKFGK-LNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         7 ~~~~~lfV~nLp~~---~te~~L~~~F~~~G~-V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .+...|.|+.....   .+.+.|++++++-+- ++.+..-.   .-..|.|++.|+..+|.+.|+...-+.-.|.+.++.
T Consensus        33 gedpavQIs~~~~g~~~~~~~~v~~~L~~~gI~~ksi~~~~---~~~~irf~~~~~Ql~Ak~vL~~~L~~~y~VAlnl~p  109 (127)
T PRK10629         33 QQESTLAIRAVHQGASLPDGFYVYQHLDANGIHIKSITPEN---DSLLIRFDSPEQSAAAKEVLDRTLPHGYIIAQQDDN  109 (127)
T ss_pred             CCCceEEEecCCCCCccchHHHHHHHHHHCCCCcceEEeeC---CEEEEEECCHHHHHHHHHHHHHHcCCCCEEEEecCC
Confidence            45567788766333   456778888887763 44554433   378899999999999988876555455566666554

>KOG2891|consensus

Probab=81.59  E-value=0.53  Score=39.98  Aligned_cols=37  Identities=24%  Similarity=0.470  Sum_probs=28.8

Q ss_pred             CCCcEEEEcCCCcC------------CcHHHHHHHHHhCCCeeEEEEee
Q psy2347           7 ERGTRVYVGGLTET------------VKKEDLELEFEKFGKLNSVWVAF   43 (207)
Q Consensus         7 ~~~~~lfV~nLp~~------------~te~~L~~~F~~~G~V~~v~i~~   43 (207)
                      +...+|++..||-.            .+|+.|+..|+.||+|..|.|+.
T Consensus       147 erpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipi  195 (445)
T KOG2891|consen  147 ERPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPI  195 (445)
T ss_pred             CCCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcc
Confidence            34568888888732            46788999999999999888753

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	207
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		4e-08
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		2e-07
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		3e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		4e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		6e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		6e-04

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 38/70 (54%)
Query: 11 RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          +VYVG L                    +VW+A NPPGFAFVEF +  DAE A   ++ + 
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 71 LMGSKLRVEI 80
          + GS++RVE+
Sbjct: 62 ICGSRVRVEL 71

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 36/70 (51%)
Query: 11  RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
           +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 71  LMGSKLRVEI 80
           L G ++RVE+
Sbjct: 135 LCGCRVRVEL 144

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 36/70 (51%)
Query: 11  RVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
           +VYVG L                    SVWVA NPPGFAFVEF +  DA  A   ++ + 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 71  LMGSKLRVEI 80
           L G ++RVE+
Sbjct: 135 LCGCRVRVEL 144

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 2  SDGMMERGTRVYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQ 56
          S GM      +YVGGL E V                 + +  +       GFAFVEF   
Sbjct: 5  SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 57 IDAEAACDSMNDQDLMGSKLRVEI 80
           DA AA D+MN+ +L G  +RV +
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNL 88

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 4  GMMERGTRV-YVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQI 57
          G M    RV YVGGL E V                 + +  +       GFAFVEF    
Sbjct: 1  GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 58 DAEAACDSMNDQDLMGSKLRVEI 80
          DA AA D+MN+ +L G  +RV +
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNL 83

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          +YVGGL E V                 + +  +       GFAFVEF    DA AA D+M
Sbjct: 8  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 67 NDQDLMGSKLRVEI 80
          N+ +L G  +RV +
Sbjct: 68 NESELFGRTIRVNL 81

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 12 VYVGGLTETVXXXXXXXXXXXXXXXNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSM 66
          +YVGGL E V                 + +  +       GFAFVEF    DA AA D+M
Sbjct: 5  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 67 NDQDLMGSKLRVEI 80
          N+ +L G  +RV +
Sbjct: 65 NESELFGRTIRVNL 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	207
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.88
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.88
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.87
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.87
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.87
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.87
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.87
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.86
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.86
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.86
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.86
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.86
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.86
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.86
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.86
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.86
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.86
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.86
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.86
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.85
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.85
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.85
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.85
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.85
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.85
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.85
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.85
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.85
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.85
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.84
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.84
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.84
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.84
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.84
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.84
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.84
2div_A	99	TRNA selenocysteine associated protein; structural	99.84
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.84
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.84
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.84
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.84
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.84
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.84
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.83
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.83
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.83
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.83
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.83
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.83
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.83
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.83
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.83
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.82
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.82
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.82
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.82
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.82
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.82
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.82
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.82
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.82
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.82
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.82
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.82
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.81
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.81
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.81
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.81
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.81
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.81
1x5p_A	97	Negative elongation factor E; structure genomics,	99.81
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.81
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.81
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.81
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.8
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.8
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.8
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.8
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.8
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.8
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.8
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.68
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.79
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.79
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.79
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.79
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.79
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.79
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.79
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.79
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.79
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.79
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.79
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.78
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.78
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.78
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.78
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.78
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.78
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.78
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.78
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.78
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.77
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.77
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.77
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.77
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.76
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.76
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.76
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.75
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.75
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.74
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.74
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.73
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.73
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.73
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.73
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.73
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.73
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.72
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.72
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.71
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.7
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.7
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.7
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.69
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.68
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.68
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.68
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.68
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.68
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.65
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.65
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.65
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.64
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.64
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.64
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.63
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.63
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.63
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.62
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.61
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.61
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.59
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.58
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.56
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.56
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.54
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.5
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.43
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.43
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.25
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.02
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.95
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.62
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.43
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	98.12
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.99
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.77
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.73
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.6
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	97.47
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.54
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.44
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.24
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	94.47
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	90.97
2cu1_A	103	Mitogen-activated protein kinase kinase kinase 2;	84.72
3fry_A	73	Probable copper-exporting P-type ATPase A; transpo	82.74

>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=99.88  E-value=1.3e-22  Score=145.50  Aligned_cols=80  Identities=24%  Similarity=0.430  Sum_probs=73.9

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .+..+.++|||+|||+++||++|+++|++||+|++|+|++|     +++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        14 n~~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V   93 (99)
T 4fxv_A           14 NLYFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV   93 (99)
T ss_dssp             --CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999987     5689999999999999999999999999999999


Q ss_pred             EEeec
Q psy2347          79 EISRG   83 (207)
Q Consensus        79 ~~a~~   83 (207)
                      ++|+|
T Consensus        94 ~~AkP   98 (99)
T 4fxv_A           94 SYARP   98 (99)
T ss_dssp             EECCB
T ss_pred             EEeeC
Confidence            99986

>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=99.88  E-value=1.7e-22  Score=155.55  Aligned_cols=84  Identities=27%  Similarity=0.486  Sum_probs=77.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|+
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4457899999999999999999999999999999999887     46899999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q psy2347          80 ISRGRGRGR   88 (207)
Q Consensus        80 ~a~~k~~~~   88 (207)
                      +|+++.+..
T Consensus       115 ~a~~~~~~~  123 (156)
T 1h2v_Z          115 WDAGFKEGR  123 (156)
T ss_dssp             EESCCCTTC
T ss_pred             ECCCCCCcC
Confidence            998866543

>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=99.87  E-value=1.6e-21  Score=141.50  Aligned_cols=83  Identities=23%  Similarity=0.295  Sum_probs=77.1

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC-----cEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG-----SKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g-----~~l~V~~   80 (207)
                      ....++|||.|||+++|+++|+++|++|++|+.|+|+++  +||||+|+++++|++||+.||+++|.+     ++|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~   89 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   89 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT--TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC--CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEe
Confidence            456789999999999999999999999999999999987  899999999999999999999999999     9999999


Q ss_pred             eecCCCCCCC
Q psy2347          81 SRGRGRGRGG   90 (207)
Q Consensus        81 a~~k~~~~~~   90 (207)
                      |+++++...+
T Consensus        90 a~~~~~~~~r   99 (108)
T 1x4c_A           90 DGPRSPSYGR   99 (108)
T ss_dssp             SSCCSCCCCC
T ss_pred             CCCCCCCCCC
Confidence            9998766544

>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=99.87  E-value=9.6e-22  Score=142.55  Aligned_cols=83  Identities=34%  Similarity=0.517  Sum_probs=76.8

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ...+.++|||.|||+++|+++|+++|++|++|+.|+|+.+  +++||||+|+++++|++||+.||+++|++++|+|++++
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   97 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   97 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcc
Confidence            3456789999999999999999999999999999999877  68999999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      ++.+.
T Consensus        98 ~~~~~  102 (109)
T 1x4a_A           98 SGRGT  102 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.87  E-value=1.8e-21  Score=138.60  Aligned_cols=86  Identities=29%  Similarity=0.380  Sum_probs=78.9

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||.|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus         4 ~~~~~~~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            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3567889999999999999999999999999999999887     57999999999999999999999999999999999


Q ss_pred             EeecCCCCCCC
Q psy2347          80 ISRGRGRGRGG   90 (207)
Q Consensus        80 ~a~~k~~~~~~   90 (207)
                      +++++......
T Consensus        84 ~a~~~~~~~~~   94 (99)
T 1whw_A           84 PSTIKKEASQS   94 (99)
T ss_dssp             ECCCCSTTCCC
T ss_pred             EcCCCcccccC
Confidence            99998765443

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=8.7e-22  Score=140.93  Aligned_cols=87  Identities=32%  Similarity=0.557  Sum_probs=80.0

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ..+.++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+
T Consensus         6 ~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 1x5s_A            6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   85 (102)
T ss_dssp             CCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            345678899999999999999999999999999999999886     678999999999999999999999999999999


Q ss_pred             EEEeecCCCCCC
Q psy2347          78 VEISRGRGRGRG   89 (207)
Q Consensus        78 V~~a~~k~~~~~   89 (207)
                      |++++++...+.
T Consensus        86 v~~a~~~~~~~~   97 (102)
T 1x5s_A           86 VDQAGKSSDNRS   97 (102)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEECCCCCCCCC
Confidence            999998776543

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

Probab=99.87  E-value=1.9e-21  Score=137.28  Aligned_cols=83  Identities=28%  Similarity=0.462  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||.|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            457889999999999999999999999999999999987     578999999999999999999999999999999999


Q ss_pred             eecCCCCC
Q psy2347          81 SRGRGRGR   88 (207)
Q Consensus        81 a~~k~~~~   88 (207)
                      ++++....
T Consensus        82 a~~~~~~~   89 (95)
T 2dnz_A           82 VTERLDGG   89 (95)
T ss_dssp             SSCCCCCC
T ss_pred             cccccCCC
Confidence            98876643

>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=99.86  E-value=3.4e-21  Score=138.18  Aligned_cols=85  Identities=24%  Similarity=0.356  Sum_probs=78.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ...+.++|||+|||+++|+++|+++|++|++|+.|+|+.+   +++||||+|+++++|++||+.||++.|.+++|+|+++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            3456789999999999999999999999999999999987   6799999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q psy2347          82 RGRGRGRG   89 (207)
Q Consensus        82 ~~k~~~~~   89 (207)
                      +++.....
T Consensus        91 ~~~~~~~~   98 (103)
T 2cqi_A           91 TTPSSQKS   98 (103)
T ss_dssp             CCTTCCCC
T ss_pred             CCCccccc
Confidence            98765543

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

Probab=99.86  E-value=1e-21  Score=140.55  Aligned_cols=87  Identities=36%  Similarity=0.613  Sum_probs=79.9

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ..+.++.++|||.|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+
T Consensus         6 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2cqb_A            6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   85 (102)
T ss_dssp             SCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            345678899999999999999999999999999999999887     689999999999999999999999999999999


Q ss_pred             EEEeecCCCCCC
Q psy2347          78 VEISRGRGRGRG   89 (207)
Q Consensus        78 V~~a~~k~~~~~   89 (207)
                      |++++++.....
T Consensus        86 V~~a~~~~~~~~   97 (102)
T 2cqb_A           86 VNLAKPMRIKES   97 (102)
T ss_dssp             EEECCCCCCCCC
T ss_pred             EEeCCCCCCCCC
Confidence            999998766543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=1.5e-21  Score=138.12  Aligned_cols=85  Identities=21%  Similarity=0.375  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEE-EEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v-~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..+.++|||.|||+++|+++|+++|++|++|+.| +|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3578899999999999999999999999999999 99887     68999999999999999999999999999999999


Q ss_pred             EeecCCCCCCC
Q psy2347          80 ISRGRGRGRGG   90 (207)
Q Consensus        80 ~a~~k~~~~~~   90 (207)
                      +++++.....+
T Consensus        82 ~a~~~~~~~~~   92 (96)
T 1x5t_A           82 YAFKKDSKGSG   92 (96)
T ss_dssp             ESCCCCCCCCC
T ss_pred             EecccCCCCCC
Confidence            99988765443

>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=99.86  E-value=3.7e-21  Score=137.95  Aligned_cols=86  Identities=28%  Similarity=0.429  Sum_probs=79.3

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ....+.++|||.|||+++|+++|+++|++|++|+.|+|+.+   +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999987   589999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q psy2347          81 SRGRGRGRG   89 (207)
Q Consensus        81 a~~k~~~~~   89 (207)
                      ++++.....
T Consensus        90 a~~~~~~~~   98 (103)
T 2cq3_A           90 ATARVMTNS   98 (103)
T ss_dssp             CCSSCCCCC
T ss_pred             cccCCCCCC
Confidence            998876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=2.9e-21  Score=137.55  Aligned_cols=85  Identities=26%  Similarity=0.575  Sum_probs=78.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ....+.++|||+|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+ ||++.|.+++|+|
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V   83 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEV   83 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEE
Confidence            34567899999999999999999999999999999999887     68999999999999999998 8999999999999


Q ss_pred             EEeecCCCCCC
Q psy2347          79 EISRGRGRGRG   89 (207)
Q Consensus        79 ~~a~~k~~~~~   89 (207)
                      ++++++.....
T Consensus        84 ~~a~~~~~~~~   94 (99)
T 2dgs_A           84 KRAEPRDSKSS   94 (99)
T ss_dssp             EECCCCCCCCC
T ss_pred             EECCCCcccCC
Confidence            99998776543

>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=99.86  E-value=2e-21  Score=138.01  Aligned_cols=83  Identities=28%  Similarity=0.502  Sum_probs=77.3

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC--CcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM--GSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~--g~~l~V~~a   81 (207)
                      ...++.++|||.|||+++|+++|+++|++|++|++|+|+++ ++||||+|+++++|++||+.||+++|.  +++|+|+++
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a   90 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEEC
Confidence            45567899999999999999999999999999999999987 899999999999999999999999999  999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      ++++++
T Consensus        91 ~~~~~~   96 (97)
T 1why_A           91 KSGPSS   96 (97)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987653

>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=2.5e-21  Score=139.26  Aligned_cols=85  Identities=28%  Similarity=0.400  Sum_probs=78.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            4567889999999999999999999999999999999887     57899999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q psy2347          80 ISRGRGRGRG   89 (207)
Q Consensus        80 ~a~~k~~~~~   89 (207)
                      +++++.....
T Consensus        91 ~a~~~~~~~~  100 (105)
T 1x5u_A           91 KASAHNKNLS  100 (105)
T ss_dssp             ETTTTSCCCC
T ss_pred             ECCCCCcCCC
Confidence            9998776544

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=9.7e-22  Score=142.43  Aligned_cols=84  Identities=15%  Similarity=0.167  Sum_probs=76.4

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcC--CceeCCcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN--DQDLMGSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~--g~~i~g~~l~V~~a   81 (207)
                      ...++.++|||+|||+++||++|+++|++||+|++|+|+++ |+||||+|+++++|++||+.|+  ..+|.+++|+|++|
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A   89 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS   89 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            35678899999999999999999999999999999999998 9999999999999999999876  47899999999999


Q ss_pred             ecCCCCC
Q psy2347          82 RGRGRGR   88 (207)
Q Consensus        82 ~~k~~~~   88 (207)
                      ++++...
T Consensus        90 ~~~~~~~   96 (105)
T 1sjq_A           90 NHKELKT   96 (105)
T ss_dssp             SSSSCCC
T ss_pred             CCCCCCc
Confidence            8876553

>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=99.86  E-value=5.5e-21  Score=137.29  Aligned_cols=84  Identities=30%  Similarity=0.461  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+.+.++|||.|||+++|+++|+++|++|++|+.|+|+   ++||||+|+++++|++||+.||+++|.+++|+|+++++
T Consensus         6 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~---~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   82 (103)
T 2dgu_A            6 SGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP   82 (103)
T ss_dssp             CCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC---SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCC
Confidence            456678999999999999999999999999999999997   45999999999999999999999999999999999998


Q ss_pred             CCCCCCC
Q psy2347          84 RGRGRGG   90 (207)
Q Consensus        84 k~~~~~~   90 (207)
                      +......
T Consensus        83 ~~~~~~~   89 (103)
T 2dgu_A           83 PDQKRKE   89 (103)
T ss_dssp             CCCCCCC
T ss_pred             Ccccchh
Confidence            7765443

>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=3e-21  Score=137.71  Aligned_cols=83  Identities=24%  Similarity=0.407  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ...+.++|||.|||+++|+++|+++|++|++|+.|+|+.+    +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4456789999999999999999999999999999999987    468999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      +++++++
T Consensus        93 a~~~~~~   99 (100)
T 2do4_A           93 SNSGPSS   99 (100)
T ss_dssp             CCCCSCC
T ss_pred             CCCCCCC
Confidence            9987654

>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=3.5e-21  Score=136.76  Aligned_cols=86  Identities=24%  Similarity=0.317  Sum_probs=78.9

Q ss_pred             CCCCCCCCcEEEEcCCCcCCcHHHHH----HHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           2 SDGMMERGTRVYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         2 s~~~~~~~~~lfV~nLp~~~te~~L~----~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      |..+..+.++|||+|||+++|+++|+    ++|++||+|++|+|+.+  .++||||+|+++++|++||+.||+++|.+++
T Consensus         2 ss~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            2 SSGSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCCCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34556778999999999999999999    99999999999999977  4889999999999999999999999999999


Q ss_pred             EEEEEeecCCCC
Q psy2347          76 LRVEISRGRGRG   87 (207)
Q Consensus        76 l~V~~a~~k~~~   87 (207)
                      |+|++|++++..
T Consensus        82 l~V~~a~~~~~~   93 (96)
T 2dgx_A           82 ILVSLATGASGP   93 (96)
T ss_dssp             EEEEECCCSSCC
T ss_pred             EEEEEcCCCCCC
Confidence            999999887654

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

Probab=99.86  E-value=3.9e-21  Score=145.01  Aligned_cols=85  Identities=22%  Similarity=0.412  Sum_probs=77.7

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||+|||+++|+++|+++|++|++|++|+|+++     +++||||+|+++++|++||+.||+.+|.+++|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999877     47899999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q psy2347          80 ISRGRGRGRG   89 (207)
Q Consensus        80 ~a~~k~~~~~   89 (207)
                      +++++..+..
T Consensus       118 ~a~~~~~~~~  127 (139)
T 1u6f_A          118 LAASGHQRPG  127 (139)
T ss_dssp             ESSCCCCCCC
T ss_pred             ECCCCCCCCC
Confidence            9998766543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.86  E-value=9.1e-21  Score=138.85  Aligned_cols=84  Identities=26%  Similarity=0.416  Sum_probs=76.1

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      +....+.++|||.|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+.|+. +|.+++|+
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            344567899999999999999999999999999999999987     678999999999999999999997 89999999


Q ss_pred             EEEeecCCCC
Q psy2347          78 VEISRGRGRG   87 (207)
Q Consensus        78 V~~a~~k~~~   87 (207)
                      |++++++.+.
T Consensus        90 V~~a~~~~~~   99 (116)
T 2cqd_A           90 VNLAYLGAKP   99 (116)
T ss_dssp             EEESTTTCCC
T ss_pred             EEEcccCCCc
Confidence            9999875443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=5.6e-21  Score=134.43  Aligned_cols=84  Identities=23%  Similarity=0.432  Sum_probs=77.0

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .....+.++|||+|||+++|+++|+++|++||+|++|+|+++   ||||+|+++++|++||+.||+++|.+++|+|++++
T Consensus         4 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~---~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   80 (92)
T 2dgt_A            4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD---YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST   80 (92)
T ss_dssp             SCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS---EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC---EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            445677899999999999999999999999999999999854   99999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q psy2347          83 GRGRGRG   89 (207)
Q Consensus        83 ~k~~~~~   89 (207)
                      ++.+...
T Consensus        81 ~~~~~~~   87 (92)
T 2dgt_A           81 SRLRTAS   87 (92)
T ss_dssp             CCCSCCC
T ss_pred             CCCCCCC
Confidence            8766543

>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=1.9e-21  Score=139.49  Aligned_cols=85  Identities=24%  Similarity=0.380  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            3566899999999999999999999999999999999987     46899999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q psy2347          80 ISRGRGRGRG   89 (207)
Q Consensus        80 ~a~~k~~~~~   89 (207)
                      +++++.....
T Consensus        91 ~a~~~~~~~~  100 (103)
T 2cq0_A           91 WAKPSTNSGP  100 (103)
T ss_dssp             ESSCCCCSCC
T ss_pred             ECCCCCCCCC
Confidence            9998776543

>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=2e-21  Score=139.34  Aligned_cols=86  Identities=31%  Similarity=0.512  Sum_probs=78.4

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ...++.++|||+|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            34567899999999999999999999999999999999876     5799999999999999999999999999999999


Q ss_pred             EEeecCCCCCC
Q psy2347          79 EISRGRGRGRG   89 (207)
Q Consensus        79 ~~a~~k~~~~~   89 (207)
                      ++++++.+...
T Consensus        88 ~~a~~~~~~~~   98 (103)
T 2dnm_A           88 QVARYGRRDLS   98 (103)
T ss_dssp             EECSSCCSCCC
T ss_pred             EECCcCCCCCC
Confidence            99988665433

>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=99.85  E-value=1.6e-21  Score=143.18  Aligned_cols=80  Identities=26%  Similarity=0.388  Sum_probs=73.9

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .+++|||+|||+++||++|+++|++||+|++|+|+.+   +++||||+|+++++|++||+.||+++|.+++|+|++++++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            4568999999999999999999999999999999987   5789999999999999999999999999999999999876


Q ss_pred             CCC
Q psy2347          85 GRG   87 (207)
Q Consensus        85 ~~~   87 (207)
                      ..+
T Consensus        84 ~~~   86 (115)
T 4f25_A           84 KER   86 (115)
T ss_dssp             CC-
T ss_pred             ccc
Confidence            554

>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=4e-21  Score=138.18  Aligned_cols=85  Identities=27%  Similarity=0.389  Sum_probs=78.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCC---cEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMG---SKLR   77 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g---~~l~   77 (207)
                      ..++.++|||+|||+++|+++|+++|++|++|+.|+|+.+    +++||||+|+++++|++||+.||+..|.+   ++|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3456899999999999999999999999999999999987    47899999999999999999999999998   9999


Q ss_pred             EEEeecCCCCCC
Q psy2347          78 VEISRGRGRGRG   89 (207)
Q Consensus        78 V~~a~~k~~~~~   89 (207)
                      |++++++.++..
T Consensus        91 V~~a~~~~~~~~  102 (105)
T 2dnh_A           91 VKFADTDKESGP  102 (105)
T ss_dssp             EEESCSSCCCSC
T ss_pred             EEECccCcccCC
Confidence            999998876544

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.6e-21  Score=138.75  Aligned_cols=87  Identities=26%  Similarity=0.404  Sum_probs=79.4

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ....+.++|||.|||+++|+++|+++|++|++|+.|+|+.+   +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            34567899999999999999999999999999999999976   678999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q psy2347          81 SRGRGRGRGG   90 (207)
Q Consensus        81 a~~k~~~~~~   90 (207)
                      ++++.++..+
T Consensus        90 a~~~~~~~~~   99 (103)
T 2d9p_A           90 AQRKEERQSG   99 (103)
T ss_dssp             CSSCCCCCCC
T ss_pred             ecccccCCCC
Confidence            9988765443

>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=2.8e-21  Score=141.36  Aligned_cols=84  Identities=26%  Similarity=0.438  Sum_probs=77.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||.|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            346689999999999999999999999999999999987     458999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q psy2347          81 SRGRGRGRG   89 (207)
Q Consensus        81 a~~k~~~~~   89 (207)
                      ++++.....
T Consensus       102 a~~~~~~~~  110 (115)
T 2cpz_A          102 KRSKNDSKS  110 (115)
T ss_dssp             CCCSCCCCC
T ss_pred             cCCCCcCCC
Confidence            998876543

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

Probab=99.85  E-value=2.5e-21  Score=141.35  Aligned_cols=80  Identities=18%  Similarity=0.242  Sum_probs=74.7

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++||++|+++|++||+|++|+|+.|     +++||||+|+++++|++||+.||+++|.+++|+|++
T Consensus         3 ~~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            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            357789999999999999999999999999999999987     579999999999999999999999999999999999


Q ss_pred             eecCC
Q psy2347          81 SRGRG   85 (207)
Q Consensus        81 a~~k~   85 (207)
                      +..+.
T Consensus        83 a~~~~   87 (110)
T 3s8s_A           83 DIKGQ   87 (110)
T ss_dssp             CSTTH
T ss_pred             CCCCc
Confidence            97543

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

Probab=99.85  E-value=3.7e-21  Score=135.55  Aligned_cols=82  Identities=28%  Similarity=0.483  Sum_probs=76.1

Q ss_pred             CCCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           1 MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         1 ms~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      |+....++.++|||.|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++||+.||+++|.+++
T Consensus         8 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   87 (94)
T 2e5h_A            8 MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRV   87 (94)
T ss_dssp             CCCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEE
T ss_pred             CCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            34556678899999999999999999999999999999999887     5789999999999999999999999999999


Q ss_pred             EEEEEee
Q psy2347          76 LRVEISR   82 (207)
Q Consensus        76 l~V~~a~   82 (207)
                      |+|++|+
T Consensus        88 l~v~~ak   94 (94)
T 2e5h_A           88 IKASIAI   94 (94)
T ss_dssp             EEEEECC
T ss_pred             EEEEecC
Confidence            9999985

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.85  E-value=2.8e-21  Score=138.80  Aligned_cols=81  Identities=25%  Similarity=0.294  Sum_probs=74.3

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCce--eCCcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD--LMGSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~--i~g~~l~V~~a   81 (207)
                      ...+++++|||+|||+++|+++|+++|++||+|++|.|+++ |+||||+|+++++|++|++.|+...  |.+++|.|+++
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~-kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S   94 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK-KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS   94 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEEC
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEec
Confidence            34578899999999999999999999999999999999876 8999999999999999999998765  78999999999


Q ss_pred             ecCC
Q psy2347          82 RGRG   85 (207)
Q Consensus        82 ~~k~   85 (207)
                      ++++
T Consensus        95 ~~k~   98 (100)
T 3r27_A           95 TSQK   98 (100)
T ss_dssp             SCSC
T ss_pred             cccc
Confidence            8764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=8.1e-22  Score=139.06  Aligned_cols=79  Identities=24%  Similarity=0.377  Sum_probs=72.4

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCC-CeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcC-CceeCCcEEEEEEe
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFG-KLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN-DQDLMGSKLRVEIS   81 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G-~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~-g~~i~g~~l~V~~a   81 (207)
                      +++|||+|||+++||++|+++|++|| +|++|+|++|     +++||||+|+++++|++||+.|+ ...|.+++|+|++|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            47999999999999999999999999 7999999887     78999999999999999999875 56799999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +|+++.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.85  E-value=2.5e-21  Score=134.40  Aligned_cols=80  Identities=28%  Similarity=0.485  Sum_probs=71.6

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++|++.||++.|.+++|+|++
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            467889999999999999999999999999999999987     478999999999999999999999999999999999


Q ss_pred             eecCC
Q psy2347          81 SRGRG   85 (207)
Q Consensus        81 a~~k~   85 (207)
                      +++++
T Consensus        83 a~~kp   87 (87)
T 3bs9_A           83 ATRKP   87 (87)
T ss_dssp             EC---
T ss_pred             cCCCC
Confidence            98864

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.6e-21  Score=140.29  Aligned_cols=87  Identities=26%  Similarity=0.443  Sum_probs=79.0

Q ss_pred             CCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCee--------EEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCC
Q psy2347           2 SDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLN--------SVWVAFN-----PPGFAFVEFSNQIDAEAACDSMND   68 (207)
Q Consensus         2 s~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~--------~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g   68 (207)
                      +.....+.++|||.|||+++|+++|+++|++|+.|+        .|+|+.+     +++||||+|+++++|++||+.||+
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   87 (113)
T 2cpe_A            8 DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG   87 (113)
T ss_dssp             CCCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT
T ss_pred             CcccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC
Confidence            344566789999999999999999999999999999        6998877     578999999999999999999999


Q ss_pred             ceeCCcEEEEEEeecCCCCC
Q psy2347          69 QDLMGSKLRVEISRGRGRGR   88 (207)
Q Consensus        69 ~~i~g~~l~V~~a~~k~~~~   88 (207)
                      ++|.+++|+|++++++....
T Consensus        88 ~~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           88 KDFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             CEETTEECEEECSSCCCCST
T ss_pred             CccCCCEEEEEECCCCCCCC
Confidence            99999999999999876653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.85  E-value=1.4e-20  Score=137.54  Aligned_cols=86  Identities=28%  Similarity=0.456  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ....+.++|||.|||+++|+++|+++|++|+.|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567899999999999999999999999999999999987     4689999999999999999999999999999999


Q ss_pred             EEeecCCCCCC
Q psy2347          79 EISRGRGRGRG   89 (207)
Q Consensus        79 ~~a~~k~~~~~   89 (207)
                      ++++++.....
T Consensus        90 ~~a~~~~~~~~  100 (115)
T 2dgo_A           90 NWATRKPPAPK  100 (115)
T ss_dssp             EESSCCCCCSC
T ss_pred             EEccCCCCCCc
Confidence            99998766543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=8.8e-21  Score=132.88  Aligned_cols=81  Identities=20%  Similarity=0.425  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ..++.++|||+|||+++|+++|+++|++|++|++|+|+   ++||||+|+++++|++||+.||+.+|++++|+|++++++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   80 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII---KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNK   80 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE---TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCC
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE---CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCC
Confidence            45678999999999999999999999999999999998   679999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy2347          85 GRGR   88 (207)
Q Consensus        85 ~~~~   88 (207)
                      .+..
T Consensus        81 ~~~~   84 (90)
T 2dnq_A           81 SKAS   84 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6653

>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=99.85  E-value=3.9e-21  Score=142.69  Aligned_cols=85  Identities=28%  Similarity=0.558  Sum_probs=78.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|+
T Consensus        18 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           18 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            3456789999999999999999999999999999999877     48999999999999999999999999999999999


Q ss_pred             EeecCCCCCC
Q psy2347          80 ISRGRGRGRG   89 (207)
Q Consensus        80 ~a~~k~~~~~   89 (207)
                      +++++.....
T Consensus        98 ~a~~~~~~~~  107 (126)
T 3ex7_B           98 WCFVRGPPKG  107 (126)
T ss_dssp             ESEESSSCCC
T ss_pred             EecCCCCCCC
Confidence            9998776543

>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=9.7e-21  Score=137.31  Aligned_cols=85  Identities=25%  Similarity=0.414  Sum_probs=78.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcC------CceeCC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN------DQDLMG   73 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~------g~~i~g   73 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||      ++.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            4467889999999999999999999999999999999977     58999999999999999999999      999999


Q ss_pred             cEEEEEEeecCCCCCC
Q psy2347          74 SKLRVEISRGRGRGRG   89 (207)
Q Consensus        74 ~~l~V~~a~~k~~~~~   89 (207)
                      ++|+|++++++.....
T Consensus        91 ~~l~v~~a~~~~~~~~  106 (111)
T 1x4h_A           91 RQLKVDLAVTRDEAAS  106 (111)
T ss_dssp             CEEEEECCCCCCCCCC
T ss_pred             EEEEEEECCCCccCCC
Confidence            9999999998766543

>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=3.1e-21  Score=139.18  Aligned_cols=81  Identities=23%  Similarity=0.263  Sum_probs=74.1

Q ss_pred             CCCCCcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC--ceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND--QDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g--~~i~g~~l~V~~a   81 (207)
                      ..+++++|||+|||+ ++||++|+++|++||+|++|.|+++ ++||||+|+++++|++||+.||.  .+|.+++|.|++|
T Consensus        11 ~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   89 (102)
T 1x4d_A           11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   89 (102)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEEC
Confidence            456789999999999 9999999999999999999999987 79999999999999999998885  4699999999999


Q ss_pred             ecCCC
Q psy2347          82 RGRGR   86 (207)
Q Consensus        82 ~~k~~   86 (207)
                      +++.+
T Consensus        90 ~~~~~   94 (102)
T 1x4d_A           90 QKYKR   94 (102)
T ss_dssp             CCCTT
T ss_pred             CCCCC
Confidence            87544

>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=9.7e-21  Score=136.35  Aligned_cols=83  Identities=13%  Similarity=0.111  Sum_probs=75.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc--CCceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM--NDQDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l--~g~~i~g~~l~V~~a~   82 (207)
                      ..+++++|||+|||+++||++|+++|++||+|++|.|+++ |+||||+|+++++|++||+.|  +..+|.+++|+|++++
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~   89 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   89 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcC
Confidence            4567899999999999999999999999999999999987 999999999999999999976  4678999999999998


Q ss_pred             cCCCCC
Q psy2347          83 GRGRGR   88 (207)
Q Consensus        83 ~k~~~~   88 (207)
                      ++....
T Consensus        90 ~~~~~~   95 (101)
T 2cq1_A           90 HKELKT   95 (101)
T ss_dssp             CSSCCC
T ss_pred             cccCcC
Confidence            876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=9.9e-21  Score=132.62  Aligned_cols=83  Identities=24%  Similarity=0.451  Sum_probs=76.1

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .....+.++|||+|||+++|+++|+++|++||+|++|+|+++   ||||+|+++++|++||+.||++.|.+++|+|++++
T Consensus         3 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~---~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   79 (90)
T 2dnp_A            3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD---YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST   79 (90)
T ss_dssp             CCSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS---CEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC---EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECC
Confidence            445678899999999999999999999999999999999854   99999999999999999999999999999999998


Q ss_pred             cCCCCC
Q psy2347          83 GRGRGR   88 (207)
Q Consensus        83 ~k~~~~   88 (207)
                      ++....
T Consensus        80 ~~~~~~   85 (90)
T 2dnp_A           80 KGQKKS   85 (90)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            875543

>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=99.84  E-value=6.7e-21  Score=131.08  Aligned_cols=77  Identities=35%  Similarity=0.517  Sum_probs=73.1

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++|++.||++.|.+++|+|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            468999999999999999999999999999999977     478999999999999999999999999999999999998


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

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

Probab=99.84  E-value=9.1e-21  Score=136.48  Aligned_cols=85  Identities=22%  Similarity=0.416  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCcee---CCcE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDL---MGSK   75 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i---~g~~   75 (207)
                      ....+.++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++||+.||+..+   .+++
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            34567899999999999999999999999999999999987     679999999999999999999999988   8999


Q ss_pred             EEEEEeecCCCCC
Q psy2347          76 LRVEISRGRGRGR   88 (207)
Q Consensus        76 l~V~~a~~k~~~~   88 (207)
                      |+|++++++.+..
T Consensus        88 l~v~~a~~~~~~~  100 (106)
T 2dgp_A           88 IQVKPADSESRGG  100 (106)
T ss_dssp             CEEEECCCCSCCC
T ss_pred             EEEEECCcccccC
Confidence            9999998876543

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

Probab=99.84  E-value=1.4e-20  Score=135.64  Aligned_cols=84  Identities=21%  Similarity=0.408  Sum_probs=77.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhc-CCceeCCcEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSM-NDQDLMGSKLR   77 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l-~g~~i~g~~l~   77 (207)
                      ...+.++|||.|||+++|+++|+++|++|++|+.|+|+.+      +++||||+|+++++|++||+.| |++.|.+++|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            4467789999999999999999999999999999999876      4899999999999999999999 99999999999


Q ss_pred             EEEeecCCCCC
Q psy2347          78 VEISRGRGRGR   88 (207)
Q Consensus        78 V~~a~~k~~~~   88 (207)
                      |++++++....
T Consensus        91 v~~a~~~~~~~  101 (107)
T 2cph_A           91 LEWADSEVTVQ  101 (107)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEeCCCCCCCC
Confidence            99999876654

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

Probab=99.84  E-value=8.4e-21  Score=133.18  Aligned_cols=83  Identities=23%  Similarity=0.317  Sum_probs=77.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|+.|+|+++   +++||||+|+++++|++||+.||++.|.+++|+|+++
T Consensus         4 ~~~~~~~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            4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4567899999999999999999999999999999999986   5799999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++...
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            887654

>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=99.84  E-value=8.2e-21  Score=137.39  Aligned_cols=83  Identities=28%  Similarity=0.266  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC--ceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND--QDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g--~~i~g~~l~V~~a~   82 (207)
                      ..+++++|||+|||+++||++|+++|++||+|++|.|+++ |+||||+|+++++|++||+.|+.  .+|.+++|+|++++
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~   89 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST   89 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcc
Confidence            3467899999999999999999999999999999999886 89999999999999999998865  45999999999998


Q ss_pred             cCCCCC
Q psy2347          83 GRGRGR   88 (207)
Q Consensus        83 ~k~~~~   88 (207)
                      ++....
T Consensus        90 ~~~~~~   95 (104)
T 1wex_A           90 SKRITR   95 (104)
T ss_dssp             SSSCCC
T ss_pred             CccccC
Confidence            876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=2.7e-20  Score=132.57  Aligned_cols=82  Identities=29%  Similarity=0.430  Sum_probs=75.2

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhC--CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKF--GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~--G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      +..+.+.++|||+|||+++|+++|+++|++|  +.|+.|+++   ++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI---RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   85 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC---SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe---CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456778999999999999999999999999  999999875   67999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      ++++.+.
T Consensus        86 a~~~~~~   92 (99)
T 2cpd_A           86 AKPVDKD   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9987654

>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=2.3e-20  Score=137.22  Aligned_cols=82  Identities=28%  Similarity=0.529  Sum_probs=76.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .++.++|||+|||+++|+++|+++|++|++|+.|+|+.+    +++||||+|+++++|++||+.||+..|.+++|+|+++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            356789999999999999999999999999999999987    5799999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            887654

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

Probab=99.84  E-value=1.5e-20  Score=133.47  Aligned_cols=84  Identities=24%  Similarity=0.383  Sum_probs=76.6

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      .++.++|||+|||+++|+++|+++|++|++|+.|+|+.+        +++||||+|+++++|++||+.||++.|.+++|+
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            357789999999999999999999999999999999865        357999999999999999999999999999999


Q ss_pred             EEEeecCCCCCC
Q psy2347          78 VEISRGRGRGRG   89 (207)
Q Consensus        78 V~~a~~k~~~~~   89 (207)
                      |++++++.....
T Consensus        82 V~~a~~~~~~~~   93 (98)
T 2cpf_A           82 VRISERATKPAS   93 (98)
T ss_dssp             EECSSCSSCCCC
T ss_pred             EEEccCCCCCCC
Confidence            999988766543

>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=9.5e-21  Score=134.99  Aligned_cols=83  Identities=27%  Similarity=0.487  Sum_probs=77.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ....+.++|||+|||+++|+++|+++|++|++|+.|+|+++ ++||||+|+++++|++||+.||+++|.+++|+|+++++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   88 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCC
Confidence            34567789999999999999999999999999999999987 89999999999999999999999999999999999988


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      +...
T Consensus        89 ~~~~   92 (99)
T 2cpj_A           89 SASL   92 (99)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.84  E-value=1.2e-20  Score=131.13  Aligned_cols=80  Identities=26%  Similarity=0.426  Sum_probs=74.2

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .+.++|||+|||+++|+++|+++|++||+|+.|+|+.+      +++||||+|+++++|++|++.||+.+|.+++|+|++
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            35689999999999999999999999999999999775      578999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      ++++..
T Consensus        82 a~~~~~   87 (88)
T 4a8x_A           82 VLAPWP   87 (88)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=5.4e-21  Score=137.59  Aligned_cols=86  Identities=21%  Similarity=0.358  Sum_probs=78.3

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ....++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+. +++.|++++|+
T Consensus        10 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   88 (105)
T 2dh8_A           10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNID   88 (105)
T ss_dssp             CCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEB
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEE
Confidence            345577899999999999999999999999999999999987     468999999999999999998 99999999999


Q ss_pred             EEEeecCCCCCC
Q psy2347          78 VEISRGRGRGRG   89 (207)
Q Consensus        78 V~~a~~k~~~~~   89 (207)
                      |++++++.....
T Consensus        89 V~~a~~~~~~~~  100 (105)
T 2dh8_A           89 PKPCTPRGMQPS  100 (105)
T ss_dssp             CCCSCCSSCCTT
T ss_pred             EEEccCCCCCCC
Confidence            999998876543

>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=8e-21  Score=140.63  Aligned_cols=83  Identities=14%  Similarity=0.148  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC--ceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND--QDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g--~~i~g~~l~V~~a~   82 (207)
                      ..+++++|||+|||+++||++|+++|++||+|++|+|+++ |+||||+|+++++|++||+.|+.  .+|.+++|+|++|+
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~  105 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN  105 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEcc
Confidence            4567899999999999999999999999999999999987 89999999999999999998874  68999999999998


Q ss_pred             cCCCCC
Q psy2347          83 GRGRGR   88 (207)
Q Consensus        83 ~k~~~~   88 (207)
                      +++...
T Consensus       106 ~k~~~~  111 (119)
T 2ad9_A          106 HKELKT  111 (119)
T ss_dssp             SSSCCC
T ss_pred             CCCCCc
Confidence            876554

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=9.7e-21  Score=134.71  Aligned_cols=84  Identities=24%  Similarity=0.436  Sum_probs=76.9

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCee-EEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcE-
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLN-SVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK-   75 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~-~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~-   75 (207)
                      .....+.++|||+|||+++|+++|+++|++|++|+ +|+|+.+     +++||||+|+++++|++||+.||++.|.++. 
T Consensus         3 s~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   82 (99)
T 2div_A            3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATP   82 (99)
T ss_dssp             CCCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSS
T ss_pred             CCCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCc
Confidence            45567889999999999999999999999999999 9999987     4589999999999999999999999999999 


Q ss_pred             ---EEEEEeecCCC
Q psy2347          76 ---LRVEISRGRGR   86 (207)
Q Consensus        76 ---l~V~~a~~k~~   86 (207)
                         |+|++|++...
T Consensus        83 ~~~l~v~~a~~~~~   96 (99)
T 2div_A           83 AKRFKLNYATYSGP   96 (99)
T ss_dssp             CEECCEEETTCCSS
T ss_pred             ceeEEEeecCCCCC
Confidence               99999987543

>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=3.8e-20  Score=134.92  Aligned_cols=83  Identities=22%  Similarity=0.230  Sum_probs=76.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|++|+|+.+    +++||||+|+++++|++||+.||+++|.+++|+|++
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            4566889999999999999999999999999999999987    478999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      +++....
T Consensus        91 a~~~~~~   97 (114)
T 2do0_A           91 DERALPK   97 (114)
T ss_dssp             CSCCCCC
T ss_pred             cccCCCC
Confidence            9765443

>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=99.84  E-value=1e-20  Score=130.76  Aligned_cols=78  Identities=38%  Similarity=0.683  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      +.++.++|||.|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++|++.||++.|.+++|+|+
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4567899999999999999999999999999999999876     68999999999999999999999999999999999


Q ss_pred             Eee
Q psy2347          80 ISR   82 (207)
Q Consensus        80 ~a~   82 (207)
                      +|+
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            985

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

Probab=99.84  E-value=1.1e-20  Score=134.34  Aligned_cols=81  Identities=22%  Similarity=0.407  Sum_probs=73.8

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+..++|||+|||+++|+++|+++|++|+.|+ ++|+.+ +++||||+|+++++|++||+.||++.|.+++|+|+++++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            345578999999999999999999999999997 666665 789999999999999999999999999999999999988


Q ss_pred             CCC
Q psy2347          84 RGR   86 (207)
Q Consensus        84 k~~   86 (207)
                      +.+
T Consensus        94 ~~~   96 (97)
T 2e5j_A           94 QRD   96 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.84  E-value=7.3e-21  Score=139.27  Aligned_cols=82  Identities=18%  Similarity=0.144  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCC-CeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFG-KLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G-~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .....++|||+|||+++|+++|+++|++|| +|+.|+|+.+ +++||||+|+++++|++||+.||+.+|++++|+|++++
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            345678999999999999999999999999 8999999644 79999999999999999999999999999999999997


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      .++.
T Consensus       104 ~~p~  107 (111)
T 2jvr_A          104 NPPP  107 (111)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            6543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=1.7e-20  Score=134.63  Aligned_cols=82  Identities=27%  Similarity=0.409  Sum_probs=75.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||+++|+++|+++|++|+ |++|+|+.+     +++||||+|+++++|++|| .||+++|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVD   88 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEE
Confidence            456778999999999999999999999995 999999987     4689999999999999999 899999999999999


Q ss_pred             EeecCCCCC
Q psy2347          80 ISRGRGRGR   88 (207)
Q Consensus        80 ~a~~k~~~~   88 (207)
                      +++++....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dng_A           89 IAEGRKQDK   97 (103)
T ss_dssp             ECCCCCCCC
T ss_pred             EecCCCCCC
Confidence            999876544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.4e-20  Score=135.07  Aligned_cols=86  Identities=20%  Similarity=0.301  Sum_probs=78.8

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHh-CCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCce-eCCcEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEK-FGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQD-LMGSKLR   77 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~-~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~-i~g~~l~   77 (207)
                      ....+.++|||+|||+++|+++|+++|++ |++|+.|+|+.+    +++||||+|+++++|++||+.||++. |.+++|+
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             CCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            34567899999999999999999999999 999999999987    67999999999999999999999999 9999999


Q ss_pred             EEEeecCCCCCC
Q psy2347          78 VEISRGRGRGRG   89 (207)
Q Consensus        78 V~~a~~k~~~~~   89 (207)
                      |++++++.....
T Consensus        84 v~~a~~~~~~~~   95 (104)
T 2dhg_A           84 LSVAIPKASRVK   95 (104)
T ss_dssp             CCBCCCCCSCCC
T ss_pred             EEEccCCCcCCC
Confidence            999988766544

>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=99.84  E-value=1.7e-20  Score=134.82  Aligned_cols=82  Identities=20%  Similarity=0.333  Sum_probs=75.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..++.++|||.|||+++|+++|+++|++|+ |++|+|+.+      +++||||+|+++++|++|| .||+++|.+++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   88 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRV   88 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEE
Confidence            445779999999999999999999999999 999999877      3789999999999999999 89999999999999


Q ss_pred             EEeecCCCCC
Q psy2347          79 EISRGRGRGR   88 (207)
Q Consensus        79 ~~a~~k~~~~   88 (207)
                      ++++++....
T Consensus        89 ~~a~~~~~~~   98 (104)
T 1wi8_A           89 DVADQAQDKD   98 (104)
T ss_dssp             EECCCCCCCC
T ss_pred             EEccCCCCCC
Confidence            9999876653

>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=1.4e-20  Score=136.52  Aligned_cols=82  Identities=21%  Similarity=0.494  Sum_probs=76.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+.++|||+|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  102 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  102 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            345689999999999999999999999999999999877     479999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      +++++.+
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9987654

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

Probab=99.83  E-value=1.2e-20  Score=132.94  Aligned_cols=80  Identities=30%  Similarity=0.424  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ...++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567889999999999999999999999999999999987     4689999999999999999999999999999999


Q ss_pred             EEeec
Q psy2347          79 EISRG   83 (207)
Q Consensus        79 ~~a~~   83 (207)
                      +++++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99864

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

Probab=99.83  E-value=1.2e-20  Score=135.88  Aligned_cols=80  Identities=29%  Similarity=0.573  Sum_probs=75.0

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||+|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            45678999999999999999999999999999999987     4699999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy2347          82 RGRGR   86 (207)
Q Consensus        82 ~~k~~   86 (207)
                      ++++.
T Consensus       101 ~~~~~  105 (106)
T 1p27_B          101 FVRGP  105 (106)
T ss_dssp             EESSC
T ss_pred             cCCCC
Confidence            98764

>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=99.83  E-value=2.9e-20  Score=134.79  Aligned_cols=82  Identities=22%  Similarity=0.378  Sum_probs=76.9

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ..+.++|||+|||+++|+++|+++|++||+|+.|+|+.+ ++||||+|+++++|++||+.||+++|.+++|+|+++++++
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP  100 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCC
Confidence            456789999999999999999999999999999999988 8999999999999999999999999999999999999876


Q ss_pred             CCC
Q psy2347          86 RGR   88 (207)
Q Consensus        86 ~~~   88 (207)
                      ...
T Consensus       101 ~~~  103 (109)
T 1x4g_A          101 DMT  103 (109)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1e-20  Score=137.53  Aligned_cols=83  Identities=29%  Similarity=0.456  Sum_probs=77.2

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      .....+.++|||+|||+++|+++|+++|++||+|+.|+|+.+   +++||||+|+++++|++|++.||++.|++++|+|+
T Consensus        23 ~~~~~~~~~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           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            445667899999999999999999999999999999999887   68999999999999999999999999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      +++++.
T Consensus       103 ~a~~~~  108 (109)
T 2err_A          103 NATARV  108 (109)
T ss_dssp             ECCCSC
T ss_pred             ECCCCc
Confidence            998864

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

Probab=99.83  E-value=2e-20  Score=132.57  Aligned_cols=79  Identities=20%  Similarity=0.322  Sum_probs=74.4

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ++++|||+|||+++++++|+++|++||.|++|+|+.+     +++||||+|+++++|++||+.||+..|.++.|+|++++
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            5689999999999999999999999999999999887     47999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      ++..
T Consensus        81 ~~~~   84 (96)
T 2x1f_A           81 NSDI   84 (96)
T ss_dssp             CSSG
T ss_pred             CCCC
Confidence            8653

>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=99.83  E-value=9.6e-21  Score=138.04  Aligned_cols=84  Identities=23%  Similarity=0.330  Sum_probs=76.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHH---HHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLE---LEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLM   72 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~---~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~   72 (207)
                      ....+.++|||+|||+++++++|+   ++|++||+|++|+|+++        +++||||+|+++++|++||+.||+++|+
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            344567899999999999999999   99999999999999877        2379999999999999999999999999


Q ss_pred             CcEEEEEEeecCCCC
Q psy2347          73 GSKLRVEISRGRGRG   87 (207)
Q Consensus        73 g~~l~V~~a~~k~~~   87 (207)
                      +++|+|++|++++..
T Consensus        90 gr~l~V~~a~~k~~~  104 (111)
T 2cpi_A           90 GRTLKASLGTTKYCS  104 (111)
T ss_dssp             TEEEEEESCCCCSCS
T ss_pred             CEEEEEEeccccccc
Confidence            999999999988743

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.83  E-value=1e-20  Score=135.21  Aligned_cols=79  Identities=46%  Similarity=0.792  Sum_probs=74.7

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCCCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRGR   88 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~~~   88 (207)
                      ++|||+|||+++|+++|+++|++|++|++|+|+.++++||||+|+++++|++||+.||+++|.+++|+|++++++++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~   79 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPRRS   79 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCCcc
Confidence            5899999999999999999999999999999998888999999999999999999999999999999999999877543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=2.8e-20  Score=130.46  Aligned_cols=82  Identities=18%  Similarity=0.220  Sum_probs=75.5

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ....+.++|||+|||+++|+++|+++|++| .|+.|+|+.+    +++||||+|+++++|++||+ ||++.|.++.|+|+
T Consensus         5 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEE
T ss_pred             CCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEE
Confidence            345678899999999999999999999999 9999999987    57899999999999999999 99999999999999


Q ss_pred             EeecCCCC
Q psy2347          80 ISRGRGRG   87 (207)
Q Consensus        80 ~a~~k~~~   87 (207)
                      ++++++..
T Consensus        83 ~a~~~~~s   90 (91)
T 2dgw_A           83 REKSGPSS   90 (91)
T ss_dssp             EESSCCCC
T ss_pred             ECCcCCCC
Confidence            99887653

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

Probab=99.83  E-value=9.2e-21  Score=133.75  Aligned_cols=80  Identities=28%  Similarity=0.352  Sum_probs=73.9

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...++.++|||.|||+++|+++|+++|++|++|++|+|+.+    +++||||+|+++++|++||+.||+++|.+++|+|+
T Consensus        11 ~~~~~~~~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           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            34567789999999999999999999999999999999987    47899999999999999999999999999999999


Q ss_pred             Eeec
Q psy2347          80 ISRG   83 (207)
Q Consensus        80 ~a~~   83 (207)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9864

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

Probab=99.83  E-value=5.5e-21  Score=136.14  Aligned_cols=83  Identities=14%  Similarity=0.318  Sum_probs=74.3

Q ss_pred             CCCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCC--eeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCc----
Q psy2347           1 MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGK--LNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQ----   69 (207)
Q Consensus         1 ms~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~--V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~----   69 (207)
                      |-......-.+|||+|||+++|+++|+++|++||.  |++|+|++|     +++||||+|+++++|++||+.||+.    
T Consensus         1 mg~~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~   80 (95)
T 2lkz_A            1 MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPL   80 (95)
T ss_dssp             CCCCSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCE
T ss_pred             CCcccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCc
Confidence            44556667789999999999999999999999995  678999887     7899999999999999999999986    


Q ss_pred             eeCCcEEEEEEeec
Q psy2347          70 DLMGSKLRVEISRG   83 (207)
Q Consensus        70 ~i~g~~l~V~~a~~   83 (207)
                      .|++++|.|++|++
T Consensus        81 ~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           81 KIDGKTIGVDFAKS   94 (95)
T ss_dssp             EETTEEEEEEECCC
T ss_pred             eECCEEEEEEEccC
Confidence            58999999999975

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.83  E-value=2.3e-20  Score=130.47  Aligned_cols=76  Identities=18%  Similarity=0.216  Sum_probs=71.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+..|||+||++.+||++|+++|.+||+|++++|+.+ |+||||+|.++++|++|++.||+.+|.+++|+|++|++
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~-kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-QGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC-CcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            45779999999999999999999999999999999884 99999999999999999999999999999999999853

>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=99.83  E-value=1.6e-20  Score=140.83  Aligned_cols=82  Identities=30%  Similarity=0.440  Sum_probs=76.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||+.+|.+++|+|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567889999999999999999999999999999999976     68999999999999999999999999999999999


Q ss_pred             EeecCCC
Q psy2347          80 ISRGRGR   86 (207)
Q Consensus        80 ~a~~k~~   86 (207)
                      +++++..
T Consensus       122 ~a~~~~p  128 (129)
T 2kxn_B          122 FSITKRP  128 (129)
T ss_dssp             CCSSSSC
T ss_pred             EecCCCC
Confidence            9988653

>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=99.82  E-value=3.9e-20  Score=133.39  Aligned_cols=78  Identities=27%  Similarity=0.393  Sum_probs=73.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|++|+|+.+    +++||||+|+++++|++||+.||+++|.+++|+|++
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4567899999999999999999999999999999999987    578999999999999999999999999999999999


Q ss_pred             ee
Q psy2347          81 SR   82 (207)
Q Consensus        81 a~   82 (207)
                      ++
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.82  E-value=4.2e-20  Score=127.73  Aligned_cols=77  Identities=31%  Similarity=0.500  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc-CCceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM-NDQDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l-~g~~i~g~~l~V~~a~   82 (207)
                      ...+.++|||+|||+++|+++|+++|++||+|+.|+|+++ ++||||+|+++++|++|++.| +++.|.+++|+|++|+
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~ak   85 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            4466789999999999999999999999999999999986 899999999999999999999 9999999999999985

>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=99.82  E-value=3.9e-20  Score=130.21  Aligned_cols=82  Identities=23%  Similarity=0.345  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCC-eeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC-ceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGK-LNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND-QDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~-V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g-~~i~g~~l~V~~a~   82 (207)
                      ..++.++|||+|||+++|+++|+++|++|++ |+.+.|+  +++||||+|+++++|++||+.||+ ++|.+++|+|++++
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~   81 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL--KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   81 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE--ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc--CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEcc
Confidence            3567789999999999999999999999999 6666554  379999999999999999999999 99999999999999


Q ss_pred             cCCCCC
Q psy2347          83 GRGRGR   88 (207)
Q Consensus        83 ~k~~~~   88 (207)
                      ++..+.
T Consensus        82 ~~~~~~   87 (93)
T 2cqh_A           82 SKKLRS   87 (93)
T ss_dssp             CCCCCC
T ss_pred             CccccC
Confidence            876543

>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=99.82  E-value=1.9e-20  Score=137.49  Aligned_cols=81  Identities=23%  Similarity=0.322  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE-----EEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK-----LRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~-----l~V~~a   81 (207)
                      ...++|||.|||+++|+++|+++|++|++|++|+|+.+  +||||+|+++++|++||++||+++|++++     |+|+.+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~   91 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD   91 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC--CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccC
Confidence            45689999999999999999999999999999999876  89999999999999999999999999988     777777


Q ss_pred             ecCCCCCC
Q psy2347          82 RGRGRGRG   89 (207)
Q Consensus        82 ~~k~~~~~   89 (207)
                      +++.....
T Consensus        92 ~~~~~~~~   99 (115)
T 3beg_B           92 GPRSPSYG   99 (115)
T ss_dssp             C----CCC
T ss_pred             CCCCCCCC
Confidence            76655443

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

Probab=99.82  E-value=3e-20  Score=131.82  Aligned_cols=82  Identities=26%  Similarity=0.438  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           5 MMERGTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..++.++|||+|||+ ++|+++|+++|++||+|++|+|.   ++||||+|+++++|++||+.||+..|.+++|+|+++++
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 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSS   82 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE---TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEEC
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCc
Confidence            456889999999998 99999999999999999999995   78999999999999999999999999999999999988


Q ss_pred             CCCCCC
Q psy2347          84 RGRGRG   89 (207)
Q Consensus        84 k~~~~~   89 (207)
                      +.+...
T Consensus        83 ~~~~~~   88 (96)
T 2kvi_A           83 NARPQF   88 (96)
T ss_dssp             CCC---
T ss_pred             CCCCCC
Confidence            765443

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

Probab=99.82  E-value=1.4e-20  Score=134.42  Aligned_cols=79  Identities=20%  Similarity=0.324  Sum_probs=73.7

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .....++|||+|||+++|+++|+++|++||+|++|+|++. ++||||+|++.++|++||+.||++.|++++|+|++++++
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~-~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETT-TTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecC-CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            3455789999999999999999999999999999999865 899999999999999999999999999999999999874

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

Probab=99.82  E-value=5e-20  Score=131.59  Aligned_cols=81  Identities=28%  Similarity=0.427  Sum_probs=72.1

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ....+.++|||.|||+++|+++|+++|++|++|   +|+.+    +++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            345678999999999999999999999999987   34443    68999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy2347          80 ISRGRGRG   87 (207)
Q Consensus        80 ~a~~k~~~   87 (207)
                      +++++.+.
T Consensus        87 ~a~~~~~~   94 (101)
T 2fc9_A           87 LQGPRGSP   94 (101)
T ss_dssp             ECSSCCCC
T ss_pred             EcCCCCCC
Confidence            99887554

>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=99.82  E-value=4.9e-20  Score=133.79  Aligned_cols=78  Identities=33%  Similarity=0.546  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           7 ERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         7 ~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ...++|||+|||++ +|+++|+++|++|++|++|+|   +++||||+|+++++|++||+.||+++|++++|+|++++++.
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i---~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV---HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE---ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCCC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE---eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCCC
Confidence            34589999999999 999999999999999999998   47899999999999999999999999999999999998654


Q ss_pred             CC
Q psy2347          86 RG   87 (207)
Q Consensus        86 ~~   87 (207)
                      ..
T Consensus       102 ~~  103 (110)
T 1wf1_A          102 PD  103 (110)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>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=2.5e-20  Score=136.58  Aligned_cols=82  Identities=20%  Similarity=0.201  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcC--CceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN--DQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~--g~~i~g~~l~V~~a   81 (207)
                      ..+++++|||+|||++ +||++|+++|++||+|++|.|+++ ++||||+|+++++|++||+.|+  ..+|.+++|+|++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~-kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a   99 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   99 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC-CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEC
Confidence            4567899999999998 999999999999999999999875 8999999999999999999885  45699999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++.+.
T Consensus       100 ~~~~~~  105 (112)
T 1x4f_A          100 EKYKKL  105 (112)
T ss_dssp             CSCSSS
T ss_pred             cccccc
Confidence            876654

>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=99.82  E-value=4.2e-20  Score=134.21  Aligned_cols=81  Identities=27%  Similarity=0.470  Sum_probs=75.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999876     46899999999999999999999999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            998875

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=2.7e-20  Score=133.98  Aligned_cols=80  Identities=21%  Similarity=0.234  Sum_probs=72.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ...+.++|||+|||+++||++|+++|++|+. ++|+|+++    +++||||+|+++++|++||+ +|+++|.++.|+|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            4456789999999999999999999999994 59999887    57899999999999999995 799999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      +++++.
T Consensus        89 ~~~~~~   94 (102)
T 1wez_A           89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            887654

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

Probab=99.82  E-value=1.7e-20  Score=133.16  Aligned_cols=81  Identities=21%  Similarity=0.220  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..+..++|||.|||+++|+++|+++|++|+.|+.+.++.+     +++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            4456789999999999999999999999999987776655     57999999999999999999999999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      +++.+.
T Consensus        91 ~a~~~~   96 (98)
T 2cqp_A           91 LGSGPS   96 (98)
T ss_dssp             ESSCSS
T ss_pred             EcCCCC
Confidence            997654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=7.8e-20  Score=133.82  Aligned_cols=79  Identities=25%  Similarity=0.442  Sum_probs=74.0

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+. +++.|.+++|+|+++++
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            489999999999999999999999999999999987     579999999999999999997 99999999999999998


Q ss_pred             CCCCC
Q psy2347          84 RGRGR   88 (207)
Q Consensus        84 k~~~~   88 (207)
                      +....
T Consensus       106 ~~~~~  110 (116)
T 1x4b_A          106 REESG  110 (116)
T ss_dssp             CCCCC
T ss_pred             CccCC
Confidence            87654

>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=99.82  E-value=7.5e-21  Score=133.41  Aligned_cols=78  Identities=23%  Similarity=0.304  Sum_probs=66.9

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCC--CeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFG--KLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G--~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      .+|||+|||+++|+++|+++|++||  +|++|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|++++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5899999999999999999999999  9999999987     57899999999999999999999999999999999998


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      +++..
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            87654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=8.6e-20  Score=132.67  Aligned_cols=82  Identities=23%  Similarity=0.435  Sum_probs=72.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++||+.++ +.|+++.|+|+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEEEEE
Confidence            3456789999999999999999999999999999999987     57999999999999999999875 99999999999


Q ss_pred             EeecCCCC
Q psy2347          80 ISRGRGRG   87 (207)
Q Consensus        80 ~a~~k~~~   87 (207)
                      ++.++...
T Consensus       100 ~a~~~~~~  107 (109)
T 2rs2_A          100 VAFPRRAQ  107 (109)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99987654

>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=5.3e-20  Score=140.68  Aligned_cols=81  Identities=44%  Similarity=0.751  Sum_probs=76.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ...+.++|||+|||+++|+++|+++|++||+|++|+|+.++++||||+|+++++|++||+.||++.|.+++|+|++++++
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999886


Q ss_pred             C
Q psy2347          85 G   85 (207)
Q Consensus        85 ~   85 (207)
                      .
T Consensus       149 ~  149 (150)
T 2i2y_A          149 K  149 (150)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.81  E-value=7.6e-20  Score=127.37  Aligned_cols=77  Identities=26%  Similarity=0.515  Sum_probs=72.1

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||+|||+++|+++|+++|++|++|++|+|+.+     +++||||+|+++++|++|+ .||++.|.+++|+|++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            4579999999999999999999999999999999987     5899999999999999999 899999999999999998


Q ss_pred             cCC
Q psy2347          83 GRG   85 (207)
Q Consensus        83 ~k~   85 (207)
                      ++.
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            753

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

Probab=99.81  E-value=5.4e-20  Score=131.50  Aligned_cols=81  Identities=27%  Similarity=0.530  Sum_probs=71.7

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ...++.++|||.|||+++|+++|+++|++|.   .|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3456789999999999999999999999873   5666665     4689999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy2347          79 EISRGRGRG   87 (207)
Q Consensus        79 ~~a~~k~~~   87 (207)
                      ++++++.+.
T Consensus        87 ~~a~~~~~~   95 (102)
T 2fc8_A           87 DWAKPKGEG   95 (102)
T ss_dssp             EECCCCCSS
T ss_pred             EEecCCCCC
Confidence            999987764

>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=1.7e-19  Score=129.29  Aligned_cols=82  Identities=20%  Similarity=0.297  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.  .+.|++++|+|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCeEEEEE
Confidence            4467789999999999999999999999999999999987     468999999999999999984  679999999999


Q ss_pred             EeecCCCCC
Q psy2347          80 ISRGRGRGR   88 (207)
Q Consensus        80 ~a~~k~~~~   88 (207)
                      ++++++...
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cqg_A           89 LPNSKQSQD   97 (103)
T ss_dssp             CCCTTCCCC
T ss_pred             ecCCCCcCC
Confidence            999876653

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

Probab=99.81  E-value=1.1e-20  Score=135.34  Aligned_cols=79  Identities=24%  Similarity=0.267  Sum_probs=74.0

Q ss_pred             CCCcEEEEcCCCc------CCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCC-c
Q psy2347           7 ERGTRVYVGGLTE------TVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMG-S   74 (207)
Q Consensus         7 ~~~~~lfV~nLp~------~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g-~   74 (207)
                      ...++|||+|||.      ++++++|+++|++||+|++|+|+.+     +++||||+|+++++|++||+.||++.|.+ +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      9999999999999999999999877     67999999999999999999999999999 9


Q ss_pred             EEEEEEeecCC
Q psy2347          75 KLRVEISRGRG   85 (207)
Q Consensus        75 ~l~V~~a~~k~   85 (207)
                      +|+|++++++.
T Consensus        84 ~l~V~~a~~~~   94 (100)
T 3ns6_A           84 RLFLYTMKDVE   94 (100)
T ss_dssp             BCEEEESHHHH
T ss_pred             EEEEEECchhh
Confidence            99999998764

>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=138.88  Aligned_cols=84  Identities=35%  Similarity=0.522  Sum_probs=77.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+.++|||+|||+++|+++|+++|++||+|+.|+|+.|     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            345789999999999999999999999999999999887     689999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q psy2347          81 SRGRGRGRG   89 (207)
Q Consensus        81 a~~k~~~~~   89 (207)
                      ++++.+...
T Consensus       147 a~~~~~~~~  155 (158)
T 2kn4_A          147 ARYGRPPDS  155 (158)
T ss_dssp             ECCSSCCCC
T ss_pred             CCCCCCCCC
Confidence            998765443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.81  E-value=8.8e-20  Score=129.93  Aligned_cols=79  Identities=23%  Similarity=0.368  Sum_probs=73.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE--------EEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCce
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS--------VWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQD   70 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~--------v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~   70 (207)
                      ....+.++|||+|||+++|+++|+++|++|+.|+.        |+|+.+     +++||||+|+++++|++||+.||+..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999999        999887     46899999999999999999999999


Q ss_pred             eCCcEEEEEEee
Q psy2347          71 LMGSKLRVEISR   82 (207)
Q Consensus        71 i~g~~l~V~~a~   82 (207)
                      |.+++|+|++|+
T Consensus        88 ~~g~~l~V~~A~   99 (99)
T 2la6_A           88 FSGNPIKVSFAT   99 (99)
T ss_dssp             SSSSBCEEEECC
T ss_pred             eCCcEEEEEecC
Confidence            999999999984

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=5.9e-20  Score=134.79  Aligned_cols=77  Identities=26%  Similarity=0.412  Sum_probs=71.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||.|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            345689999999999999999999999999999999877     589999999999999999999999999999999998


Q ss_pred             ee
Q psy2347          81 SR   82 (207)
Q Consensus        81 a~   82 (207)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
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=99.81  E-value=8.4e-20  Score=132.66  Aligned_cols=80  Identities=26%  Similarity=0.388  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ...+.++|||+|||+++|+++|+++|++||+|+.|+|+   ++||||+|+++++|++|++.||+..|.+++|+|++++++
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~---kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE---TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE---CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            34567899999999999999999999999999999998   789999999999999999999999999999999999887


Q ss_pred             CCC
Q psy2347          85 GRG   87 (207)
Q Consensus        85 ~~~   87 (207)
                      .++
T Consensus       104 ~~r  106 (108)
T 2jvo_A          104 AKR  106 (108)
T ss_dssp             C--
T ss_pred             CCC
Confidence            654

>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=99.81  E-value=1.1e-19  Score=132.71  Aligned_cols=84  Identities=24%  Similarity=0.298  Sum_probs=74.9

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCe----eEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKL----NSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V----~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++|+++|+++|++|+.|    ..++++.. +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3467899999999999999999999999998    56666644 789999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q psy2347          81 SRGRGRGRG   89 (207)
Q Consensus        81 a~~k~~~~~   89 (207)
                      ++++.....
T Consensus       102 a~~~~~~~~  110 (115)
T 2cpx_A          102 GKNKKQRSS  110 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             ccCCCCCCC
Confidence            998776543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=7e-20  Score=132.17  Aligned_cols=78  Identities=17%  Similarity=0.210  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ...+.++|||+|||+++|+++|+++|++||+|++|.|+.+    +++||||+|+++++|++||+ +++++|.++.|.|++
T Consensus         7 ~~~~~~~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            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999987    78999999999999999999 899999999999998


Q ss_pred             eec
Q psy2347          81 SRG   83 (207)
Q Consensus        81 a~~   83 (207)
                      +++
T Consensus        86 ~~~   88 (103)
T 1s79_A           86 KDD   88 (103)
T ss_dssp             HHH
T ss_pred             chH
Confidence            764

>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=3.7e-19  Score=126.29  Aligned_cols=81  Identities=23%  Similarity=0.350  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ...+.++|||+||  ++|+++|+++|++||+|+.|+|.. +++||||+|+++++|++||+.||++.|.+++|+|++++++
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~-~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~   87 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP-PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   87 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEET-TTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecC-CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCC
Confidence            3456789999996  899999999999999999999975 4899999999999999999999999999999999999887


Q ss_pred             CCCC
Q psy2347          85 GRGR   88 (207)
Q Consensus        85 ~~~~   88 (207)
                      +...
T Consensus        88 ~~~~   91 (97)
T 1x5p_A           88 PMLD   91 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.81  E-value=2.8e-19  Score=132.42  Aligned_cols=83  Identities=24%  Similarity=0.334  Sum_probs=76.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..++.++|||+|||+++|+++|+++|++||+|+.|+|+.+    +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3456789999999999999999999999999999999987    689999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      |.++...
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9876543

>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=99.81  E-value=1.4e-19  Score=132.92  Aligned_cols=85  Identities=16%  Similarity=0.264  Sum_probs=76.3

Q ss_pred             CCCCCcEEEE--cCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCcee-----CCcEEE
Q psy2347           5 MMERGTRVYV--GGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL-----MGSKLR   77 (207)
Q Consensus         5 ~~~~~~~lfV--~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i-----~g~~l~   77 (207)
                      ..+++++|||  +||++++||++|+++|++||+|++|.|+.+ ++||||+|+++++|++|++.||+++|     .+++|.
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~-rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~   99 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   99 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEE
Confidence            4567889999  779999999999999999999999988876 89999999999999999999999998     689999


Q ss_pred             EEEeecCCCCCCC
Q psy2347          78 VEISRGRGRGRGG   90 (207)
Q Consensus        78 V~~a~~k~~~~~~   90 (207)
                      |.+++..+...++
T Consensus       100 v~~a~~~p~~~~~  112 (114)
T 2cq2_A          100 LNFVEKVQWSGPS  112 (114)
T ss_dssp             EEEESCCCCSSCC
T ss_pred             EEecccCcccCCC
Confidence            9999877665543

>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=99.81  E-value=1.3e-19  Score=132.31  Aligned_cols=82  Identities=21%  Similarity=0.297  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++.++|||+|||+++|+++|+++|++||.|+.|.|+.+  +++||||+|+++++|++||+.||+..|.++.|.|++++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4567889999999999999999999999999999999987  68999999999999999999999999999999999998


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      ++..
T Consensus        84 ~~~~   87 (115)
T 3lqv_A           84 ANRA   87 (115)
T ss_dssp             HHHH
T ss_pred             CChh
Confidence            7543

>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=130.83  Aligned_cols=82  Identities=24%  Similarity=0.356  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCC-eeEEEEe-eC-----CCcEEEEEEcCHHHHHHHHHhcC--CceeCCcEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGK-LNSVWVA-FN-----PPGFAFVEFSNQIDAEAACDSMN--DQDLMGSKL   76 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~-V~~v~i~-~d-----~rG~afV~F~~~e~A~~Al~~l~--g~~i~g~~l   76 (207)
                      ..+.++|||+|||+++|+++|+++|++|+. |++|.|+ .+     +++||||+|+++++|++||+.|+  ...|.+++|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            456789999999999999999999999998 9999998 43     68999999999999999999996  589999999


Q ss_pred             EEEEeecCCCC
Q psy2347          77 RVEISRGRGRG   87 (207)
Q Consensus        77 ~V~~a~~k~~~   87 (207)
                      +|++++++...
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999987654

>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=99.80  E-value=2.4e-19  Score=127.71  Aligned_cols=78  Identities=26%  Similarity=0.443  Sum_probs=72.6

Q ss_pred             CCCCCcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           5 MMERGTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..++.++|||+|||+ ++++++|+++|++||+|++|+|.   ++||||+|+++++|++||+.||+..|.+++|+|+++++
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~---~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC---SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe---CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            456789999999998 99999999999999999999984   78999999999999999999999999999999999987


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      +.
T Consensus        95 ~~   96 (97)
T 2xnq_A           95 NA   96 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=1.9e-20  Score=153.37  Aligned_cols=77  Identities=22%  Similarity=0.324  Sum_probs=71.6

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCC--CeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFG--KLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G--~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      +.++|||+|||+++||++|+++|++|+  +|++|+|++|     +|+||||+|+++++|++||+.||+++|.+++|+|++
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  9999999988     579999999999999999999999999999999999


Q ss_pred             eecC
Q psy2347          81 SRGR   84 (207)
Q Consensus        81 a~~k   84 (207)
                      |+++
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            9764

>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=99.80  E-value=8.5e-20  Score=128.15  Aligned_cols=82  Identities=24%  Similarity=0.446  Sum_probs=64.4

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .+..+.++|||+|||+++||++|+++|++||+|++|+|++++++||||+|+++++|+++..  ....+.+++|.|++|++
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~A~~~~~--~~~~~~g~~v~v~~a~~   83 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCG--EDLIIKGISVHISNAEP   83 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHHHHHHTT--CEEEETTEEEEEEECC-
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHHHHHHcC--CCcccCCEEEEEEEcCC
Confidence            4566789999999999999999999999999999999999899999999999999984321  13345699999999988


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      +..+
T Consensus        84 k~~~   87 (89)
T 3d2w_A           84 KHNK   87 (89)
T ss_dssp             ----
T ss_pred             CCcC
Confidence            7653

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

Probab=99.80  E-value=4.7e-20  Score=139.18  Aligned_cols=83  Identities=35%  Similarity=0.522  Sum_probs=76.3

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++.++|||+|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+++
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  124 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  124 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45679999999999999999999999999999999876     6789999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q psy2347          82 RGRGRGRG   89 (207)
Q Consensus        82 ~~k~~~~~   89 (207)
                      +++.+...
T Consensus       125 ~~~~~~~~  132 (135)
T 2lea_A          125 RYGRPPDS  132 (135)
T ss_dssp             CCCCCCTT
T ss_pred             CCCCCCcc
Confidence            88765443

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.1e-19  Score=132.51  Aligned_cols=81  Identities=19%  Similarity=0.283  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCcee--------
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDL--------   71 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i--------   71 (207)
                      ....+.++|||.|||+++|+++|+++|++|++|+.|+|+.+    +++||||+|+++++|++||+.||++.|        
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            34456789999999999999999999999999999999987    578999999999999999999999999        


Q ss_pred             CCcEEEEEEeecC
Q psy2347          72 MGSKLRVEISRGR   84 (207)
Q Consensus        72 ~g~~l~V~~a~~k   84 (207)
                      .+++|.|++++|+
T Consensus       100 ~~~~l~v~~a~p~  112 (114)
T 1x5o_A          100 PTEPLLCKFSGPS  112 (114)
T ss_dssp             CSSCBEEEECCCS
T ss_pred             CCCceeEEccCCC
Confidence            5788999999865

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

Probab=99.80  E-value=1.7e-19  Score=134.95  Aligned_cols=82  Identities=21%  Similarity=0.289  Sum_probs=74.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHH----HHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~----~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..++.++|||+|||+.+++++|+    ++|++||+|++|.|+.+  +++||||+|+++++|++||+.||+..|.+++|+|
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            34567899999999999999876    69999999999988765  7899999999999999999999999999999999


Q ss_pred             EEeecCCC
Q psy2347          79 EISRGRGR   86 (207)
Q Consensus        79 ~~a~~k~~   86 (207)
                      ++|+++..
T Consensus       105 ~~a~~~~~  112 (127)
T 2a3j_A          105 TFSETPQS  112 (127)
T ss_dssp             EECCCCCH
T ss_pred             EEccCcch
Confidence            99987643

>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=99.80  E-value=4.2e-19  Score=157.90  Aligned_cols=81  Identities=22%  Similarity=0.530  Sum_probs=75.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||+|||++||+++|+++|++||+|+.|.|+.+     +++||||+|+++++|++||++||+++|.+++|+|+++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45689999999999999999999999999999999877     6899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++...
T Consensus       180 ~~~~~~  185 (437)
T 3pgw_S          180 RGRTVK  185 (437)
T ss_pred             CCCCCC
Confidence            986553

>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=99.80  E-value=6.9e-20  Score=133.68  Aligned_cols=78  Identities=19%  Similarity=0.207  Sum_probs=72.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ...++|||.|||+++|+++|+++|++||.|+.|.|+.+ ++||||+|+++++|++||+.||++.|.+++|.|++++...
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~-~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   85 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-CCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCCc
Confidence            35679999999999999999999999999999998875 8999999999999999999999999999999999997643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.80  E-value=4.2e-20  Score=136.24  Aligned_cols=80  Identities=20%  Similarity=0.185  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCC---eeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGK---LNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~---V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ...+.++|||+|||+++|+++|+++|++|+.   |+.|+|+.+    +++||||+|+++++|++||+ ||+++|.++.|+
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            3456789999999999999999999999999   899999987    57899999999999999999 899999999999


Q ss_pred             EEEeecCC
Q psy2347          78 VEISRGRG   85 (207)
Q Consensus        78 V~~a~~k~   85 (207)
                      |.++++++
T Consensus        92 V~~a~~~~   99 (118)
T 2db1_A           92 VFKSHRTE   99 (118)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99997653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.80  E-value=1.2e-19  Score=140.32  Aligned_cols=77  Identities=21%  Similarity=0.260  Sum_probs=71.7

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCC--CeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFG--KLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G--~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      +.++|||+|||+++||++|+++|++||  +|++|+|+.|     +++||||+|+++++|++||+.||+++|.+++|+|++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            567999999999999999999999999  9999999987     578999999999999999999999999999999999


Q ss_pred             eecC
Q psy2347          81 SRGR   84 (207)
Q Consensus        81 a~~k   84 (207)
                      |+++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.80  E-value=1.7e-19  Score=133.36  Aligned_cols=79  Identities=28%  Similarity=0.519  Sum_probs=73.1

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++|| .||++.|.+++|+|+++++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            579999999999999999999999999999999876     5899999999999999999 7999999999999999987


Q ss_pred             CCCCC
Q psy2347          84 RGRGR   88 (207)
Q Consensus        84 k~~~~   88 (207)
                      .....
T Consensus       115 ~~~~~  119 (124)
T 2jwn_A          115 NMPGI  119 (124)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            65543

>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=99.80  E-value=2.4e-20  Score=131.54  Aligned_cols=78  Identities=21%  Similarity=0.199  Sum_probs=69.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||.|||+++|+++|+++|++|+.|+.+.++.+     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            345689999999999999999999999999988877764     579999999999999999999999999999999998


Q ss_pred             eec
Q psy2347          81 SRG   83 (207)
Q Consensus        81 a~~   83 (207)
                      +++
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            864

>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=1.6e-19  Score=140.32  Aligned_cols=84  Identities=21%  Similarity=0.487  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+.++|||.|||+++|+++|+++|++||+|+.|.|+.+     +++||||+|.++++|++||+.||++.|.+++|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345678999999999999999999999999999999987     479999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q psy2347          81 SRGRGRGRG   89 (207)
Q Consensus        81 a~~k~~~~~   89 (207)
                      ++++.....
T Consensus       149 a~~~~~~~~  157 (165)
T 1rk8_A          149 CFVKGPKRV  157 (165)
T ss_dssp             SEECC----
T ss_pred             ecCCCCCCC
Confidence            998776543

>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=99.80  E-value=1.1e-19  Score=128.69  Aligned_cols=82  Identities=24%  Similarity=0.424  Sum_probs=74.8

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHH----HHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~----~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..++.++|||+|||+++|+++|+    ++|++||+|+.|.|+.+  +++||||+|+++++|++|++.||+..|.+++|+|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34678999999999999999999    99999999999998854  6899999999999999999999999999999999


Q ss_pred             EEeecCCC
Q psy2347          79 EISRGRGR   86 (207)
Q Consensus        79 ~~a~~k~~   86 (207)
                      ++++++..
T Consensus        84 ~~a~~~~~   91 (97)
T 1nu4_A           84 QYAKTDSD   91 (97)
T ss_dssp             EECSSCCT
T ss_pred             EEccCCCc
Confidence            99988654

>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=99.80  E-value=2.4e-19  Score=124.47  Aligned_cols=77  Identities=26%  Similarity=0.468  Sum_probs=70.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ....+.++|||+|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++||+. ++++|++++|+|
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v   84 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDP   84 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEE
Confidence            34567889999999999999999999999999999999987     478999999999999999975 888999999999


Q ss_pred             EEe
Q psy2347          79 EIS   81 (207)
Q Consensus        79 ~~a   81 (207)
                      ++|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            876

>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=99.80  E-value=1.7e-19  Score=129.84  Aligned_cols=81  Identities=20%  Similarity=0.174  Sum_probs=73.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||+|||+++|+++|+++|++|+.|++ |+|+.+    +++||||+|+++++|++||+. |++.|.++.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            3456789999999999999999999999999987 888776    689999999999999999997 9999999999999


Q ss_pred             EeecCCC
Q psy2347          80 ISRGRGR   86 (207)
Q Consensus        80 ~a~~k~~   86 (207)
                      ++++++-
T Consensus        90 ~~~~~~~   96 (104)
T 1wg5_A           90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHH
Confidence            9987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=3.4e-21  Score=141.25  Aligned_cols=85  Identities=22%  Similarity=0.330  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE--------EEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCce
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS--------VWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQD   70 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~--------v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~   70 (207)
                      +...+.++|||+|||+++|+++|+++|++|+.|+.        |+|+.+     +++||||+|+++++|++||+.||+..
T Consensus         2 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   81 (116)
T 2lcw_A            2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   81 (116)
Confidence            34567889999999999999999999999999998        888876     57999999999999999999999999


Q ss_pred             eCCcEEEEEEeecCCCCC
Q psy2347          71 LMGSKLRVEISRGRGRGR   88 (207)
Q Consensus        71 i~g~~l~V~~a~~k~~~~   88 (207)
                      |.+++|+|+++++++...
T Consensus        82 ~~g~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           82 FSGNPIKVSFATRRADFN   99 (116)
Confidence            999999999999887653

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=5.6e-20  Score=134.19  Aligned_cols=78  Identities=26%  Similarity=0.399  Sum_probs=72.7

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||.|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++|| .||++.|.++.|+|+++++
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            479999999999999999999999999999999976     6799999999999999999 8999999999999999987


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      +..+
T Consensus       104 ~~~~  107 (114)
T 2cq4_A          104 EKNR  107 (114)
T ss_dssp             HHHH
T ss_pred             CccC
Confidence            6543

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.1e-19  Score=133.03  Aligned_cols=80  Identities=20%  Similarity=0.170  Sum_probs=74.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCe-eEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKL-NSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V-~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||+|||+++|+++|+++|++|+.| +.|+|+.|    +++||||+|+++++|++||+. |++.|.+++|+|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            45667899999999999999999999999999 88999887    689999999999999999987 9999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      ++++++
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            998765

>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=6.4e-20  Score=138.85  Aligned_cols=81  Identities=20%  Similarity=0.167  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCC---eeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGK---LNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKL   76 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~---V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l   76 (207)
                      ....+.++|||+|||+++||++|+++|++|+.   |+.|+|++|    +++||||+|+++++|++||+ ||+++|.++.|
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            34566789999999999999999999999999   889999987    57899999999999999999 99999999999


Q ss_pred             EEEEeecCC
Q psy2347          77 RVEISRGRG   85 (207)
Q Consensus        77 ~V~~a~~k~   85 (207)
                      +|.++++++
T Consensus       118 ~V~~a~~~e  126 (136)
T 2hgl_A          118 EVFKSHRTE  126 (136)
T ss_dssp             EEEECCHHH
T ss_pred             EEEECChHH
Confidence            999987653

>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=99.79  E-value=1.1e-19  Score=126.73  Aligned_cols=81  Identities=21%  Similarity=0.401  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|+.++++||||+|+++++|++|+..  ...+.+++|+|++++++.
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCC
Confidence            356799999999999999999999999999999999988899999999999999875432  456699999999998876


Q ss_pred             CCC
Q psy2347          86 RGR   88 (207)
Q Consensus        86 ~~~   88 (207)
                      ...
T Consensus        80 ~~~   82 (88)
T 1wf0_A           80 NSN   82 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

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

Probab=99.79  E-value=1.4e-19  Score=129.75  Aligned_cols=80  Identities=25%  Similarity=0.471  Sum_probs=74.5

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||+|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            45689999999999999999999999999999999876     4799999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy2347          82 RGRGR   86 (207)
Q Consensus        82 ~~k~~   86 (207)
                      +++..
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            87654

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

Probab=99.79  E-value=3.1e-20  Score=128.47  Aligned_cols=77  Identities=18%  Similarity=0.331  Sum_probs=70.9

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.++.|+|++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            467889999999999999999999999999999999987     589999999999999999999999999999887765


Q ss_pred             ee
Q psy2347          81 SR   82 (207)
Q Consensus        81 a~   82 (207)
                      ++
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=3.6e-19  Score=125.82  Aligned_cols=80  Identities=19%  Similarity=0.213  Sum_probs=73.1

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEE-EEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v-~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ....++|||+|||+++|+++|+++|++||+|+.| .|+.+ ..+.|||+|+++++|++||+.||++.|.+++|+|+++++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            3457899999999999999999999999999999 47777 445699999999999999999999999999999999998


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      +.
T Consensus        92 ~~   93 (96)
T 2e44_A           92 EM   93 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            74

>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=99.79  E-value=5.3e-19  Score=137.38  Aligned_cols=80  Identities=21%  Similarity=0.272  Sum_probs=72.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEEEeec
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVEISRG   83 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~~a~~   83 (207)
                      .+..+|||.||++++|+++|+++|++||+|++|.|+.+ +++||||+|+++++|++|++.||+.+|.+  ++|+|+++++
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~~Ak~  123 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  123 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecC
Confidence            34467899999999999999999999999999999866 57899999999999999999999999966  9999999998


Q ss_pred             CCC
Q psy2347          84 RGR   86 (207)
Q Consensus        84 k~~   86 (207)
                      +.-
T Consensus       124 ~~l  126 (164)
T 1sjr_A          124 TSL  126 (164)
T ss_dssp             SSC
T ss_pred             Ccc
Confidence            753

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=1.6e-19  Score=131.63  Aligned_cols=75  Identities=19%  Similarity=0.208  Sum_probs=70.0

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .++|||+|||+++||++|+++|++| .|+.|+|+.|    +++||||+|+++++|++|| .||++.|.++.|+|..++++
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            4799999999999999999999999 9999999987    7899999999999999999 58999999999999998765


Q ss_pred             C
Q psy2347          85 G   85 (207)
Q Consensus        85 ~   85 (207)
                      +
T Consensus        94 ~   94 (109)
T 2dnn_A           94 Q   94 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

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

Probab=99.79  E-value=5.3e-19  Score=132.94  Aligned_cols=77  Identities=38%  Similarity=0.655  Sum_probs=71.8

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3457889999999999999999999999999999999877     68999999999999999999999999999999998


Q ss_pred             Ee
Q psy2347          80 IS   81 (207)
Q Consensus        80 ~a   81 (207)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.79  E-value=3.8e-19  Score=128.26  Aligned_cols=80  Identities=19%  Similarity=0.305  Sum_probs=73.0

Q ss_pred             CCCcEEEEcCCCcCC------cHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCc-EE
Q psy2347           7 ERGTRVYVGGLTETV------KKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGS-KL   76 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~------te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~-~l   76 (207)
                      ...++|||+|||+.+      |+++|+++|++||+|+.|.|+.+   +++||||+|+++++|++||+.||++.|.++ +|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            346899999999999      88999999999999999998843   689999999999999999999999999998 99


Q ss_pred             EEEEeecCCC
Q psy2347          77 RVEISRGRGR   86 (207)
Q Consensus        77 ~V~~a~~k~~   86 (207)
                      +|+++++..+
T Consensus        93 ~V~~a~~~~k  102 (105)
T 2nlw_A           93 RVNLFTDFDK  102 (105)
T ss_dssp             EEECSCCCCC
T ss_pred             EEEEcchHhh
Confidence            9999986543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.79  E-value=5.6e-20  Score=131.30  Aligned_cols=79  Identities=18%  Similarity=0.397  Sum_probs=71.0

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||+|||+++|+++|+++|++|+.|+. .++.+     +++||||+|+++++|++||+ ||++.|.+++|+|+++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            46789999999999999999999999998877 34433     78999999999999999999 9999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++...
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            887654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.79  E-value=7.2e-20  Score=137.16  Aligned_cols=81  Identities=20%  Similarity=0.336  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE--EEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCc----eeCCc
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNS--VWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQ----DLMGS   74 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~--v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~----~i~g~   74 (207)
                      ..+.++|||+|||+++||++|+++|++||.|+.  |+|++|     +++||||+|+++ +|++||+.||++    +|+++
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            356789999999999999999999999999976  999988     689999999999 999999999999    99999


Q ss_pred             EEEEEEeecCCCC
Q psy2347          75 KLRVEISRGRGRG   87 (207)
Q Consensus        75 ~l~V~~a~~k~~~   87 (207)
                      +|+|++++++.+.
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999886544

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

Probab=99.78  E-value=2.6e-19  Score=126.54  Aligned_cols=81  Identities=17%  Similarity=0.318  Sum_probs=72.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ..+.++|||+|||+++|+++|+++|++|++|+.+ .... +++||||+|+++++|++||+.||++.|.+++|+|++++++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            4567899999999999999999999999988777 2222 6899999999999999999999999999999999999887


Q ss_pred             CCC
Q psy2347          85 GRG   87 (207)
Q Consensus        85 ~~~   87 (207)
                      .+.
T Consensus        92 ~~~   94 (96)
T 1fjc_A           92 GGT   94 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.78  E-value=1.1e-19  Score=129.90  Aligned_cols=79  Identities=20%  Similarity=0.351  Sum_probs=70.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .....++|||+|||+++|+++|+++|++|| |++|+|+.+      +++||||+|+++++|++|| .||+..|.++.|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            446679999999999999999999999999 999999876      4799999999999999999 89999999999999


Q ss_pred             EEeecCC
Q psy2347          79 EISRGRG   85 (207)
Q Consensus        79 ~~a~~k~   85 (207)
                      ++++++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998864

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.78  E-value=1.9e-19  Score=121.63  Aligned_cols=70  Identities=27%  Similarity=0.605  Sum_probs=66.2

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++|++ ||++.|++++|+|++|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            5999999999999999999999999999999877     57999999999999999998 8999999999999875

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=9.8e-19  Score=123.41  Aligned_cols=82  Identities=26%  Similarity=0.286  Sum_probs=70.7

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .....++|||+|||+++|+++|+++|++||+|++|.+..+ .+ ||||+|+++++|++||+ ||+++|.+++|+|+++.+
T Consensus         4 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~-~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            4 GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             CCTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCC-EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCC
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCc-EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCc
Confidence            3456789999999999999999999999999998822222 23 99999999999999999 999999999999999887


Q ss_pred             CCCCC
Q psy2347          84 RGRGR   88 (207)
Q Consensus        84 k~~~~   88 (207)
                      +....
T Consensus        82 ~~~~~   86 (94)
T 2e5g_A           82 KEFQS   86 (94)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            65543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.78  E-value=7.5e-19  Score=131.78  Aligned_cols=79  Identities=23%  Similarity=0.330  Sum_probs=72.4

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcE-EEEEEcCHHHHHHHHHhcCCceeCC--cEEEEEEeecC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF-AFVEFSNQIDAEAACDSMNDQDLMG--SKLRVEISRGR   84 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~-afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~~a~~k   84 (207)
                      +..+|||.||++.+|+++|+++|++||+|++|.|+.++++| |||+|++.++|++|++.||+++|.+  ++|+|++++++
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~  106 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  106 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCS
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCC
Confidence            44577799999999999999999999999999998777788 9999999999999999999999988  89999999876


Q ss_pred             CC
Q psy2347          85 GR   86 (207)
Q Consensus        85 ~~   86 (207)
                      .-
T Consensus       107 ~l  108 (130)
T 3zzy_A          107 SL  108 (130)
T ss_dssp             SC
T ss_pred             ce
Confidence            43

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.7e-19  Score=122.25  Aligned_cols=71  Identities=23%  Similarity=0.480  Sum_probs=67.6

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++|++.++ +.|++++|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            57999999999999999999999999999999887     57999999999999999999999 9999999999987

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.78  E-value=7.9e-20  Score=138.83  Aligned_cols=80  Identities=21%  Similarity=0.231  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ...+.++|||+|||+++||++|+++|++|+ |++|+|++|    +++||||+|+++++|++|| +||+++|.++.|+|.+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            345678999999999999999999999999 779999887    6899999999999999999 7899999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      +++++.
T Consensus       120 a~~~~~  125 (139)
T 2hgn_A          120 NSTTGA  125 (139)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            987654

>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=99.78  E-value=3.9e-19  Score=124.06  Aligned_cols=77  Identities=17%  Similarity=0.245  Sum_probs=71.3

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ...++|||+|||+++|+++|+++|++| +|++|+|.+ +++||||+|+++++|++|++.||+.+|.+++|+|++++.+.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~-~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~   79 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDR-NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA   79 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEG-GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeC-CCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCCc
Confidence            467899999999999999999999999 999999864 58999999999999999999999999999999999997643

>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=99.78  E-value=9.2e-20  Score=127.44  Aligned_cols=77  Identities=29%  Similarity=0.557  Sum_probs=68.5

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ++|||+|||+++++++|+++|++||+|++|+|+.+     +++||||+|++++ |++|++.||++.|.+++|+|++|.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999877     5899999999999 99999999999999999999999886


Q ss_pred             CCC
Q psy2347          85 GRG   87 (207)
Q Consensus        85 ~~~   87 (207)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.77  E-value=1.1e-18  Score=137.54  Aligned_cols=80  Identities=25%  Similarity=0.380  Sum_probs=74.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .++.++|||.|||+++|+++|+++|++|++|++|+|+.+    +++||||+|+++++|++||+.||++.|.+++|+|++|
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456789999999999999999999999999999999886    6899999999999999999999999999999999999


Q ss_pred             ecCC
Q psy2347          82 RGRG   85 (207)
Q Consensus        82 ~~k~   85 (207)
                      .+..
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=8.9e-20  Score=135.32  Aligned_cols=80  Identities=25%  Similarity=0.260  Sum_probs=70.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||+|||+++|+++|+++|++|+.|+.+.++.+     +++||||+|+++++|++||+ ||++.|.++.|+|.
T Consensus        21 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~   99 (124)
T 1wel_A           21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVH   99 (124)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            3456689999999999999999999999999987444432     57999999999999999999 99999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      +++++.
T Consensus       100 ~a~~~~  105 (124)
T 1wel_A          100 PITKKG  105 (124)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            998653

>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=1.7e-19  Score=130.59  Aligned_cols=82  Identities=16%  Similarity=0.127  Sum_probs=74.9

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCC---eeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGK---LNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~---V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      .....+.++|||+|||+++|+++|+++|++|+.   |+.|+|+.+    +++||||+|+++++|++||+ ||++.|.++.
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~   83 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRY   83 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSC
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeE
Confidence            345567889999999999999999999999998   899999887    68999999999999999999 8999999999


Q ss_pred             EEEEEeecCC
Q psy2347          76 LRVEISRGRG   85 (207)
Q Consensus        76 l~V~~a~~k~   85 (207)
                      |+|.++++++
T Consensus        84 i~V~~a~~~~   93 (107)
T 2lmi_A           84 VEVYEINNED   93 (107)
T ss_dssp             CCCEECCHHH
T ss_pred             EEEEECCHHH
Confidence            9999998754

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.77  E-value=5.6e-19  Score=121.32  Aligned_cols=70  Identities=21%  Similarity=0.361  Sum_probs=65.2

Q ss_pred             CcEEEEcCCCcCC------cHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCc-EEEE
Q psy2347           9 GTRVYVGGLTETV------KKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGS-KLRV   78 (207)
Q Consensus         9 ~~~lfV~nLp~~~------te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~-~l~V   78 (207)
                      +++|||+|||+++      |+++|+++|++||+|++|+|+.+   +++||||+|+++++|++||+.||+..|.++ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4799999999999      78999999999999999998854   789999999999999999999999999999 8876

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.76  E-value=2.8e-18  Score=127.84  Aligned_cols=76  Identities=20%  Similarity=0.256  Sum_probs=69.1

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcE-EEEEEcCHHHHHHHHHhcCCceeCC--cEEEEEEeecCCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF-AFVEFSNQIDAEAACDSMNDQDLMG--SKLRVEISRGRGR   86 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~-afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~~a~~k~~   86 (207)
                      ..|||.||++.+|+++|+++|++||+|++|.|+.. .+| |||+|+++++|++|+++||+.+|.+  ++|+|++|+++.-
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~l  104 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRL  104 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSCC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCcc
Confidence            34679999999999999999999999999999875 586 9999999999999999999999987  6899999988753

>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=99.76  E-value=2e-18  Score=138.92  Aligned_cols=79  Identities=22%  Similarity=0.327  Sum_probs=74.5

Q ss_pred             CCCcEEEEcCCC-cCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           7 ERGTRVYVGGLT-ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         7 ~~~~~lfV~nLp-~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      .++++|||+||| +++|+++|+++|++||+|++|+|++++++||||+|+++++|++||+.||+++|.+++|+|.+++.+.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~   81 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA   81 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCc
Confidence            367899999999 8999999999999999999999999889999999999999999999999999999999999997543

>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=99.76  E-value=1.9e-18  Score=119.72  Aligned_cols=73  Identities=22%  Similarity=0.379  Sum_probs=68.6

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhC----C-------CeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKF----G-------KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~----G-------~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      ..+.++|||+|||+++|+++|+++|++|    +       +|++|+++++ ++||||+|+++++|++|+ .||++.|.++
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-kg~afV~f~~~~~a~~A~-~l~g~~~~g~   80 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVDETTQAM-AFDGIIFQGQ   80 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-SSEEEEEESSHHHHHHHG-GGTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-CcEEEEEcCCHHHHHHHH-hcCCCEECCe
Confidence            4567899999999999999999999999    8       8999999887 899999999999999999 9999999999


Q ss_pred             EEEEEE
Q psy2347          75 KLRVEI   80 (207)
Q Consensus        75 ~l~V~~   80 (207)
                      +|+|+.
T Consensus        81 ~l~V~r   86 (87)
T 2hzc_A           81 SLKIRR   86 (87)
T ss_dssp             ECEEEC
T ss_pred             EEEEeC
Confidence            999873

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=6.8e-19  Score=131.01  Aligned_cols=78  Identities=22%  Similarity=0.187  Sum_probs=70.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCe----eEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKL----NSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V----~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ++.++|||+|||+++|+++|+++|++|++|    +.|+|+++    +++||||+|+++++|++||+. |++.|.++.|+|
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~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            567899999999999999999999999875    68888876    679999999999999999986 999999999999


Q ss_pred             EEeecCC
Q psy2347          79 EISRGRG   85 (207)
Q Consensus        79 ~~a~~k~   85 (207)
                      ..+++++
T Consensus       100 ~~a~~~e  106 (123)
T 2dha_A          100 FRSTAAE  106 (123)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9987643

>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=99.75  E-value=8.4e-19  Score=131.03  Aligned_cols=79  Identities=22%  Similarity=0.193  Sum_probs=71.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCee--EEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLN--SVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~--~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ...+.++|||+|||+++||++|+++|++| .|+  .|+|++|    +++||||+|+++++|++||+. ++++|.++.|+|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            34567899999999999999999999999 777  8999887    789999999999999999985 779999999999


Q ss_pred             EEeecCC
Q psy2347          79 EISRGRG   85 (207)
Q Consensus        79 ~~a~~k~   85 (207)
                      .++++++
T Consensus       116 ~~a~~~e  122 (126)
T 2hgm_A          116 FKSSQEE  122 (126)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9987654

>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=99.75  E-value=2.6e-18  Score=130.17  Aligned_cols=82  Identities=26%  Similarity=0.384  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE--------EEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS--------VWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~--------v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      ...+.++|||+|||+++|+++|+++|++||.|+.        |.+...  +++||||+|.++++|++||+.||+..|.++
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            3467889999999999999999999999999876        433333  789999999999999999999999999999


Q ss_pred             EEEEEEeecCCC
Q psy2347          75 KLRVEISRGRGR   86 (207)
Q Consensus        75 ~l~V~~a~~k~~   86 (207)
                      +|.|++|+++..
T Consensus       121 ~l~V~~a~~~~~  132 (143)
T 3egn_A          121 PMVVQFARSARP  132 (143)
T ss_dssp             ECEEEECCCSCC
T ss_pred             EEEEEECCCCCC
Confidence            999999977543

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.74  E-value=2.9e-18  Score=138.07  Aligned_cols=79  Identities=27%  Similarity=0.382  Sum_probs=74.1

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ..++|||.|||+++|+++|+++|++||+|+.|+|+.|   +++||||+|+++++|++||+.||+++|.+++|+|++|+++
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCH
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            4578999999999999999999999999999999987   6899999999999999999999999999999999999876


Q ss_pred             CC
Q psy2347          85 GR   86 (207)
Q Consensus        85 ~~   86 (207)
                      .+
T Consensus       182 ~~  183 (213)
T 4f02_A          182 KE  183 (213)
T ss_dssp             HH
T ss_pred             cc
Confidence            43

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.74  E-value=4.3e-18  Score=137.07  Aligned_cols=81  Identities=30%  Similarity=0.379  Sum_probs=72.5

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      +..+.++|||+|||+++||++|+++|++||+|++|+|++|     +++||||+|+++++|++||+.||...+.++.|+|.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            4457789999999999999999999999999999999987     56899999999999999999999999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      ++.+..
T Consensus        91 ~~~~~~   96 (213)
T 4f02_A           91 WSQRDP   96 (213)
T ss_dssp             ECCCCT
T ss_pred             cccccc
Confidence            886543

>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=99.74  E-value=9.5e-19  Score=118.07  Aligned_cols=70  Identities=21%  Similarity=0.492  Sum_probs=65.8

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++|++. +++.|.+++|+|++|
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-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            6999999999999999999999999999999876     589999999999999999985 889999999999875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.73  E-value=1.8e-18  Score=123.61  Aligned_cols=80  Identities=20%  Similarity=0.438  Sum_probs=72.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ..+.++|||+|||+++|+++|+++|++||+|+.|+|+.+    +++||||+|+++++|++||+  +++.|++++|.|.++
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            345689999999999999999999999999999999987    57999999999999999998  899999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      .++...
T Consensus        84 ~~~~~~   89 (102)
T 2xs2_A           84 IRKQNL   89 (102)
T ss_dssp             EECC--
T ss_pred             CcCcch
Confidence            877554

>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=99.73  E-value=1e-17  Score=128.54  Aligned_cols=79  Identities=24%  Similarity=0.456  Sum_probs=74.0

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|.++++|++|++.|++..|.+++|+|++++
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            5789999999999999999999999999999999876     56899999999999999999999999999999999998


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      ++..
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            7654

>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=99.73  E-value=1.6e-17  Score=138.36  Aligned_cols=85  Identities=25%  Similarity=0.409  Sum_probs=79.3

Q ss_pred             CCCCCCCCCcEEEEcCCCcCCcHHHHH----HHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           1 MSDGMMERGTRVYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         1 ms~~~~~~~~~lfV~nLp~~~te~~L~----~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      |+....++.++|||+|||+++|+++|+    ++|++||+|++|+|+++  +++||||+|+++++|++||+.||+..|.++
T Consensus         1 m~~~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            777788899999999999999999977    89999999999999876  789999999999999999999999999999


Q ss_pred             EEEEEEeecCC
Q psy2347          75 KLRVEISRGRG   85 (207)
Q Consensus        75 ~l~V~~a~~k~   85 (207)
                      .|+|++++++.
T Consensus        81 ~l~v~~a~~~~   91 (282)
T 3pgw_A           81 PMRIQYAKTDS   91 (282)
T ss_pred             EEEEEEeccCc
Confidence            99999997755

>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=99.73  E-value=1.4e-17  Score=127.42  Aligned_cols=79  Identities=23%  Similarity=0.395  Sum_probs=73.5

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|.++++|++|++.||+..|.+++|+|++++
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            3689999999999999999999999999999999987     34899999999999999999999999999999999998


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      ++..
T Consensus        81 ~~~~   84 (167)
T 1fxl_A           81 PSSA   84 (167)
T ss_dssp             CCCG
T ss_pred             CCcc
Confidence            7653

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

Probab=99.73  E-value=1.1e-17  Score=131.95  Aligned_cols=81  Identities=20%  Similarity=0.400  Sum_probs=76.0

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++|++.||+..|.+++|+|+++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            56799999999999999999999999999999999987     3789999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++.+.
T Consensus       192 ~~~~~~  197 (198)
T 2yh0_A          192 SVGAKN  197 (198)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987653

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.3e-17  Score=117.60  Aligned_cols=77  Identities=23%  Similarity=0.276  Sum_probs=68.2

Q ss_pred             CCCCCcE-EEEcCCCcCCcHHH----HHHHHHhC-CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTR-VYVGGLTETVKKED----LELEFEKF-GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~-lfV~nLp~~~te~~----L~~~F~~~-G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..+++.+ |||.|||+.+++++    |+++|++| |+|.+|     ..++|||+|++.++|++|++.||+.+|.+++|+|
T Consensus         4 ~~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-----tgG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v   78 (96)
T 2diu_A            4 GSSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-----TGCSAILRFINQDSAERAQKRMENEDVFGNRIIV   78 (96)
T ss_dssp             SCCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-----CTTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-----ecCEEEEEECCHHHHHHHHHHhcCCccCCceEEE
Confidence            3455666 99999999999988    55899999 599988     2499999999999999999999999999999999


Q ss_pred             EEeecCCC
Q psy2347          79 EISRGRGR   86 (207)
Q Consensus        79 ~~a~~k~~   86 (207)
                      ++|+++..
T Consensus        79 ~~A~~~sd   86 (96)
T 2diu_A           79 SFTPKNRE   86 (96)
T ss_dssp             ESSCCSCC
T ss_pred             EecCCCcc
Confidence            99988754

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

Probab=99.73  E-value=1.7e-17  Score=126.75  Aligned_cols=79  Identities=34%  Similarity=0.515  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+.++|||.|||+++|+++|+++|++|+.|+.|+|+.+     ++++|||+|+++++|++|++.||+..|.+++|+|+
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            3456789999999999999999999999999999999877     46899999999999999999999999999999999


Q ss_pred             Eeec
Q psy2347          80 ISRG   83 (207)
Q Consensus        80 ~a~~   83 (207)
                      +|++
T Consensus       163 ~a~~  166 (166)
T 3md3_A          163 WAAK  166 (166)
T ss_dssp             ESCC
T ss_pred             ecCC
Confidence            9864

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

Probab=99.72  E-value=1.7e-17  Score=132.52  Aligned_cols=82  Identities=29%  Similarity=0.438  Sum_probs=75.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|+++++|++||+.||+++|.+++|+|+++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45689999999999999999999999999999999987     3789999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy2347          82 RGRGRGR   88 (207)
Q Consensus        82 ~~k~~~~   88 (207)
                      ++++...
T Consensus       203 ~~~~~~~  209 (216)
T 2qfj_A          203 VTPPMPL  209 (216)
T ss_dssp             SSCSSTT
T ss_pred             cCCCCCC
Confidence            9876543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.72  E-value=1.2e-17  Score=137.30  Aligned_cols=80  Identities=24%  Similarity=0.446  Sum_probs=72.1

Q ss_pred             CCCCcEEEEcCCCcCC---------cHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCcee-----
Q psy2347           6 MERGTRVYVGGLTETV---------KKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL-----   71 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~---------te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i-----   71 (207)
                      ..+.++|||+||+.++         +|++|+++|++||+|++|+|+.+ ++||||+|+++++|++|+++|+++.|     
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~-kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~  209 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-KNCGFVKFKYQANAEFAKEAMSNQTLLLPSD  209 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG-GTEEEEEESSHHHHHHHHHHHTTCCCCCTTS
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC-CCEEEEEeCCHHHHHHHHHHhCCCEEecccc
Confidence            4567899999999998         79999999999999999999986 99999999999999999999999999     


Q ss_pred             -------CCcEEEEEEeecCCC
Q psy2347          72 -------MGSKLRVEISRGRGR   86 (207)
Q Consensus        72 -------~g~~l~V~~a~~k~~   86 (207)
                             .++.|.|++|++++.
T Consensus       210 ~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          210 KEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TTGGGGGGSCCCEEEECC----
T ss_pred             ccccccCCCCEEEEEEccCCCC
Confidence                   899999999987654

>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=2.5e-17  Score=129.62  Aligned_cols=83  Identities=20%  Similarity=0.382  Sum_probs=70.1

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||.|||+++|+++|+++|++||.|+.|+|+.+     +++||||+|+++++|++||+. +++.|.++.|+|+++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            34589999999999999999999999999999999987     478999999999999999986 799999999999999


Q ss_pred             ecCCCCCCC
Q psy2347          82 RGRGRGRGG   90 (207)
Q Consensus        82 ~~k~~~~~~   90 (207)
                      .++......
T Consensus       181 ~~k~~~~~~  189 (196)
T 1l3k_A          181 LSKQEMASA  189 (196)
T ss_dssp             C--------
T ss_pred             CChhHhccc
Confidence            998776543

>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=99.71  E-value=2.8e-17  Score=133.64  Aligned_cols=81  Identities=22%  Similarity=0.365  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           5 MMERGTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+++++|||+|||+ ++|+++|+++|++||+|++|+|+.+.++||||+|.++++|++||+.||+..|.+++|+|+++++
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~  109 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH  109 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecC
Confidence            345688999999999 9999999999999999999999999889999999999999999999999999999999999986


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      +.
T Consensus       110 ~~  111 (229)
T 2adc_A          110 QN  111 (229)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

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

Probab=99.71  E-value=3.1e-17  Score=125.33  Aligned_cols=77  Identities=19%  Similarity=0.393  Sum_probs=72.4

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ++|||+|||+++|+++|+++|++||+|++|+|+.+    +++||||+|.++++|++|++.|++..|.++.|.|+++.++.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999877    56899999999999999999999999999999999997765


Q ss_pred             C
Q psy2347          86 R   86 (207)
Q Consensus        86 ~   86 (207)
                      .
T Consensus        81 ~   81 (166)
T 3md3_A           81 Q   81 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.70  E-value=1.8e-17  Score=127.16  Aligned_cols=77  Identities=19%  Similarity=0.475  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||.|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++|++ |++..|.+++|+|++|+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            4679999999999999999999999999999999876     57899999999999999998 89999999999999999


Q ss_pred             cCC
Q psy2347          83 GRG   85 (207)
Q Consensus        83 ~k~   85 (207)
                      ||+
T Consensus       165 pk~  167 (167)
T 2cjk_A          165 PRH  167 (167)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            874

>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=99.70  E-value=9.5e-17  Score=133.74  Aligned_cols=77  Identities=21%  Similarity=0.381  Sum_probs=73.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEEEEEEee
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKLRVEISR   82 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l~V~~a~   82 (207)
                      ..+.++|||.|||+++|+++|+++|++|+.|++|+|+.+.++||||+|+++++|++||+.||+.+|. +++|+|++++
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            3467899999999999999999999999999999999887799999999999999999999999999 9999999986

>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=99.70  E-value=1.7e-16  Score=115.60  Aligned_cols=83  Identities=20%  Similarity=0.337  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCcCC-----------cHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2347           5 MMERGTRVYVGGLTETV-----------KKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLM   72 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~-----------te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~   72 (207)
                      ...++++|+|.||....           ++++|+++|++||+|++|.|+.. +++||||+|+++++|++||+.||++.|.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            45678999999994433           26899999999999999966422 7899999999999999999999999999


Q ss_pred             CcEEEEEEeecCCCC
Q psy2347          73 GSKLRVEISRGRGRG   87 (207)
Q Consensus        73 g~~l~V~~a~~k~~~   87 (207)
                      +++|+|++++++..-
T Consensus        91 gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           91 GRQITAQAWDGTTDY  105 (112)
T ss_dssp             TEECEEEECCSCCCS
T ss_pred             CcEEEEEEeCCCCCc
Confidence            999999999887654

>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=99.70  E-value=4.2e-17  Score=128.27  Aligned_cols=80  Identities=24%  Similarity=0.441  Sum_probs=71.7

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|.++++|++||+. +++.|.++.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            456789999999999999999999999999999999987     468999999999999999986 88999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      +.++..
T Consensus        89 ~~~~~~   94 (196)
T 1l3k_A           89 AVSRED   94 (196)
T ss_dssp             CCC---
T ss_pred             ccCccc
Confidence            877644

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

Probab=99.69  E-value=5.4e-17  Score=125.11  Aligned_cols=76  Identities=21%  Similarity=0.412  Sum_probs=71.5

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ...++|||.|||+++|+++|+++|++||+|+.|+|+.+     +++||||+|+++++|++|++.||++.|.+++|+|++|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            44689999999999999999999999999999999988     3789999999999999999999999999999999987


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=4.3e-17  Score=119.11  Aligned_cols=74  Identities=26%  Similarity=0.442  Sum_probs=62.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKL   76 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l   76 (207)
                      .....++|||+|||+++|+++|+++|++||+|+ +.++.+        +++||||+|+++++|++||++|  +.++++.|
T Consensus         4 ~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~--~~~~G~~~   80 (114)
T 2dnl_A            4 GSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC--LEEDGKLY   80 (114)
T ss_dssp             SSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS--EEETTEEE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh--hhcCCcEE
Confidence            345678999999999999999999999999999 777764        3799999999999999999988  24566655


Q ss_pred             EEEEe
Q psy2347          77 RVEIS   81 (207)
Q Consensus        77 ~V~~a   81 (207)
                      .|..+
T Consensus        81 ~~~~~   85 (114)
T 2dnl_A           81 LCVSS   85 (114)
T ss_dssp             EEECC
T ss_pred             EeccC
Confidence            55443

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.69  E-value=7e-17  Score=127.76  Aligned_cols=79  Identities=19%  Similarity=0.289  Sum_probs=74.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCC-CeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEEEEEEeec
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFG-KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKLRVEISRG   83 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G-~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l~V~~a~~   83 (207)
                      .++.++|||.|||+++|+++|+++|++|| +|+.|+|+.+.+++|||+|+++++|++|++.||+..|. +++|+|+++++
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            35688999999999999999999999999 99999998777899999999999999999999999999 99999999987


Q ss_pred             C
Q psy2347          84 R   84 (207)
Q Consensus        84 k   84 (207)
                      +
T Consensus       197 ~  197 (198)
T 1qm9_A          197 T  197 (198)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.68  E-value=1.3e-16  Score=129.80  Aligned_cols=79  Identities=19%  Similarity=0.289  Sum_probs=74.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCC-CeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEEEEEEeec
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFG-KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKLRVEISRG   83 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G-~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l~V~~a~~   83 (207)
                      .++.++|||.|||+++|+++|+++|++|| +|+.|+|+.+.+++|||+|+++++|++||+.||+..|. +++|+|+++++
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            34578999999999999999999999999 99999997766899999999999999999999999999 99999999987


Q ss_pred             C
Q psy2347          84 R   84 (207)
Q Consensus        84 k   84 (207)
                      +
T Consensus       228 ~  228 (229)
T 2adc_A          228 T  228 (229)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.68  E-value=7.2e-17  Score=125.03  Aligned_cols=77  Identities=18%  Similarity=0.362  Sum_probs=70.4

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .+.++|||.|||+++|+++|+++|++|++|..+  ..+  +++||||+|+++++|++||+.||++.|.+++|+|++|++|
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~--~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE--CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe--cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            456899999999999999999999999988877  222  7899999999999999999999999999999999999887


Q ss_pred             C
Q psy2347          85 G   85 (207)
Q Consensus        85 ~   85 (207)
                      +
T Consensus       175 ~  175 (175)
T 1fje_B          175 G  175 (175)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=99.68  E-value=9.1e-17  Score=128.19  Aligned_cols=78  Identities=29%  Similarity=0.492  Sum_probs=71.5

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|+++++|++||+.||++.|.+++|+|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4579999999999999999999999999999999876     68999999999999999999999999999999998876


Q ss_pred             cCC
Q psy2347          83 GRG   85 (207)
Q Consensus        83 ~k~   85 (207)
                      ++.
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.68  E-value=6.7e-17  Score=127.88  Aligned_cols=78  Identities=23%  Similarity=0.396  Sum_probs=73.9

Q ss_pred             CCcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           8 RGTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         8 ~~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      .+++|||+|||+ ++|+++|+++|++||+|++|+|+.+.++||||+|+++++|++||+.||+..|.+++|+|.+++++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~   80 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   80 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCC
Confidence            357999999999 999999999999999999999999888999999999999999999999999999999999998654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.68  E-value=1.7e-16  Score=114.74  Aligned_cols=79  Identities=16%  Similarity=0.088  Sum_probs=70.5

Q ss_pred             CCCCCcEEEEcCCCc-----CCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           5 MMERGTRVYVGGLTE-----TVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~-----~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ...++++|+|.||..     +.++++|+++|++||+|++|.|+++      +++|+||+|+++++|++|++.||+..|.+
T Consensus         4 ~~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            4 GKCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             GGSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            456889999999952     2378999999999999999999875      47999999999999999999999999999


Q ss_pred             cEEEEEEeec
Q psy2347          74 SKLRVEISRG   83 (207)
Q Consensus        74 ~~l~V~~a~~   83 (207)
                      ++|+|+++.+
T Consensus        84 r~i~v~~a~~   93 (105)
T 2pe8_A           84 RVVKACFYNL   93 (105)
T ss_dssp             EECEEEECCH
T ss_pred             cEEEEEEcCH
Confidence            9999999975

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.67  E-value=1.2e-16  Score=123.20  Aligned_cols=76  Identities=21%  Similarity=0.462  Sum_probs=70.0

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeC---CcEEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLM---GSKLRVE   79 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~---g~~l~V~   79 (207)
                      .+.++|||.|||+++|+++|+++|++||+|+.|+|+.+    +++||||+|+++++|++|++.||+..+.   +++|+|+
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            35689999999999999999999999999999999987    5789999999999999999999998876   4999999


Q ss_pred             Eee
Q psy2347          80 ISR   82 (207)
Q Consensus        80 ~a~   82 (207)
                      +|.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            974

>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=99.67  E-value=1.9e-16  Score=121.42  Aligned_cols=76  Identities=26%  Similarity=0.471  Sum_probs=70.7

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRV   78 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V   78 (207)
                      ..+.++|||.|||.++|+++|+++|++|++|+.|+|+.+     ++++|||+|+++++|++|++.||+..|.+  ++|+|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            456789999999999999999999999999999999987     36899999999999999999999999987  99999


Q ss_pred             EEe
Q psy2347          79 EIS   81 (207)
Q Consensus        79 ~~a   81 (207)
                      ++|
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=99.65  E-value=3.1e-16  Score=120.86  Aligned_cols=79  Identities=19%  Similarity=0.374  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCceeC---CcEEE
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQDLM---GSKLR   77 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~~i~---g~~l~   77 (207)
                      +.++|||+|||+++|+++|+++|++||+|++|+|+.+       +++||||+|.++++|++|++.|++..+.   .+.|.
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            5789999999999999999999999999999999876       3579999999999999999999998875   67788


Q ss_pred             EEEeecCCC
Q psy2347          78 VEISRGRGR   86 (207)
Q Consensus        78 V~~a~~k~~   86 (207)
                      |.+++++..
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            887766543

>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=99.65  E-value=3.1e-16  Score=129.97  Aligned_cols=78  Identities=24%  Similarity=0.490  Sum_probs=73.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ...+.++|||+|||+++|+++|+++|++||+|+.|.|+++ ++||||+|.++++|++||+.||++.|.++.|+|.++.+
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~   95 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH   95 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT-TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC-CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc
Confidence            3455689999999999999999999999999999999876 89999999999999999999999999999999999875

>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=99.65  E-value=3.7e-16  Score=119.36  Aligned_cols=75  Identities=28%  Similarity=0.589  Sum_probs=68.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcE--EEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSK--LRVE   79 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~--l~V~   79 (207)
                      .+.++|||.|||+++|+++|+++|++|++|+.|+|+.+     ++++|||+|+++++|++|++.||+..|.++.  |+|+
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            45689999999999999999999999999999999887     3789999999999999999999999999965  7777


Q ss_pred             Ee
Q psy2347          80 IS   81 (207)
Q Consensus        80 ~a   81 (207)
                      +|
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>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=99.64  E-value=5.7e-16  Score=119.31  Aligned_cols=77  Identities=21%  Similarity=0.340  Sum_probs=70.2

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhC----C-------CeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKF----G-------KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~----G-------~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      .+.++|||+|||+++|+++|+++|++|    +       .|.++++..+ ++||||+|.++++|++|+ +||++.|.+++
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~-~g~afV~f~~~~~A~~A~-~~~~~~~~g~~   79 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT-TTEEEEEESSHHHHHHHG-GGTTCEETTEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC-CCEEEEEeCCHHHHHHHH-HhCCcEecCce
Confidence            467899999999999999999999999    6       7888888776 999999999999999999 89999999999


Q ss_pred             EEEEEeecCC
Q psy2347          76 LRVEISRGRG   85 (207)
Q Consensus        76 l~V~~a~~k~   85 (207)
                      |+|+++++..
T Consensus        80 i~v~~~~~~~   89 (172)
T 2g4b_A           80 LKIRRPHDYQ   89 (172)
T ss_dssp             CEEECCSSCC
T ss_pred             eeecCCcccC
Confidence            9999876654

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.64  E-value=4.8e-16  Score=123.93  Aligned_cols=75  Identities=17%  Similarity=0.232  Sum_probs=68.8

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .++|||.|||+++|+++|+++|++||+|+.|+|+++    +++||||+|+++++|++||+.+ +++|.+++|.|.+++.-
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHH
Confidence            479999999999999999999999999999999986    6799999999999999999865 46999999999987653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=3.2e-15  Score=107.17  Aligned_cols=82  Identities=20%  Similarity=0.244  Sum_probs=68.5

Q ss_pred             CCCCcEEEEcCCC-------cCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           6 MERGTRVYVGGLT-------ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         6 ~~~~~~lfV~nLp-------~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .....+|.|.-.+       .++|+++|+++|++||+|++|.|+..+++||||+|+++++|++||+.++  .+.+++|+|
T Consensus         7 ~~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l~V   84 (100)
T 2d9o_A            7 GQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEV--GLVDNPLKI   84 (100)
T ss_dssp             CCSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBCEE
T ss_pred             CCccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeEEE
Confidence            3445677776543       4589999999999999999999987789999999999999999999854  467999999


Q ss_pred             EEeecCCCCCC
Q psy2347          79 EISRGRGRGRG   89 (207)
Q Consensus        79 ~~a~~k~~~~~   89 (207)
                      +++++++....
T Consensus        85 ~~a~~~~~~~~   95 (100)
T 2d9o_A           85 SWLEGQPQDAS   95 (100)
T ss_dssp             ECSSCCCCCCS
T ss_pred             EEccCCCCCCC
Confidence            99988765443

>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=99.64  E-value=3e-16  Score=120.35  Aligned_cols=75  Identities=19%  Similarity=0.421  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ++++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|.++++|++||+.  .+.|.++.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            5789999999999999999999999999999999887     679999999999999999985  578999999999886


Q ss_pred             cC
Q psy2347          83 GR   84 (207)
Q Consensus        83 ~k   84 (207)
                      ++
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            54

>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=99.63  E-value=4.2e-16  Score=125.27  Aligned_cols=75  Identities=13%  Similarity=0.115  Sum_probs=68.1

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCe--eEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCc----EEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKL--NSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGS----KLR   77 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V--~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~----~l~   77 (207)
                      +++++|||.|||+++||++|+++|++||.|  ++|+|+.+   ++++|||+|+++++|++||+.||+++|.++    ++.
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~  200 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYT  200 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEE
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceE
Confidence            467799999999999999999999999999  89999876   468999999999999999999999999876    577


Q ss_pred             EEEe
Q psy2347          78 VEIS   81 (207)
Q Consensus        78 V~~a   81 (207)
                      |++|
T Consensus       201 vk~~  204 (205)
T 3tyt_A          201 LKLC  204 (205)
T ss_dssp             CEEE
T ss_pred             EEec
Confidence            7775

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

Probab=99.63  E-value=1e-15  Score=120.54  Aligned_cols=78  Identities=21%  Similarity=0.329  Sum_probs=68.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhC----C-------CeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKF----G-------KLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK   75 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~----G-------~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~   75 (207)
                      ...++|||+|||+++|+++|+++|++|    +       .|.++++..+ ++||||+|.++++|++|| .||++.|.+++
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~-~g~afV~F~~~~~A~~Al-~l~g~~~~g~~   79 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-KNFAFLEFRSVDETTQAM-AFDGIIFQGQS   79 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETT-TTEEEEEESCSHHHHHHG-GGTTEEETTEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCC-CCEEEEEeCCHHHHHHHH-HhcCCEEcCce
Confidence            457899999999999999999999999    5       6777777655 899999999999999999 89999999999


Q ss_pred             EEEEEeecCCC
Q psy2347          76 LRVEISRGRGR   86 (207)
Q Consensus        76 l~V~~a~~k~~   86 (207)
                      |+|++++++..
T Consensus        80 i~v~~~~~~~~   90 (198)
T 2yh0_A           80 LKIRRPHDYQP   90 (198)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEeCCCCCCC
Confidence            99999876543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.63  E-value=4.5e-16  Score=115.86  Aligned_cols=73  Identities=18%  Similarity=0.260  Sum_probs=66.0

Q ss_pred             cEEEEcCC----CcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcC----HHH----HHHHHH--hcCCce
Q psy2347          10 TRVYVGGL----TETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSN----QID----AEAACD--SMNDQD   70 (207)
Q Consensus        10 ~~lfV~nL----p~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~----~e~----A~~Al~--~l~g~~   70 (207)
                      ++|||+||    |+.++|++|+++|++||+|.+|+++.|     +++||||+|.+    +++    |.+|++  .|++..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    999999999999999999999999999     78999999995    322    888988  789999


Q ss_pred             eCCcEEEEEEee
Q psy2347          71 LMGSKLRVEISR   82 (207)
Q Consensus        71 i~g~~l~V~~a~   82 (207)
                      |.+++|+|++.+
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999864

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

Probab=99.63  E-value=6.9e-16  Score=129.09  Aligned_cols=80  Identities=23%  Similarity=0.334  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           5 MMERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ...+.++|||.|||++ +|+++|+++|++||.|+.|+|+.+      +++||||+|.++++|++|| .||++.|.+++|+
T Consensus       206 ~~~~~~~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          206 ATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREIS  284 (292)
T ss_dssp             -CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEE
T ss_pred             cCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEE
Confidence            3456789999999999 999999999999999999999876      4789999999999999999 9999999999999


Q ss_pred             EEEeecCC
Q psy2347          78 VEISRGRG   85 (207)
Q Consensus        78 V~~a~~k~   85 (207)
                      |++|++|+
T Consensus       285 V~~a~~k~  292 (292)
T 2ghp_A          285 VSLADKKP  292 (292)
T ss_dssp             EEECCCCC
T ss_pred             EEEecCCC
Confidence            99999874

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.62  E-value=9.6e-16  Score=127.75  Aligned_cols=82  Identities=22%  Similarity=0.215  Sum_probs=75.8

Q ss_pred             CCCCcEEEEcCCCcCC-cHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETV-KKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~-te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+.++|||.|||+++ |+++|+++|++|+.|+.|+|+.+    ++++|||+|+++++|++|++.||+..|.+++|+|++
T Consensus       181 ~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            3467899999999995 99999999999999999999987    578999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      ++++..+
T Consensus       261 a~~~~~~  267 (284)
T 3smz_A          261 CAPGPPG  267 (284)
T ss_dssp             CCSSSCH
T ss_pred             ecCCCcc
Confidence            9987653

>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=99.61  E-value=2e-15  Score=109.07  Aligned_cols=78  Identities=18%  Similarity=0.255  Sum_probs=68.8

Q ss_pred             CCCcEEEEcCC--CcCCc--------HHHHHHHHHhCCCeeEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCc
Q psy2347           7 ERGTRVYVGGL--TETVK--------KEDLELEFEKFGKLNSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQ   69 (207)
Q Consensus         7 ~~~~~lfV~nL--p~~~t--------e~~L~~~F~~~G~V~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~   69 (207)
                      .+++.|.|.|+  |.++.        +++|+++|++||+|++|+|+++       +++++||+|+++++|++|+++||++
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            47889999998  44443        4689999999999999999876       4799999999999999999999999


Q ss_pred             eeCCcEEEEEEeecC
Q psy2347          70 DLMGSKLRVEISRGR   84 (207)
Q Consensus        70 ~i~g~~l~V~~a~~k   84 (207)
                      .+.+++|+|+++.+.
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998653

>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=99.61  E-value=4.1e-16  Score=120.76  Aligned_cols=81  Identities=19%  Similarity=0.364  Sum_probs=69.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEee----CCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAF----NPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~----d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ...+.++|||+|||+++|+++|+++|++|+.|..+.|..    .+++||||+|.++++|++||+ ||++.|.+++|+|++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            456789999999999999999999999998765522211    178999999999999999995 999999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      ++++..
T Consensus        88 ~~~~~~   93 (175)
T 1fje_B           88 PKGRDS   93 (175)
T ss_dssp             CCCSSC
T ss_pred             CCCccc
Confidence            987654

>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=99.59  E-value=4.3e-15  Score=123.76  Aligned_cols=82  Identities=17%  Similarity=0.291  Sum_probs=75.4

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||.|||+++|+++|+++|++|++|+.|+|+.+     +++||||+|.++++|++|++.|++..|.+++|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            356789999999999999999999999999999999877     468999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      +.++...
T Consensus       172 a~~~~~~  178 (284)
T 3smz_A          172 TDAGQLT  178 (284)
T ss_dssp             CCGGGCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.58  E-value=4.7e-15  Score=124.01  Aligned_cols=81  Identities=11%  Similarity=0.215  Sum_probs=71.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCC-CeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFG-KLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G-~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .+.++|||.|||+++|+++|+++|++|+ +|+.|+|+.+    +++||||+|.++++|++|++.||++.|.+++|.|+++
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            3578999999999999999999999999 9999999876    6899999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      .++...
T Consensus       195 ~~~~~~  200 (292)
T 2ghp_A          195 NPLEKS  200 (292)
T ss_dssp             CCC---
T ss_pred             CCCccc
Confidence            876543

>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=99.56  E-value=7.5e-15  Score=126.56  Aligned_cols=77  Identities=16%  Similarity=0.304  Sum_probs=67.0

Q ss_pred             CCCCCcEEEEcC--CCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC---Cc--EEE
Q psy2347           5 MMERGTRVYVGG--LTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM---GS--KLR   77 (207)
Q Consensus         5 ~~~~~~~lfV~n--Lp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~---g~--~l~   77 (207)
                      ..+++++|||+|  |+..+||++|+++|++||+|++|.|.. .|+||||+|++.++|++||++||++++.   ++  .|.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly   92 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY   92 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEE
Confidence            467889999999  578999999999999999999988766 5999999999999999999999999883   34  566


Q ss_pred             EEEee
Q psy2347          78 VEISR   82 (207)
Q Consensus        78 V~~a~   82 (207)
                      |.+++
T Consensus        93 ~~~~~   97 (345)
T 3tht_A           93 LNFVE   97 (345)
T ss_dssp             EEECS
T ss_pred             EEEee
Confidence            66663

>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=99.56  E-value=8.2e-15  Score=108.08  Aligned_cols=76  Identities=22%  Similarity=0.293  Sum_probs=67.5

Q ss_pred             CCcEEEEcCC--CcCC---cHHHHHHHHHhCCCeeEEEEeeCC---------CcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           8 RGTRVYVGGL--TETV---KKEDLELEFEKFGKLNSVWVAFNP---------PGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         8 ~~~~lfV~nL--p~~~---te~~L~~~F~~~G~V~~v~i~~d~---------rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ++++|+|.||  |.++   .+++|+++|++||+|++|+|+++.         ++++||+|+++++|++|++.||+..+.+
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            7889999998  3332   468999999999999999998761         3899999999999999999999999999


Q ss_pred             cEEEEEEeec
Q psy2347          74 SKLRVEISRG   83 (207)
Q Consensus        74 ~~l~V~~a~~   83 (207)
                      ++|+|+++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999865

>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=99.54  E-value=3.4e-15  Score=107.67  Aligned_cols=68  Identities=28%  Similarity=0.467  Sum_probs=59.4

Q ss_pred             EcCCCcCCcHHHHHHHH------------HhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347          14 VGGLTETVKKEDLELEF------------EKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus        14 V~nLp~~~te~~L~~~F------------~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      +.+||+++++++|+++|            ++||+|++|+|+++    +++||||+|+++++|++|++.||++.|.+++|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            34555666777777666            99999999999987    589999999999999999999999999999999


Q ss_pred             EEEe
Q psy2347          78 VEIS   81 (207)
Q Consensus        78 V~~a   81 (207)
                      |+++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9986

>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=99.54  E-value=1.4e-14  Score=119.98  Aligned_cols=80  Identities=28%  Similarity=0.354  Sum_probs=71.1

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCC-ceeC---CcEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMND-QDLM---GSKLRV   78 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g-~~i~---g~~l~V   78 (207)
                      .+.++|||.|||+++|+++|+++|++||+|+.|+|+.+    +++||||+|+++++|++||+.||+ ..+.   +++|.|
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            45789999999999999999999999999999999887    578999999999999999999954 4444   999999


Q ss_pred             EEeecCCC
Q psy2347          79 EISRGRGR   86 (207)
Q Consensus        79 ~~a~~k~~   86 (207)
                      +++++...
T Consensus       174 ~~~~~~~~  181 (261)
T 3sde_A          174 EPMEQFDD  181 (261)
T ss_dssp             EECCCEES
T ss_pred             eeccccCc
Confidence            99987543

>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=99.50  E-value=8.7e-14  Score=101.95  Aligned_cols=78  Identities=18%  Similarity=0.195  Sum_probs=67.4

Q ss_pred             CCCCcEEEEcCC--CcCC--------cHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           6 MERGTRVYVGGL--TETV--------KKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         6 ~~~~~~lfV~nL--p~~~--------te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      ..+++.|.|.|+  |.+.        .+++|+++|++||+|++|.|+++ +++++||+|+++++|++|++.||+.++.++
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            346778999987  2221        24588999999999999999887 689999999999999999999999999999


Q ss_pred             EEEEEEeec
Q psy2347          75 KLRVEISRG   83 (207)
Q Consensus        75 ~l~V~~a~~   83 (207)
                      +|+|+++.+
T Consensus        84 ~i~v~~~~~   92 (114)
T 3s6e_A           84 MITAAYVPL   92 (114)
T ss_dssp             ECEEEEECH
T ss_pred             EEEEEEEcH
Confidence            999999864

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.43  E-value=4.9e-13  Score=98.74  Aligned_cols=78  Identities=15%  Similarity=0.180  Sum_probs=70.6

Q ss_pred             CCCCCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcC-HHHHHHHHHhcC--CceeCCcEEEEE
Q psy2347           4 GMMERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSN-QIDAEAACDSMN--DQDLMGSKLRVE   79 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~-~e~A~~Al~~l~--g~~i~g~~l~V~   79 (207)
                      ..+++.+.|+|.||+++ +++++|+++|++|++|..|.++.+ .-.|||+|.+ +++|++|+++|+  +.+|++..++++
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g-~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~e   91 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   91 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecC-CCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEE
Confidence            46788999999999999 999999999999999999999998 4489999999 899999999995  678899999988


Q ss_pred             Eee
Q psy2347          80 ISR   82 (207)
Q Consensus        80 ~a~   82 (207)
                      +.+
T Consensus        92 vL~   94 (121)
T 1owx_A           92 VLE   94 (121)
T ss_dssp             ECC
T ss_pred             ECC
Confidence            764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=3.4e-13  Score=94.20  Aligned_cols=76  Identities=17%  Similarity=0.280  Sum_probs=65.1

Q ss_pred             CCCCcEEEEcCCCc----CCcH----HHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           6 MERGTRVYVGGLTE----TVKK----EDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         6 ~~~~~~lfV~nLp~----~~te----~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      =++..+|+|.-++.    ++.+    .+|++.|++||+|..++|+.+   .+||+|++.++|.+||+ ||+.+|.++.|+
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d---~~fVtF~d~~sAlaAi~-mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVED---KMWVTFLEGSSALNVLS-LNGKELLNRTIT   79 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSS---SEEEEESSHHHHHHGGG-GTTCEETTEEEE
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecC---CEEEEECChHHHHHHHh-cCCeEeCCeEEE
Confidence            35677888887662    2323    678999999999999999988   49999999999999998 999999999999


Q ss_pred             EEEeecCC
Q psy2347          78 VEISRGRG   85 (207)
Q Consensus        78 V~~a~~k~   85 (207)
                      |++++|.-
T Consensus        80 V~lkt~dW   87 (91)
T 2dnr_A           80 IALKSPSG   87 (91)
T ss_dssp             EEECCCSS
T ss_pred             EEeCCCCc
Confidence            99998753

>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=99.25  E-value=9e-12  Score=87.47  Aligned_cols=76  Identities=14%  Similarity=0.168  Sum_probs=64.7

Q ss_pred             CCCCCCcEEEEcCCCcC------CcH---HHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           4 GMMERGTRVYVGGLTET------VKK---EDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~------~te---~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      .+=++..||+|.-++..      ..+   .+|++.|++||+|+.++|+.|   -+||+|.+.++|.+||+ ||+.+|.++
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d---~~fVtF~d~~sAl~AI~-ldG~~v~Gr   85 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC---cEEEEEcChHHHHHHHh-cCCeeeCCe
Confidence            34577889999888632      221   568899999999999999988   49999999999999998 999999999


Q ss_pred             EEEEEEeec
Q psy2347          75 KLRVEISRG   83 (207)
Q Consensus        75 ~l~V~~a~~   83 (207)
                      .|+|++..+
T Consensus        86 ~L~V~~k~~   94 (95)
T 1ufw_A           86 AVKISGPSS   94 (95)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEeccCC
Confidence            999997654

>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=99.02  E-value=9.1e-10  Score=88.64  Aligned_cols=76  Identities=22%  Similarity=0.264  Sum_probs=63.1

Q ss_pred             CCcEEEEcCCC-----cCCcHHHHHHHHHhCCCeeEEEEeeC---------CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           8 RGTRVYVGGLT-----ETVKKEDLELEFEKFGKLNSVWVAFN---------PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         8 ~~~~lfV~nLp-----~~~te~~L~~~F~~~G~V~~v~i~~d---------~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      +...|.+.++-     .+-.+++|++.|++||+|++|.|+++         +++++||+|++.++|++|++.||+..+.+
T Consensus       123 ~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~g  202 (222)
T 3dxb_A          123 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG  202 (222)
T ss_dssp             BCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             ccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECC
Confidence            34455555542     23457889999999999999999854         46899999999999999999999999999


Q ss_pred             cEEEEEEeec
Q psy2347          74 SKLRVEISRG   83 (207)
Q Consensus        74 ~~l~V~~a~~   83 (207)
                      ++|.|+++..
T Consensus       203 r~i~~~~~~~  212 (222)
T 3dxb_A          203 RKVVAEVYDQ  212 (222)
T ss_dssp             SBCEEEECCH
T ss_pred             eEEEEEEcCH
Confidence            9999999754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.95  E-value=5e-09  Score=75.14  Aligned_cols=76  Identities=13%  Similarity=0.076  Sum_probs=69.0

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhC-----CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKF-----GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~-----G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ...+..++|-|-+||..++++.|+.+++++     +.|++|.++.| ..=|+|+|+|..+|-||.-+|++.+|.+++|+|
T Consensus        16 ~~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~   94 (117)
T 2l9w_A           16 NSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRS   94 (117)
T ss_dssp             CTTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             CCccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-CCceEEEEccchhhHHHHhhcCCeeecCeEEEe
Confidence            344557889999999999999999999999     99999999998 678999999999999999999999999999998


Q ss_pred             EE
Q psy2347          79 EI   80 (207)
Q Consensus        79 ~~   80 (207)
                      --
T Consensus        95 gT   96 (117)
T 2l9w_A           95 GT   96 (117)
T ss_dssp             EC
T ss_pred             cC
Confidence            64

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.62  E-value=4.4e-07  Score=64.37  Aligned_cols=77  Identities=29%  Similarity=0.280  Sum_probs=65.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhC-----CCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKF-----GKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~-----G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ....++|.|.|||++++++.|+-+|++-     |+|+.|+...   .-|+|+|.+.+.|+++|++ ..+.|++..|.|..
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~---~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~P   80 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLAQ-ADHELHGAQLSLRP   80 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET---TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEEE
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC---CcEEEEEcChHHHHHHhcC-CcceecCeEEEEEc
Confidence            3456799999999999999999999983     5788888764   5899999999999999975 58999999999987


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      ..++..
T Consensus        81 ~~~~~~   86 (104)
T 2dhx_A           81 APPRAP   86 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCc
Confidence            666544

>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=98.43  E-value=1.2e-06  Score=62.41  Aligned_cols=77  Identities=13%  Similarity=0.182  Sum_probs=65.6

Q ss_pred             CCcEEEEcCCCcCC-c----HHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETV-K----KEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~-t----e~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      -.++|+|.||+.++ +    .++++++|.+|.++.....++..+ -..|.|.++++|.+|-..||...+.+++|+|-++.
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR-Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YFgq   82 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK-RVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQ   82 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT-EEEEECSSTTHHHHHHHTSTTSEETTEECEEECCC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce-EEEEEeCChHHHHHHHHHhccceecCceeEEEecC
Confidence            35689999998765 2    257789999999999988887744 57899999999999999999999999999999997


Q ss_pred             cCC
Q psy2347          83 GRG   85 (207)
Q Consensus        83 ~k~   85 (207)
                      +.+
T Consensus        83 ~~~   85 (104)
T 1wey_A           83 TLH   85 (104)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            543

>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=98.12  E-value=1.5e-05  Score=58.13  Aligned_cols=73  Identities=14%  Similarity=0.202  Sum_probs=58.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC-cEEEEEEe
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG-SKLRVEIS   81 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g-~~l~V~~a   81 (207)
                      ....+.|.|-..|++.+ +.|.++|++||+|++..... ...+..|+|+++.+|++||.+ |++.|.+ ..|-|+..
T Consensus        21 ~~~~~wVtVFGFp~~~~-~~VL~~F~~~G~Iv~~~~~~-~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQASA-SYILLQFAQYGNILKHVMSN-TGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPC   94 (119)
T ss_dssp             CGGGGEEEEECCCGGGH-HHHHHHHHTTSCEEEEEECS-SSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEEC
T ss_pred             CCCCCEEEEECCCHHHH-HHHHHHHHhhCcEEEeccCC-CCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEEC
Confidence            34467888999998864 55667899999999988733 467999999999999999986 9999974 66777664

>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=98.08  E-value=1.3e-05  Score=55.89  Aligned_cols=64  Identities=20%  Similarity=0.222  Sum_probs=54.4

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ++|.|.+||+.+||+++.+.+....++.....+.-       .-.-|+|.|.+.|++....+.++++.+.+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            58999999999999999999999887776665443       23579999999999999999999998743

>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=97.99  E-value=2e-05  Score=55.32  Aligned_cols=57  Identities=23%  Similarity=0.283  Sum_probs=46.8

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN   67 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~   67 (207)
                      ...+.++| .+|+++...||.++|+.|+.| .|+.+.|  -.|||.|.+++.|..|+..++
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD--TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD--TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET--TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC--CeEEEEecCHHHHHHHHHhcc
Confidence            34556667 999999999999999999854 4555655  489999999999999998763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.77  E-value=4.6e-05  Score=53.53  Aligned_cols=76  Identities=18%  Similarity=0.142  Sum_probs=55.9

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCceeCCc----
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQDLMGS----   74 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~----   74 (207)
                      -..+.+|.|..||+.+||+++.+.+...-++.....+.-       .-.-|+|.|.+.|++....+.++++.+.+.    
T Consensus         6 ~~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~   85 (97)
T 2l08_A            6 HHHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLE   85 (97)
T ss_dssp             CCCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCE
T ss_pred             cccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCE
Confidence            345679999999999999999988877655433322211       225689999999999999999999887443    


Q ss_pred             -EEEEEEe
Q psy2347          75 -KLRVEIS   81 (207)
Q Consensus        75 -~l~V~~a   81 (207)
                       +..|++|
T Consensus        86 ~~a~VE~A   93 (97)
T 2l08_A           86 YPAVVEFA   93 (97)
T ss_dssp             EEEEEEEC
T ss_pred             eeeEEEec
Confidence             3445555

>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=97.73  E-value=2.3e-05  Score=55.14  Aligned_cols=57  Identities=21%  Similarity=0.185  Sum_probs=47.4

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN   67 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~   67 (207)
                      ...+.++| .+|+++...||.++|+.|+ -..|+.+.|  -.|||.|.+++.|..|+..+.
T Consensus         4 ~R~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD--TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            4 GSDHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD--TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET--TEEEEEEEEECHHHHHHHHHT
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC--CeEEEEecCHHHHHHHHHhcc
Confidence            34456677 9999999999999999998 445666665  489999999999999999764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.60  E-value=5.5e-05  Score=55.89  Aligned_cols=75  Identities=20%  Similarity=0.163  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEee-------------C-----CCcEEEEEEcCHHHHHHHHHhcC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAF-------------N-----PPGFAFVEFSNQIDAEAACDSMN   67 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~-------------d-----~rG~afV~F~~~e~A~~Al~~l~   67 (207)
                      .....|.|-+.|++.+...| ++|++||.|++ +.+..             .     ...+..|+|+++.+|++||.. |
T Consensus         5 ~~e~~VtVFGFp~~~~~~VI-~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETMANQVI-AYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-N   82 (132)
T ss_dssp             ---CEEEEECCCGGGHHHHH-HHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-T
T ss_pred             cCceEEEEEecCHHHHHHHH-HHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-C
Confidence            44567788899887765555 68999999876 22111             0     246889999999999999986 9


Q ss_pred             CceeCCcEEEEEEeec
Q psy2347          68 DQDLMGSKLRVEISRG   83 (207)
Q Consensus        68 g~~i~g~~l~V~~a~~   83 (207)
                      ++.|.+..|-|...++
T Consensus        83 G~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYTK   98 (132)
T ss_dssp             TCEETTEECEEEECCH
T ss_pred             CeEeCcEEEEEEECCH
Confidence            9999998888887653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=97.47  E-value=4.8e-05  Score=67.68  Aligned_cols=56  Identities=16%  Similarity=0.224  Sum_probs=44.9

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHh
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS   65 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~   65 (207)
                      .++|||. +|.++++++|.++|++||+|.++.+-++..-||.|||.++++|+++++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHHHHHHHhc
Confidence            4789997 8999999999999999999999988888778999999999999988754

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.54  E-value=0.0013  Score=49.24  Aligned_cols=32  Identities=16%  Similarity=0.109  Sum_probs=26.1

Q ss_pred             EEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCc
Q psy2347          38 SVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQ   69 (207)
Q Consensus        38 ~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~   69 (207)
                      .++|+++   +++|+||+|.++++|++|++.++..
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            3455555   7899999999999999999887653

>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=96.44  E-value=0.00095  Score=49.76  Aligned_cols=39  Identities=18%  Similarity=0.152  Sum_probs=35.7

Q ss_pred             CCcEEEEEEcCHHHHHHHHHhc-CCceeCCcEEEEEEeecC
Q psy2347          45 PPGFAFVEFSNQIDAEAACDSM-NDQDLMGSKLRVEISRGR   84 (207)
Q Consensus        45 ~rG~afV~F~~~e~A~~Al~~l-~g~~i~g~~l~V~~a~~k   84 (207)
                      .+++++|+|.++++|++|+++| |+.+|++ .|.|++++++
T Consensus        12 l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A           12 LKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             SCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             ccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            6899999999999999999999 9999999 9999987653

>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=95.24  E-value=0.04  Score=49.45  Aligned_cols=57  Identities=23%  Similarity=0.227  Sum_probs=45.8

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND   68 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g   68 (207)
                      ....++|. +|..+...+|.++|+.|+. .+|..+.+  -.|||.|.++++|..++++++.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd--t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD--TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS--SEEEEECSCHHHHHHHHHHHTT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC--CeEEEEECCHHHHHHHHHHHHh
Confidence            45566666 8888999999999999995 45555544  5799999999999999998753

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=94.47  E-value=0.09  Score=34.43  Aligned_cols=68  Identities=18%  Similarity=0.308  Sum_probs=44.5

Q ss_pred             EEEEcC-CCcCCcHHHHHHHHHhCCC-----eeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          11 RVYVGG-LTETVKKEDLELEFEKFGK-----LNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        11 ~lfV~n-Lp~~~te~~L~~~F~~~G~-----V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +|||.. -...++..+|..++..-..     |-.|+|..+   |.||+-.. +.|+++++.|+...+.+++|.|+.++
T Consensus         2 ~~~i~~Grk~~~~p~~ivg~i~~~~gi~~~~IG~I~i~d~---~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A            2 KLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDN---ASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             EEEESCCCC----CHHHHHHHHTSTTCCGGGEEEEEECSS---CEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC
T ss_pred             EEEEeCCCccCCCHHHHHHHHHHccCCChhhccEEEEeCC---cEEEEECH-HHHHHHHHHhccccCcCceEEEEECC
Confidence            566632 1345677788888876544     556777644   89999876 45778888899999999999998764

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=90.97  E-value=1.6  Score=29.98  Aligned_cols=72  Identities=14%  Similarity=0.179  Sum_probs=52.9

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCc-------eeCCcEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ-------DLMGSKLR   77 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~-------~i~g~~l~   77 (207)
                      .....+-|-|-|||..+-.+++.-.....+---.|..+   .+-|.|.|.+.++...|+.+|-.+       +|.+..+.
T Consensus         8 sikqnclikiinipqgtlkaevvlavrhlgyefycdyi---dgqamirfqnsdeqrlaiqkllnhnnnklqieirgqicd   84 (129)
T 4eyt_A            8 SIKQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI---DGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIRGQICD   84 (129)
T ss_dssp             --CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC---SSCEEEEESSHHHHHHHHHHHEETTTTEEEEEETTEEEE
T ss_pred             hhhhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee---cCeeEEEecCChHHHHHHHHHHhcCCCEEEEEEcceeee
Confidence            34567888899999999998888777777776666665   468999999999988888765332       34555555


Q ss_pred             EE
Q psy2347          78 VE   79 (207)
Q Consensus        78 V~   79 (207)
                      |-
T Consensus        85 vi   86 (129)
T 4eyt_A           85 VI   86 (129)
T ss_dssp             EE
T ss_pred             ee
Confidence            54

>2cu1_A Mitogen-activated protein kinase kinase kinase 2; PB1 domain, MAPK/ERK kinase kinase 2, MEK kinase 2, MEKK 2, signaling protein; NMR {Homo sapiens} SCOP: d.15.2.2

Probab=84.72  E-value=2.4  Score=29.41  Aligned_cols=67  Identities=18%  Similarity=0.218  Sum_probs=47.2

Q ss_pred             CCCcCCcHHHHHHHH-HhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCC
Q psy2347          16 GLTETVKKEDLELEF-EKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGR   86 (207)
Q Consensus        16 nLp~~~te~~L~~~F-~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~   86 (207)
                      .++..++-+||+... +.||.-.++..+.+   .+.|-..+.++.++||+.|+.. ..-+.|+|-+..++..
T Consensus        23 ~f~RPv~f~eL~~Kv~~~fGq~ldL~y~n~---EllIpl~sQeDLDkaIellDrs-s~~kSLrIlL~~~~~~   90 (103)
T 2cu1_A           23 QFPRPVKLEDLRSKAKIAFGQSMDLHYTNN---ELVIPLTTQDDLDKAVELLDRS-IHMKSLKILLVINGST   90 (103)
T ss_dssp             EEESSCCHHHHHHHHHHHHSSCEEEEECSS---SSCEECCSHHHHHHHHHHHHHC-SSCCSEEEEEEECCCC
T ss_pred             eccCCccHHHHHHHHHHHhCCeeeEEEecc---eEEEeccCHHHHHHHHHHHccC-CcccceEEEEecCCCC
Confidence            356677777776554 45888888877743   5788999999999999987644 3444566666666543

>3fry_A Probable copper-exporting P-type ATPase A; transport protein, metal binding domain, domain SWAP, ATP-BI cell membrane, copper transport; HET: CIT; 2.00A {Archaeoglobus fulgidus}

Probab=82.74  E-value=3.6  Score=25.64  Aligned_cols=56  Identities=11%  Similarity=-0.004  Sum_probs=42.7

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM   66 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l   66 (207)
                      ..+|.|.++.-..=...|++.+.+ -.|..+.+... ...+.|+|++.++..++|+.+
T Consensus         6 ~~~~~v~gm~C~~C~~~ie~~l~~-~gv~~~~v~~~-~~~~~v~~~~~~~i~~~i~~~   61 (73)
T 3fry_A            6 KIVLELSGLSCHHCVARVKKALEE-AGAKVEKVDLN-EAVVAGNKEDVDKYIKAVEAA   61 (73)
T ss_dssp             EEEEEEESSBCGGGHHHHHHHHHH-TTCEEEEECSS-EEEEEEEGGGHHHHHHHHHHT
T ss_pred             EEEEEECCCCCHHHHHHHHHHhcc-CCcEEEEEEcc-CCEEEEEECCHHHHHHHHHHc
Confidence            357888888766667888999999 78888877654 457788888777777888763

---

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	207
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	7e-18
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-16
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-16
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-16
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-16
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-15
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	4e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-14
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-14
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-14
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-13
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-13
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-13
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-12
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-12
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	5e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	7e-12
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-12
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-11
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-11
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-11
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	6e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	7e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-10
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	9e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-09
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-08
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	8e-08
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-07
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-07
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	5e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	8e-07
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04

>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 = 73.1 bits (179), Expect = 7e-18
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 5  MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDA 59
          ++++   +YVG L+    +E +   F K G +  + +  +       GF FVE+ ++ DA
Sbjct: 3  LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADA 62

Query: 60 EAACDSMNDQDLMGSKLRVEISRGRGRGR 88
          E A   +N   L    +R +   G   GR
Sbjct: 63 ENAMRYINGTRLDDRIIRTDWDAGFKEGR 91

>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 = 70.0 bits (171), Expect = 1e-16
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 7/87 (8%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAE 60
          +  +++ V  +     + ++   F  FG+L +V +           GF FV+F  + DA+
Sbjct: 6  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 61 AACDSM-NDQDLMGSKLRVEISRGRGR 86
           A +++ +   L G +L +E +     
Sbjct: 66 KAFNALCHSTHLYGRRLVLEWADSEVT 92

>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 = 70.0 bits (171), Expect = 1e-16
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +   VY GG+   +  + +   F  FG++  + V F   G++FV FS    A  A  S+N
Sbjct: 17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKGYSFVRFSTHESAAHAIVSVN 75

Query: 68 DQDLMGSKLRVEISRGR 84
             + G  ++    +  
Sbjct: 76 GTTIEGHVVKCYWGKES 92

>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 = 68.0 bits (166), Expect = 5e-16
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVA-----FNPPGFAFVEFSNQIDAEAACDSM 66
          +YVG L   V +  L  +F   G + S+ V          G+A+V F    DAE A D+M
Sbjct: 3  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 67 NDQDLMGSKLRVEISR 82
          N   + G  +R+  S+
Sbjct: 63 NFDVIKGKPVRIMWSQ 78

>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 = 68.5 bits (167), Expect = 6e-16
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP--GFAFVEFSNQIDAEAACD 64
          E    +Y+  L   +  E++   F K+G +  + V   P   G A+V + +  DA+ ACD
Sbjct: 5  EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 65 SMNDQDLMGSKLRVEISRGR 84
           ++  ++    L V      
Sbjct: 65 HLSGFNVCNRYLVVLYYNAN 84

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 66.6 bits (162), Expect = 2e-15
 Identities = 16/84 (19%), Positives = 37/84 (44%)

Query: 6  MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
          +     +    L+  + +++L+  FE   ++  V       G A++EF ++ DAE   + 
Sbjct: 13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 66 MNDQDLMGSKLRVEISRGRGRGRG 89
              ++ G  + +  +  +G  RG
Sbjct: 73 KQGAEIDGRSVSLYYTGEKGGTRG 96

>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 = 64.9 bits (158), Expect = 9e-15
 Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 4/89 (4%)

Query: 7  ERGTRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
             +RV++G L T  VKK D+E  F K+GK+    V     GFAFV++ N+ +A AA   
Sbjct: 13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV---HKGFAFVQYVNERNARAAVAG 69

Query: 66 MNDQDLMGSKLRVEISRGRGRGRGGGGRG 94
           + + + G  L + ++      R G   G
Sbjct: 70 EDGRMIAGQVLDINLAAEPKVNRSGPSSG 98

>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 = 64.3 bits (156), Expect = 1e-14
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEAACDS 65
          ++++GGL   +  + ++     FG L +  +  +       G+AF E+ +    + A   
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 66 MNDQDLMGSKLRVEISRGRGRG 87
          +N   L   KL V+ +    + 
Sbjct: 63 LNGMQLGDKKLLVQRASVGAKN 84

>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 = 63.4 bits (154), Expect = 2e-14
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKL-----NSVWVAFNPPGFAFVEFSNQIDAEAA 62
          + T +YV  L  T+  + L+  F K+G +         +   P G AFV ++ + +A+ A
Sbjct: 5  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 63 CDSMNDQDLMGSKLRVEISR 82
            ++N+    G    + +  
Sbjct: 65 ISALNNVIPEGGSQPLSVRL 84

>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 = 63.0 bits (153), Expect = 3e-14
 Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 4/75 (5%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP----PGFAFVEFSNQIDAEAACDSM 66
          ++ V  L   V   D++  F +FG L    V ++      G A V F  + DA  A    
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 67 NDQDLMGSKLRVEIS 81
          N   L G  + +++ 
Sbjct: 62 NGVPLDGRPMNIQLV 76

>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 = 63.1 bits (153), Expect = 4e-14
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 13 YVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP--------GFAFVEFSNQIDAEAACD 64
          ++  L  +  +E L+  F K G + S  ++            GF FVE+     A+ A  
Sbjct: 2  FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 65 SMNDQDLMGSKLRVEISRGRGR 86
           +    + G KL V IS    +
Sbjct: 62 QLQGHTVDGHKLEVRISERATK 83

>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 = 63.1 bits (153), Expect = 4e-14
 Identities = 30/85 (35%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 5  MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDA 59
          M      +YVGGL E V  + L   F  FG +  + +  +       GFAFVEF    DA
Sbjct: 1  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 60 EAACDSMNDQDLMGSKLRVEISRGR 84
           AA D+MN+ +L G  +RV +++  
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAKPM 85

>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 = 63.1 bits (153), Expect = 4e-14
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVW-----VAFNPPGFAFVEFSNQIDAEAA 62
          R   +YV GL +T+ +++LE  F ++G++ +       V     G  F+ F  +I+AE A
Sbjct: 5  RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 63 CDSMNDQDLMGSKLRVEIS 81
             +N Q   G+   + + 
Sbjct: 65 IKGLNGQKPSGATEPITVK 83

>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 = 62.7 bits (152), Expect = 5e-14
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 6  MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
          M     +YV  L  +  +E +E EF          V      +AFV FSN+ DA  A  +
Sbjct: 5  MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-KKIRDYAFVHFSNREDAVEAMKA 63

Query: 66 MNDQDLMGSKLRVEISRGRGRG 87
          +N + L GS + V +++   + 
Sbjct: 64 LNGKVLDGSPIEVTLAKPVDKD 85

>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 = 62.7 bits (152), Expect = 5e-14
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
          T + V  L + +   +L   F   G +N+  +  +       G+AFV+F++++D++ A  
Sbjct: 3  TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 65 SMNDQDLMGSKLRVEISR 82
           +N   +   +L+V  +R
Sbjct: 63 VLNGITVRNKRLKVSYAR 80

>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 = 62.7 bits (152), Expect = 6e-14
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          +R++VG L   + +E++   FEK+GK   V++     GF F+    +  AE A   +++ 
Sbjct: 9  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-HKDKGFGFIRLETRTLAEIAKVELDNM 67

Query: 70 DLMGSKLRVEISR 82
           L G +LRV  + 
Sbjct: 68 PLRGKQLRVRFAC 80

>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 = 62.8 bits (152), Expect = 6e-14
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVA-----FNPPGFAFVEFSNQIDAEAACD 64
            + V  L+E  ++ DL+  F  FG ++ +++A         GFAF+ F  + DA  A  
Sbjct: 9  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 65 SMNDQDLMGSKLRVEISRGR 84
           ++        L VE ++  
Sbjct: 69 GVSGFGYDHLILNVEWAKPS 88

>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 = 62.4 bits (151), Expect = 9e-14
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 10 TRVYVGGLTETVKKEDLELE----FEKFGKLNS--VWVAFNPPGFAFVEFSNQIDAEAAC 63
            +Y+  L E +KK++L+      F +FG++    V  +    G AFV F     A  A 
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 64 DSMNDQDLMGSKLRVEISRGR 84
           SM         +R++ ++  
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTD 84

>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 = 62.0 bits (150), Expect = 1e-13
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSM 66
           R++V  +    +  DL   F +FGK+  V + FN     GF FV F N  DA+ A + +
Sbjct: 12 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 71

Query: 67 NDQDLMGSKLRVEISRGRGR 86
          +   + G K+ V  +  R  
Sbjct: 72 HGTVVEGRKIEVNNATARVM 91

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 2e-13
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 4/85 (4%)

Query: 1   MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQ 56
            +DG+    + V +    +   +E      EK+G++  + V  N         +V+F  +
Sbjct: 19  SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRRE 78

Query: 57  IDAEAACDSMNDQDLMGSKLRVEIS 81
            DAE A   +N++   G  +  E+S
Sbjct: 79  EDAEKAVIDLNNRWFNGQPIHAELS 103

>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 = 61.6 bits (149), Expect = 2e-13
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 5  MME---RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP---PGFAFVEFSNQID 58
          MME   +   +YVG L+  V +  +   F + G   S  +         + FVEF    D
Sbjct: 1  MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRD 60

Query: 59 AEAACDSMNDQDLMGSKLRVEISR 82
          A AA  +MN + ++G +++V  + 
Sbjct: 61 AAAALAAMNGRKILGKEVKVNWAT 84

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (148), Expect = 2e-13
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 5/78 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACD 64
          T + V  L + + +E+    F   G++ S  +  +       G+ FV + +  DAE A +
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 65 SMNDQDLMGSKLRVEISR 82
          ++N   L    ++V  +R
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80

>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 = 61.2 bits (148), Expect = 2e-13
 Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-----VWVAFNPPGFAFVEFSNQIDAEA 61
           +   VYVGGL E V +  L   F + G + +       V     G+ FVEF ++ DA+ 
Sbjct: 7  NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 62 ACDSMNDQDLMGSKLRVEISRGRGR 86
          A   M+   L G  +RV  +    +
Sbjct: 67 AIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 61.1 bits (148), Expect = 3e-13
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 6  MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAE 60
          +++ + + V GL     ++DL+  F  FG++  V V  +       GF FV F+      
Sbjct: 5  VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 64

Query: 61 AACDSMNDQDLMGSKLRVEISRGR 84
                +   + G     ++   +
Sbjct: 65 KVMSQRH--MIDGRWCDCKLPNSK 86

>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 = 58.8 bits (142), Expect = 1e-12
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
          ++++GGL+    K+DL+  F KFG++    +  +P      GF FV F      +   D 
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD- 59

Query: 66 MNDQDLMGSKLRVE 79
            +  L G  +  +
Sbjct: 60 QKEHKLNGKVIDPK 73

>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 = 59.4 bits (143), Expect = 1e-12
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 13/89 (14%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVA-------------FNPPGFAFVEFSN 55
           + +YV GL ++V  +DL   F++ G +                     P G A V + +
Sbjct: 8  NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 56 QIDAEAACDSMNDQDLMGSKLRVEISRGR 84
             A+AA +  + +D  GSKL+V ++R +
Sbjct: 68 PPTAKAAVEWFDGKDFQGSKLKVSLARKK 96

>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 = 58.9 bits (142), Expect = 2e-12
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          + V+VG  T  + +++L   F ++G +  V++      FAFV F++   A++ C    D 
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDL 63

Query: 70 DLMGSKLRVEISRGRGRGRGGGGRG 94
           + G  + +  +  +     G   G
Sbjct: 64 IIKGISVHISNAEPKHNSNSGPSSG 88

>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 = 58.5 bits (141), Expect = 2e-12
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG---FAFVEFSNQIDAEAACDSM 66
            +++  L +++  + L   F  FG + S  V  +  G   + FV F  Q  AE A + M
Sbjct: 9  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 68

Query: 67 NDQDLMGSKLRVEISRGR 84
          N   L   K+ V   + R
Sbjct: 69 NGMLLNDRKVFVGRFKSR 86

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 3e-12
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSV-------WVAFNPPGFAFVEFSNQIDAEAA 62
           R+++GG+ +  K+E++  E  K  +                  GFAFVE+ +   A  A
Sbjct: 2  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 63 CDSMNDQD--LMGSKLRVEISRGR 84
             +      L G ++ V+ +   
Sbjct: 62 RRKLMPGRIQLWGHQIAVDWAEPE 85

>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 = 57.7 bits (139), Expect = 3e-12
 Identities = 15/75 (20%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
          +++VGGL+    +E +   F  FG++ S+ +  +       GF F+ F  +   +   + 
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59

Query: 66 MNDQDLMGSKLRVEI 80
              ++  SK  +++
Sbjct: 60 KKYHNVGLSKCEIKV 74

>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 = 57.3 bits (138), Expect = 4e-12
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNP-----PGFAFVEFSNQIDAEAACDS 65
          ++++GGL+    +E L   F +FG++    V  +P      GF FV F +Q   +    +
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 66 MNDQDLMGSKLRVEI 80
           +  +L    +  ++
Sbjct: 61 QSRHELDSKTIDPKV 75

>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 = 58.8 bits (141), Expect = 5e-12
 Identities = 24/112 (21%), Positives = 45/112 (40%), Gaps = 18/112 (16%)

Query: 7   ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGF-----AFVEFSNQIDAEA 61
           +    + V  +  TV +  L   FE++G + SV +  +          FV+F +   A+ 
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 62  ACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRGGYRGGGGGY 113
           A   +N  +++  +L+V ++    +             R G  G  G G GY
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQ-------------RPGIAGAVGDGNGY 138

>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 = 57.4 bits (138), Expect = 5e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 12 VYVGGLTETVKKEDLELEFEKFG------KLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
          +++G L   + ++ L   F  FG      K+       N  G+AF+ F++   ++AA ++
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 66 MNDQDLMGSKLRVEISRGRG-RG 87
          MN Q L    + V  +  +  +G
Sbjct: 61 MNGQYLCNRPITVSYAFKKDSKG 83

>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 = 57.0 bits (137), Expect = 7e-12
 Identities = 17/82 (20%), Positives = 45/82 (54%), Gaps = 5/82 (6%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAAC 63
          G  ++V  + E  ++++++ +F  +G++ ++ +  +       G+A VE+     A AA 
Sbjct: 7  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 66

Query: 64 DSMNDQDLMGSKLRVEISRGRG 85
          +++N  ++MG  ++V+    +G
Sbjct: 67 EALNGAEIMGQTIQVDWCFVKG 88

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (138), Expect = 8e-12
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 23 KEDLELEFEKFGKLNSVWVAFNPP-GFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS 81
          +EDL +E  KFG++  + +    P G A V F +  +A+    +++ +   G ++  +  
Sbjct: 33 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

Query: 82 RGR 84
           G 
Sbjct: 93 DGT 95

>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 = 56.7 bits (136), Expect = 9e-12
 Identities = 8/78 (10%), Positives = 28/78 (35%), Gaps = 5/78 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKL-----NSVWVAFNPPGFAFVEFSNQIDAEAACD 64
            +++     +  + ++    +    +                FA+++ +++ DA    +
Sbjct: 2  CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 65 SMNDQDLMGSKLRVEISR 82
           +N   + G  L  ++S 
Sbjct: 62 KLNGLKIEGYTLVTKVSN 79

>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 = 56.7 bits (136), Expect = 1e-11
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 11/91 (12%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEA 61
            G  V++  L+   ++E L    ++FG L  V V  +       G AF +F  Q  A+ 
Sbjct: 6  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 62 ACDSMNDQ------DLMGSKLRVEISRGRGR 86
             + + +       L G +L+V+++  R  
Sbjct: 66 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 1e-11
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 3/78 (3%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM 66
           +G  +YV G    +    L   F  FG +  + +   P   AFV +     A+ A   +
Sbjct: 3  RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-DPPRNCAFVTYEKMESADQAVAEL 59

Query: 67 NDQDLMGSKLRVEISRGR 84
          N   +   +L+V I+R +
Sbjct: 60 NGTQVESVQLKVNIARKQ 77

>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 = 56.7 bits (136), Expect = 1e-11
 Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 4/77 (5%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN 67
          +   V  GGL   V +  L    EK G ++++ +  N P ++F  +    +++ A  ++N
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-YSFARYRTTEESKRAYVTLN 77

Query: 68 DQDLM---GSKLRVEIS 81
           ++++   G K+ + ++
Sbjct: 78 GKEVVDDLGQKITLYLN 94

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEA 61
          E+  ++++GGL+    +E L   +E++GKL    V  +P      GF FV FS+  + +A
Sbjct: 18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 77

Query: 62 ACDSMNDQDLMGSKLRVEISRGR 84
          A  +     + G  +  + +  R
Sbjct: 78 AM-AARPHSIDGRVVEPKRAVAR 99

>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 = 56.6 bits (136), Expect = 2e-11
 Identities = 18/76 (23%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
           R+ V  L   V  + L   F KFG +   +    N    A +++++ + A+ A  S++ 
Sbjct: 8  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDG 67

Query: 69 QDL--MGSKLRVEISR 82
          Q++      LR++ S+
Sbjct: 68 QNIYNACCTLRIDFSK 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 = 55.8 bits (134), Expect = 3e-11
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 7  ERGTR-VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAE 60
          ER  R V+   L   ++  DLE  F   GK+  V +  +       G A+VEF       
Sbjct: 15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 61 AACDSMNDQDLMGSKLRVEISRGR 84
               +  Q L+G  + V+ S+  
Sbjct: 75 -LAIGLTGQRLLGVPIIVQASQAE 97

>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 = 54.7 bits (131), Expect = 4e-11
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 6/74 (8%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFG-----KLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
          +++VGGL+     ED++  FE+FG      L          GF FV F ++   E  C+ 
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59

Query: 66 MNDQDLMGSKLRVE 79
          ++  ++    +  +
Sbjct: 60 IHFHEINNKMVECK 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 = 54.7 bits (131), Expect = 6e-11
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEA 61
          +    + V GL+    + DL   F K+G +  V + ++       GFAFV F N  DA+ 
Sbjct: 7  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 62 ACDSMNDQDLMGSKLRV 78
          A +  N  +L G ++RV
Sbjct: 67 AKERANGMELDGRRIRV 83

>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 = 54.7 bits (131), Expect = 7e-11
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 9   GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAAC 63
           G  +++  L +    +DL   F  FG + S  V  +        F FV + N + A+AA 
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 64  DSMNDQDLMGSKLRVEISRGRGRGR 88
            SMN   +   +L+V++ R +   +
Sbjct: 78  QSMNGFQIGMKRLKVQLKRSKNDSK 102

>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 = 53.5 bits (128), Expect = 1e-10
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG-----FAFVEFSNQIDAEA 61
          E+  ++++GGL+     E L   FE++G L    V  +P       F FV ++   + +A
Sbjct: 4  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 62 ACDSMNDQDLMGSKLRVE 79
          A +      + G  +  +
Sbjct: 64 AMN-ARPHKVDGRVVEPK 80

>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 = 53.2 bits (127), Expect = 2e-10
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ- 69
          ++Y+G L+  V  +DL   F       +  V     G+AFV++ +Q  A  A ++++ + 
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSGYAFVDYPDQNWAIRAIETLSGKV 61

Query: 70 DLMGSKLRVEISRGRGR 86
          +L G  + V+ S  +  
Sbjct: 62 ELHGKIMEVDYSVSKKL 78

>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 = 52.4 bits (125), Expect = 3e-10
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 6/76 (7%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG-----FAFVEFSNQIDAEAACDS 65
          +++VGG+ E  ++  L   FE++GK+  + +  +        FAFV F +  D+      
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVI 62

Query: 66 MNDQDLMGSKLRVEIS 81
               + G    V  +
Sbjct: 63 QKYHTVNGHNCEVRKA 78

>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 = 53.2 bits (127), Expect = 3e-10
 Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 11/100 (11%)

Query: 3   DGMMERGTR-VYVGGLTETVKKEDLE-----LEFEKFGKLNSVWVAFNPPGFAFVEFSNQ 56
           D  ++R  R V+VG +     +E L+     +      +L        P G+ F E+ +Q
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 57  IDAEAACDSMNDQDLMGSKLRVEIS-----RGRGRGRGGG 91
             A +A  ++N ++  G  LRV+ +     +   +  G G
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 52.1 bits (124), Expect = 6e-10
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 5  MMERGTRVYVGGLTETVKKEDLELEFEKFG-----KLNSVWVAFNPPGFAFVEFSNQIDA 59
          M     +++VGGL+    ++ LE  F K+G      +          GF FV F N  DA
Sbjct: 1  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 60 EAACDSMNDQDLMGSKLRVEISRGRGRGR 88
          + A  +MN + + G ++RV+ +      R
Sbjct: 61 KDAMMAMNGKSVDGRQIRVDQAGKSSDNR 89

>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 = 52.4 bits (125), Expect = 6e-10
 Identities = 27/91 (29%), Positives = 38/91 (41%), Gaps = 5/91 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
           R++V  L+ T  +EDLE  F  +G L+ +    +     P GFAFV F     A  A  
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 65 SMNDQDLMGSKLRVEISRGRGRGRGGGGRGG 95
           ++ Q   G  L V  S  +      G   G
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKKEASQSGPSSG 99

>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 = 51.7 bits (123), Expect = 9e-10
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 8/83 (9%)

Query: 9  GTRVYVGGLTETVKKED-LELEFEKFGKLNSVWVAFNPPG------FAFVEFSNQIDAEA 61
          G  + +  L+  +  E+ L   FE FG +  + +             AF+ F N+  AE 
Sbjct: 4  GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 62 ACDSMNDQDLMGSKLRVEISRGR 84
          A   MN   L   ++ V ++  +
Sbjct: 64 AL-QMNRSLLGNREISVSLADKK 85

>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 = 51.3 bits (122), Expect = 2e-09
 Identities = 24/93 (25%), Positives = 38/93 (40%), Gaps = 9/93 (9%)

Query: 10  TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACD 64
           T+++VGGL        L   FE FG +    V  +       G+ FV  +++  AE AC 
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 65  SMNDQDLMGSKLRVEISRGRGR---GRGGGGRG 94
             N   + G K  V ++    +    + G   G
Sbjct: 71  DPN-PIIDGRKANVNLAYLGAKPRSLQTGFAIG 102

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 1/96 (1%)

Query: 10  TRVYVGGL-TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
           + + V  L  E V  + L + F  +G +  V + FN    A V+ ++   A+ A   +N 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 62

Query: 69  QDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRG 104
             L G  +R+ +S+ +       G+  +  ++    
Sbjct: 63  HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGN 98

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.6 bits (120), Expect = 3e-09
 Identities = 11/80 (13%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 10 TRVYVGGL-----TETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACD 64
          + +          +E+  +   E  F  + K  +    F       + FSN + A  A  
Sbjct: 6  SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQY-FKSFKRVRINFSNPLSAADARL 64

Query: 65 SMNDQDLMGSKLRVEISRGR 84
           ++  + +G ++++  ++  
Sbjct: 65 RLHKTEFLGKEMKLYFAQTL 84

>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 = 50.1 bits (119), Expect = 3e-09
 Identities = 13/85 (15%), Positives = 25/85 (29%), Gaps = 2/85 (2%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          + + V  L +    +++    + +               AFV   N   A+ A    +  
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV--DRNKRTAFVTLLNGEQAQNAIQMFHQY 63

Query: 70 DLMGSKLRVEISRGRGRGRGGGGRG 94
             G  L V++         G   G
Sbjct: 64 SFRGKDLIVQLQPTDALLCSGPSSG 88

>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 = 49.8 bits (118), Expect = 6e-09
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEA 61
          E    +Y+  L+  V + DL   F +F +     + F        G AF+ F N+  A  
Sbjct: 16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 62 ACDSMNDQDLMGSKLRVEISRGR 84
          A   +N   L G  L +E  + +
Sbjct: 76 ALHLVNGYKLYGKILVIEFGKNK 98

>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 = 51.2 bits (121), Expect = 7e-09
 Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 1   MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSN 55
              G      +++VGG+ E  ++  L   FE++GK+  + +  +       GFAFV F +
Sbjct: 89  QRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148

Query: 56  QIDAEAACDSMNDQDLMGSKLRVEISRGR 84
               +          + G    V  +  +
Sbjct: 149 HDSVDKIVI-QKYHTVNGHNCEVRKALSK 176

>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 = 43.5 bits (101), Expect = 4e-06
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQIDAEA 61
          E+  ++++GGL+     E L   FE++G L    V  +P      GF FV ++   + +A
Sbjct: 4  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 62 ACDSMN 67
          A ++  
Sbjct: 64 AMNARP 69

>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 = 47.8 bits (113), Expect = 1e-08
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 5/71 (7%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNS-----VWVAFNPPGFAFVEFSNQIDAEAACDSM 66
          +Y+ GL      +DL    + +GK+ S             G+ FV+F +   A+ A  ++
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 67 NDQDLMGSKLR 77
              +     +
Sbjct: 61 KASGVQAQMAK 71

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 10/77 (12%), Positives = 23/77 (29%), Gaps = 4/77 (5%)

Query: 10 TRVYVGGLTETVKKEDLE----LEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
          T +Y+  L  ++ +++LE       +          +    G  F    +    EA    
Sbjct: 19 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 66 MNDQDLMGSKLRVEISR 82
           N + +         + 
Sbjct: 79 FNGKFIKTPPGVSAPTE 95

>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 = 47.9 bits (113), Expect = 2e-08
 Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
            +++  L E   +  L + F +F     V +  N    AFVEF+ ++ + AA +++   
Sbjct: 9  QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGF 68

Query: 70 DLMGSK-LRVEISR 82
           +  +  +++  ++
Sbjct: 69 KITPTHAMKITFAK 82

>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 = 47.0 bits (111), Expect = 4e-08
 Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 5/76 (6%)

Query: 8  RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAAC 63
          +   VY+ G       +D++   E  G++ ++ +            FV F +   A+   
Sbjct: 5  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 64

Query: 64 DSMNDQDLMGSKLRVE 79
          +    Q    + L + 
Sbjct: 65 E-TPGQKYKETDLLIL 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 = 46.6 bits (110), Expect = 6e-08
 Identities = 32/85 (37%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVA--FNPPGFAFVEFSNQIDAEAACD 64
              R+YVG L   ++ +D+E  F K+G +  + +      P FAFVEF +  DAE A  
Sbjct: 12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVY 71

Query: 65 SMNDQDLMGSKLRVEISRGRGRGRG 89
            +  D  G +LRVE  R  GRG G
Sbjct: 72 GRDGYDYDGYRLRVEFPRS-GRGTG 95

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.1 bits (109), Expect = 8e-08
 Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 4/73 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          T V V G  +      L  +F ++G +    +  N   +  + + +++ A  A  S + +
Sbjct: 5  TWVTVFGFPQASASYILL-QFAQYGNILKHVM-SNTGNWMHIRYQSKLQARKAL-SKDGR 61

Query: 70 DLMGSKLRVEISR 82
                + + +  
Sbjct: 62 IFGE-SIMIGVKP 73

>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 = 44.9 bits (105), Expect = 2e-07
 Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL 71
          + + GL   V  +++      +             G AFV   N   AEAA ++ +   L
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDYE--LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRL 58

Query: 72 MGSKLRVEISR 82
             +L V++  
Sbjct: 59 RERELSVQLQP 69

>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 = 45.4 bits (107), Expect = 2e-07
 Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 1/81 (1%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ 69
          TR++VGGL        L  EF++FG + ++        FA++++ +   A+AAC  M   
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH-VKGDSFAYIQYESLDAAQAACAKMRGF 76

Query: 70 DLMGSKLRVEISRGRGRGRGG 90
           L G   R+ +   +     G
Sbjct: 77 PLGGPDRRLRVDFAKSGPSSG 97

>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 = 44.8 bits (105), Expect = 2e-07
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP---GFAFVEFSNQIDAEAACDSM 66
          T V V  L ++  +  +   F+  G +  V VA +      FA +EF+    A  A  + 
Sbjct: 1  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGAL-AAITK 59

Query: 67 NDQDLMGSKLRVE 79
            + +  +++ V 
Sbjct: 60 THKVVGQNEIIVS 72

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.4 bits (104), Expect = 4e-07
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 11/84 (13%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP----------GFAFVEFSNQIDAE 60
          R+YVG +   + +E +   F    +L  +  A   P           FAF+EF +  +  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 61 AACDSMNDQDLMGSKLRVEISRGR 84
           A    +     G  L++      
Sbjct: 63 QAMA-FDGIIFQGQSLKIRRPHDY 85

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 4e-07
 Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 11/79 (13%)

Query: 11 RVYVGGLTETVKKEDLELEFE---KFGKLNSVWVAFNPP--------GFAFVEFSNQIDA 59
           V+V GL++ +   ++    E   KFGK++ V +  +            A+V +    DA
Sbjct: 10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 60 EAACDSMNDQDLMGSKLRV 78
            A   +N+  + G  L+ 
Sbjct: 70 LRAIQCVNNVVVDGRTLKA 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.4 bits (104), Expect = 5e-07
 Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 2/86 (2%)

Query: 9  GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMND 68
            RV V GL  +   +DL+    + G +          G   VE+  + D E A   ++D
Sbjct: 15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYAD--VQKDGMGMVEYLRKEDMEYALRKLDD 72

Query: 69 QDLMGSKLRVEISRGRGRGRGGGGRG 94
                +      R       G   G
Sbjct: 73 TKFRSHEGETSYIRVYPERSSGPSSG 98

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.1 bits (103), Expect = 5e-07
 Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 2/84 (2%)

Query: 11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQD 70
          RV V GL  +   +DL+    + G +          G   VEF  + D   A   +++  
Sbjct: 2  RVVVSGLPPSGSWQDLKDHMREAGDVCYAD--VYRDGTGVVEFVRKEDMTYAVRKLDNTK 59

Query: 71 LMGSKLRVEISRGRGRGRGGGGRG 94
              +      R +  G      G
Sbjct: 60 FRSHEGETAYIRVKVDGPRSPSYG 83

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 6e-07
 Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 6/89 (6%)

Query: 11  RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG-----FAFVEFSNQIDAEAACDS 65
             ++G L   V +E ++  F                      F + EF +     +A  S
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75

Query: 66  MNDQDLMGSKLRVEISRGRGRGRGGGGRG 94
           +N++ L   ++RV+++        G   G
Sbjct: 76  LNEESLGNKRIRVDVADQAQDKDSGPSSG 104

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 43.4 bits (101), Expect = 8e-07
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 5/82 (6%)

Query: 7  ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPG----FAFVEFSNQIDAEAA 62
               +++G L       +L++   +    N + V     G    F +V+F +  D E A
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 70

Query: 63 CDSMNDQDLMGSKLRVEISRGR 84
           + +    + G+++++E  +GR
Sbjct: 71 LE-LTGLKVFGNEIKLEKPKGR 91

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 12 VYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACD--SMND 68
          V++         +  L    E FG +++  +  N    AF+E +   DA+AA D  +   
Sbjct: 11 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLI-LNKINEAFIEMATTEDAQAAVDYYTTTP 69

Query: 69 QDLMGSKLRVEISRGRGR 86
            + G  +RV +S+   R
Sbjct: 70 ALVFGKPVRVHLSQKYKR 87

>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 = 42.4 bits (99), Expect = 2e-06
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWV-----AFNPPGFAFVEFSNQIDAEAACD 64
          T + V  +  TV  +++   F  +  +             P G A V F ++ +A AA  
Sbjct: 10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 65 SMNDQDLMGSKLRVEI 80
           +ND+ +   K+++ +
Sbjct: 70 DLNDRPIGSRKVKLVL 85

>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 = 42.5 bits (99), Expect = 3e-06
 Identities = 24/88 (27%), Positives = 34/88 (38%), Gaps = 3/88 (3%)

Query: 6  MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDS 65
          +     V+V GL E+V + DL    EKFG +  V +       A VEF N   A+     
Sbjct: 12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM-MPFKRQALVEFENIDSAKECVTF 70

Query: 66 MNDQDLM--GSKLRVEISRGRGRGRGGG 91
            D  +   G +     S  +   R G 
Sbjct: 71 AADVPVYIAGQQAFFNYSTSKRITRPGN 98

>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 = 41.7 bits (97), Expect = 6e-06
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 2/75 (2%)

Query: 12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQI-DAEAACDSMNDQD 70
           + G L +   +EDL + F   G++  +           + F  +  +A       N+ +
Sbjct: 14 KFSGDLDDQTCREDLHILFSNHGEIKWIDF-VRGAKEGIILFKEKAKEALGKAKDANNGN 72

Query: 71 LMGSKLRVEISRGRG 85
          L      V      G
Sbjct: 73 LQLRNKEVTWEVLEG 87

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.7 bits (95), Expect = 9e-06
 Identities = 13/67 (19%), Positives = 25/67 (37%), Gaps = 7/67 (10%)

Query: 23 KEDLELEFEKFGKLNSVWVAFNPP-------GFAFVEFSNQIDAEAACDSMNDQDLMGSK 75
           ED+  E  K+G + S+ +            G  FVEF++  D + A   +  +      
Sbjct: 28 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 87

Query: 76 LRVEISR 82
          +  +   
Sbjct: 88 VVTKYCD 94

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.4 bits (88), Expect = 7e-05
 Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 2  SDGMMERG-TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAE 60
          S G   R  T +    L       +++  F +FG L  V +       A VEF   ++A 
Sbjct: 2  SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL-PEGGITAIVEFLEPLEAR 60

Query: 61 AACDSMNDQDLMGSKLRVEISR 82
           A   +         L +E + 
Sbjct: 61 KAFRHLAYSKFHHVPLYLEWAP 82

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 1e-04
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 2  SDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPP-----GFAFVEFSNQ 56
          S    E G  VY+ GL    + + +   F+K   +         P     G  FVEF N+
Sbjct: 11 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 70

Query: 57 IDAEAACDSMNDQDLMGSKLRVEISRGR 84
           D +AA    + Q +    ++V     +
Sbjct: 71 ADYKAAL-CRHKQYMGNRFIQVHPITKK 97

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.1 bits (85), Expect = 2e-04
 Identities = 15/105 (14%), Positives = 33/105 (31%), Gaps = 10/105 (9%)

Query: 5   MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDA 59
           +       ++  +  ++ K D+    E      +             G A V+F N+ DA
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 60  EAACDSMNDQDLMGSKLRVEISRGRGRGRGGGGRGGRFDSRGGRG 104
             +   ++ + L G +  V +                  ++G  G
Sbjct: 64  RKSER-LHRKKLNGREAFVHVVTLEDMREIEKNP----PAQGKSG 103

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 3e-04
 Identities = 18/89 (20%), Positives = 32/89 (35%), Gaps = 4/89 (4%)

Query: 9   GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWV---AFNPPGFAFVEFSNQIDAEAACDS 65
           G  V++ GL     + D+   F     +             G A VEF+   DA AA  +
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-A 73

Query: 66  MNDQDLMGSKLRVEISRGRGRGRGGGGRG 94
            +  ++    + + ++   G    G   G
Sbjct: 74  KDKANMQHRYVELFLNSTAGTSGSGPSSG 102

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	207
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.89
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.89
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.88
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.88
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.87
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.86
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.86
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.86
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.85
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.84
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.84
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.84
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.84
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.84
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.84
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.84
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.83
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.83
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.83
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.82
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.82
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.82
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.82
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.81
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.81
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.81
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.8
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.8
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.79
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.79
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.78
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.75
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.75
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.7
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.69
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.68
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.64
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.63
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	99.61
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.59
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.52
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.38
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.14
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.0
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.97
d1kvja_	79	Menkes copper-transporting ATPase {Human (Homo sap	91.42
d2aw0a_	72	Menkes copper-transporting ATPase {Human (Homo sap	81.88

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=5.3e-23  Score=145.78  Aligned_cols=85  Identities=29%  Similarity=0.398  Sum_probs=78.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .+.+++|||+|||+++|+++|+++|++|++|++|+|+.|     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456779999999999999999999999999999999887     689999999999999999999999999999999999


Q ss_pred             eecCCCCCCC
Q psy2347          81 SRGRGRGRGG   90 (207)
Q Consensus        81 a~~k~~~~~~   90 (207)
                      ++++.+....
T Consensus        85 a~~~~~~~~~   94 (99)
T d1whwa_          85 STIKKEASQS   94 (99)
T ss_dssp             CCCCSTTCCC
T ss_pred             CCCCCccCCC
Confidence            9988765443

>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=6.5e-23  Score=143.83  Aligned_cols=84  Identities=25%  Similarity=0.447  Sum_probs=77.5

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      +.+..++++|||+|||+++|+++|+++|++||+|++|.|+++     +++||||+|+++++|++||+.||+..|.+++|+
T Consensus         1 e~~~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   80 (93)
T d1h2vz_           1 EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR   80 (93)
T ss_dssp             CTTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECE
T ss_pred             CCccCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            356788999999999999999999999999999999999987     567999999999999999999999999999999


Q ss_pred             EEEeecCCC
Q psy2347          78 VEISRGRGR   86 (207)
Q Consensus        78 V~~a~~k~~   86 (207)
                      |+++.+..+
T Consensus        81 V~~a~~~~~   89 (93)
T d1h2vz_          81 TDWDAGFKE   89 (93)
T ss_dssp             EEEESCCCT
T ss_pred             EEEcCCCCC
Confidence            999976543

>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=99.88  E-value=2e-22  Score=141.25  Aligned_cols=83  Identities=29%  Similarity=0.446  Sum_probs=77.6

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ......++|||+|||+++|+++|+++|++||+|++|+|+.+   +++||||+|+++++|++||+.||+.+|.+++|+|++
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            44566789999999999999999999999999999999988   789999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      |++|..
T Consensus        86 A~~r~~   91 (93)
T d2cq3a1          86 ATARVM   91 (93)
T ss_dssp             CCSSCC
T ss_pred             cCcCCC
Confidence            998764

>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=99.88  E-value=9.1e-23  Score=139.54  Aligned_cols=75  Identities=24%  Similarity=0.455  Sum_probs=71.5

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +++|||+|||+++|+++|+++|++||+|++|+|+++     +++||||+|+++++|++||+.||+..|.+++|+|++|+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            578999999999999999999999999999999876     688999999999999999999999999999999999976

>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=99.88  E-value=2.9e-22  Score=139.57  Aligned_cols=81  Identities=25%  Similarity=0.386  Sum_probs=75.1

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .+.++|||+|||+++||++|+++|++||+|++|+|+.+   .++||||+|+++++|++|++.||++.|.++.|+|++|++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~   85 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   85 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            34569999999999999999999999999999999887   678999999999999999999999999999999999987


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      +..+
T Consensus        86 ~~~~   89 (90)
T d2cqia1          86 PSSQ   89 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            6543

>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=7.5e-23  Score=142.29  Aligned_cols=81  Identities=36%  Similarity=0.612  Sum_probs=75.6

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ....++|||+|||+++|+++|+++|++||+|++|+|+.|     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus         2 a~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~   81 (89)
T d2cqba1           2 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   81 (89)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456689999999999999999999999999999999887     789999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      |+|+..
T Consensus        82 a~p~~~   87 (89)
T d2cqba1          82 AKPMRI   87 (89)
T ss_dssp             CCCCCC
T ss_pred             eCCCCC
Confidence            987643

>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=1.5e-22  Score=140.84  Aligned_cols=82  Identities=30%  Similarity=0.524  Sum_probs=76.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      +....+|||+|||+++|+++|+++|++|++|+.|.++.+     +++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus         2 ~~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   81 (90)
T d1x5sa1           2 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456678999999999999999999999999999998876     789999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      |.++...
T Consensus        82 a~~~~~~   88 (90)
T d1x5sa1          82 AGKSSDN   88 (90)
T ss_dssp             EECCCCC
T ss_pred             cCCCCCC
Confidence            9887654

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.7e-22  Score=141.70  Aligned_cols=81  Identities=30%  Similarity=0.433  Sum_probs=75.7

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++|+++|+++|++|++|++|+|+.+     +++||||+|.++++|++||+.||++.|.+++|+|++
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345679999999999999999999999999999999887     678999999999999999999999999999999999


Q ss_pred             eecCCC
Q psy2347          81 SRGRGR   86 (207)
Q Consensus        81 a~~k~~   86 (207)
                      |+++.+
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            988764

>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=1.2e-22  Score=144.84  Aligned_cols=82  Identities=27%  Similarity=0.436  Sum_probs=76.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      .++.++|||+|||+++|+++|+++|++|+.|++|+++.+     +++||||+|+++++|++||++||++.|.+++|+|++
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~   94 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL   94 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            356789999999999999999999999999999999887     568999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      |+++.++
T Consensus        95 a~~k~~~  101 (102)
T d2cpza1          95 KRSKNDS  101 (102)
T ss_dssp             CCCSCCC
T ss_pred             eCCCCCC
Confidence            9998765

>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=99.87  E-value=1.6e-22  Score=140.62  Aligned_cols=79  Identities=27%  Similarity=0.382  Sum_probs=74.5

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ...+|||+|||+++|+++|+++|++||+|++|+|+.+   +++||||+|+++++|++||+.||++.|.+++|+|++|+++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~   86 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   86 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3568999999999999999999999999999999987   6899999999999999999999999999999999999987


Q ss_pred             CC
Q psy2347          85 GR   86 (207)
Q Consensus        85 ~~   86 (207)
                      ++
T Consensus        87 ~~   88 (89)
T d1cvja2          87 KE   88 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            65

>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=99.87  E-value=2.5e-22  Score=137.23  Aligned_cols=75  Identities=24%  Similarity=0.418  Sum_probs=71.2

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+++||++|+++|++||+|++|+|+++     +++||||+|+++++|++|++.||++.|.+++|+|++|+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            357999999999999999999999999999999987     568999999999999999999999999999999999986

>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=99.87  E-value=3.7e-22  Score=140.39  Aligned_cols=81  Identities=35%  Similarity=0.536  Sum_probs=75.1

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ...++.++|||+|||+++|+++|+++|++|+.|+.|+++.+  .++||||+|+++++|++||+.||+++|.+++|+|++|
T Consensus         9 p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1           9 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            34567889999999999999999999999999999998776  7899999999999999999999999999999999998


Q ss_pred             ecC
Q psy2347          82 RGR   84 (207)
Q Consensus        82 ~~k   84 (207)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=99.87  E-value=1.5e-22  Score=141.04  Aligned_cols=81  Identities=25%  Similarity=0.407  Sum_probs=76.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||.++|+++|+++|++||+|++|+|++|     +++||||+|+++++|++||+.||+..|.+++|+|+
T Consensus         4 ~~~~~~~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           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567789999999999999999999999999999999987     57899999999999999999999999999999999


Q ss_pred             EeecCC
Q psy2347          80 ISRGRG   85 (207)
Q Consensus        80 ~a~~k~   85 (207)
                      +|+|+.
T Consensus        84 ~akp~~   89 (90)
T d2cq0a1          84 WAKPST   89 (90)
T ss_dssp             ESSCCC
T ss_pred             eeeCCC
Confidence            999875

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.87  E-value=3.7e-22  Score=138.50  Aligned_cols=79  Identities=20%  Similarity=0.493  Sum_probs=73.8

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|+.|     +++||||+|+++++|++||+.||+..|.+++|+|++
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345789999999999999999999999999999999987     578999999999999999999999999999999999


Q ss_pred             eecC
Q psy2347          81 SRGR   84 (207)
Q Consensus        81 a~~k   84 (207)
                      |.+|
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9986

>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=99.86  E-value=8e-22  Score=147.72  Aligned_cols=81  Identities=22%  Similarity=0.427  Sum_probs=74.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +..++|||+|||+++||++|+++|++||+|++|+|+.+     +++||||+|.+.++|++||+.||+++|.+++|+|++|
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999876     5789999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +++.++
T Consensus       120 ~~~~~~  125 (139)
T d1u6fa1         120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            877654

>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=99.86  E-value=9.6e-22  Score=135.64  Aligned_cols=84  Identities=27%  Similarity=0.340  Sum_probs=77.1

Q ss_pred             CCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           3 DGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         3 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ++.+.+.++|||+|||+++|+++|+++|++|+.|+.+++... ++||||+|.++++|++||+.||++.|.+++|+|++|+
T Consensus         2 ~d~~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~-rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           2 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             cccccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccc-cEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            456677899999999999999999999999999988887665 8999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      |+.+.
T Consensus        81 P~~~~   85 (86)
T d2cpda1          81 PVDKD   85 (86)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=7e-22  Score=139.32  Aligned_cols=80  Identities=23%  Similarity=0.402  Sum_probs=75.3

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      .++.++|||+|||.++||++|+++|++||+|++|+|+.+ ++||||+|+++++|++||+.||+.+|.+++|+|+|+++++
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~p   93 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP   93 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            455689999999999999999999999999999999998 9999999999999999999999999999999999998865


Q ss_pred             C
Q psy2347          86 R   86 (207)
Q Consensus        86 ~   86 (207)
                      .
T Consensus        94 ~   94 (96)
T d1x4ga1          94 D   94 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.86  E-value=1.9e-21  Score=138.65  Aligned_cols=85  Identities=27%  Similarity=0.458  Sum_probs=74.0

Q ss_pred             CCCCCCC-CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCc
Q psy2347           1 MSDGMME-RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGS   74 (207)
Q Consensus         1 ms~~~~~-~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~   74 (207)
                      |+....+ ..++|||+|||+++||++|+++|++||+|++|+|+.+     +++||||+|+++++|++||+.+| ..|.++
T Consensus         1 ~h~~~~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~Gr   79 (103)
T d2cqda1           1 MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGR   79 (103)
T ss_dssp             CCCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSS-CEETTE
T ss_pred             CCCCCCCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCC-CcCCCE
Confidence            3443333 4467999999999999999999999999999999987     68999999999999999999876 479999


Q ss_pred             EEEEEEeecCCC
Q psy2347          75 KLRVEISRGRGR   86 (207)
Q Consensus        75 ~l~V~~a~~k~~   86 (207)
                      +|+|++|.++.+
T Consensus        80 ~l~V~~a~~~~~   91 (103)
T d2cqda1          80 KANVNLAYLGAK   91 (103)
T ss_dssp             ECEEEESTTTCC
T ss_pred             EEEEEEcCCCCC
Confidence            999999976543

>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=99.86  E-value=1e-21  Score=134.75  Aligned_cols=81  Identities=17%  Similarity=0.350  Sum_probs=75.1

Q ss_pred             CCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeC-CcEEEEEE
Q psy2347           2 SDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLM-GSKLRVEI   80 (207)
Q Consensus         2 s~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~-g~~l~V~~   80 (207)
                      |+...+|+++|||.|||+++|+++|+++|++||+|++|+|+++.++||||+|++.++|++|++.||+..|. +++|+|++
T Consensus         1 a~~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           1 AQTEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             CCCCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            34567789999999999999999999999999999999999888899999999999999999999999884 68999999


Q ss_pred             ee
Q psy2347          81 SR   82 (207)
Q Consensus        81 a~   82 (207)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=5.7e-22  Score=136.71  Aligned_cols=77  Identities=21%  Similarity=0.406  Sum_probs=73.2

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      .+|||+|||+++||++|+++|++||+|++|+|+.|     +++||||+|.++++|++|++.||+++|.+++|+|++|++.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            58999999999999999999999999999999987     6899999999999999999999999999999999999876


Q ss_pred             CC
Q psy2347          85 GR   86 (207)
Q Consensus        85 ~~   86 (207)
                      .+
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=1e-21  Score=133.28  Aligned_cols=73  Identities=26%  Similarity=0.390  Sum_probs=69.9

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +|||+|||+++|+++|+++|++||+|++|+|+.+    +++||||+|+++++|++|++.||++.|.+++|+|++|++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            7999999999999999999999999999999987    688999999999999999999999999999999999863

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.86  E-value=7.6e-22  Score=134.62  Aligned_cols=75  Identities=11%  Similarity=0.221  Sum_probs=69.4

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+++|+++|+++|++||+|+.+.++.+     +++||||+|+++++|++||+.||++.|.+++|+|++|+|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            379999999999999999999999999988877655     789999999999999999999999999999999999987

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=1.4e-21  Score=137.25  Aligned_cols=81  Identities=22%  Similarity=0.436  Sum_probs=75.0

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhc-CCceeCCcEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSM-NDQDLMGSKLRV   78 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l-~g~~i~g~~l~V   78 (207)
                      .+++++|||+|||++++|++|+++|++||+|+.|+|+.+      +++||||+|+++++|++||+.| |+..|.+++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            356789999999999999999999999999999999776      6899999999999999999998 889999999999


Q ss_pred             EEeecCCC
Q psy2347          79 EISRGRGR   86 (207)
Q Consensus        79 ~~a~~k~~   86 (207)
                      ++|+++..
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99988754

>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=99.85  E-value=1e-21  Score=136.93  Aligned_cols=80  Identities=20%  Similarity=0.310  Sum_probs=73.3

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..++.++|||+|||+++||++|+++|++||+|++|+|+.|     +++||||+|.++++|++||+.  .+.|+++.|.|+
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~   81 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCK   81 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEE
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEE
Confidence            4567889999999999999999999999999999999987     678999999999999999985  458999999999


Q ss_pred             EeecCCC
Q psy2347          80 ISRGRGR   86 (207)
Q Consensus        80 ~a~~k~~   86 (207)
                      +|.++..
T Consensus        82 ~a~~k~~   88 (90)
T d2cqga1          82 LPNSKQS   88 (90)
T ss_dssp             CCCTTCC
T ss_pred             eCCCCCC
Confidence            9988764

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=8.2e-22  Score=135.63  Aligned_cols=74  Identities=27%  Similarity=0.436  Sum_probs=69.5

Q ss_pred             EEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347          12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus        12 lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      |||+|||+++|+++|+++|++||+|++|+|+++        +++||||+|+++++|++||+.||++.|.+++|+|++|++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            899999999999999999999999999999876        368999999999999999999999999999999999876


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>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=1e-21  Score=135.73  Aligned_cols=79  Identities=28%  Similarity=0.538  Sum_probs=74.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ....++|||+|||+++++++|+++|++||+|++|+++++ ++||||+|+++++|++|++.||+.+|.+++|+|++|.++.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~~   83 (86)
T d2cpja1           5 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            345678999999999999999999999999999999987 8999999999999999999999999999999999998764

>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=99.85  E-value=1.8e-21  Score=133.36  Aligned_cols=74  Identities=32%  Similarity=0.473  Sum_probs=69.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      ..++.++|||+|||+++||++|+++|++||+|++|+|+.+     +++||||+|+++++|++||++||++.|.+++|+|
T Consensus         5 ~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           5 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4456789999999999999999999999999999999987     5789999999999999999999999999999987

>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=99.85  E-value=6.1e-22  Score=137.36  Aligned_cols=80  Identities=21%  Similarity=0.415  Sum_probs=73.6

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGR   86 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~   86 (207)
                      ..+++|||+|||+++||++|+++|++||+|++|+++.++++||||+|+++++|++||+  +.++|++++|+|++|+++..
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            4678999999999999999999999999999999888889999999999999999985  78899999999999988765


Q ss_pred             CC
Q psy2347          87 GR   88 (207)
Q Consensus        87 ~~   88 (207)
                      ..
T Consensus        81 ~~   82 (88)
T d1wf0a_          81 SN   82 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.6e-21  Score=132.88  Aligned_cols=73  Identities=33%  Similarity=0.476  Sum_probs=69.6

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      +|||+|||+++||++|+++|++|++|++|+|++|     +++||||+|.++++|++||+.||+..|.+++|+|++|+.
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~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            7999999999999999999999999999999987     568999999999999999999999999999999999853

>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=99.85  E-value=1.8e-21  Score=133.29  Aligned_cols=76  Identities=22%  Similarity=0.399  Sum_probs=70.0

Q ss_pred             EEEcCCCcCCcHHHHHHHHHhCCCeeEE-EEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347          12 VYVGGLTETVKKEDLELEFEKFGKLNSV-WVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus        12 lfV~nLp~~~te~~L~~~F~~~G~V~~v-~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      |||+|||+++||++|+++|++||+|+++ +|+++     +++||||+|+++++|++||+.||++.|.+++|+|++|.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999998764 67766     67999999999999999999999999999999999999876


Q ss_pred             CC
Q psy2347          86 RG   87 (207)
Q Consensus        86 ~~   87 (207)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.85  E-value=3.1e-21  Score=139.68  Aligned_cols=79  Identities=23%  Similarity=0.376  Sum_probs=74.1

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .+.+++|||+|||.++|+++|+++|++||+|++|+|+.+  +++||||+|++.++|++||+.||++.|.++.|+|+++.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            356789999999999999999999999999999999887  789999999999999999999999999999999999875


Q ss_pred             C
Q psy2347          84 R   84 (207)
Q Consensus        84 k   84 (207)
                      +
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=3.2e-21  Score=137.62  Aligned_cols=78  Identities=26%  Similarity=0.444  Sum_probs=73.3

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+++|+++|+++|++||+|+.+.|++|     +++||||+|.+.++|++||+ ++++.|+++.|.|++|++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            379999999999999999999999999999999887     78999999999999999996 799999999999999999


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      ++++
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8765

>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=2.5e-21  Score=131.57  Aligned_cols=77  Identities=23%  Similarity=0.362  Sum_probs=72.2

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ..+.++|||+||+  +||++|+++|++||+|++|++.++ ++||||+|+++++|++|++.||+.+|.+++|+|+++++++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~P   78 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   78 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSSC
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            4577899999985  899999999999999999999886 8899999999999999999999999999999999998765

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=4.6e-21  Score=134.92  Aligned_cols=82  Identities=26%  Similarity=0.442  Sum_probs=74.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcC------CceeCCc
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMN------DQDLMGS   74 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~------g~~i~g~   74 (207)
                      .++.++|||+|||+++||++|+++|++|++|+++.++.+     +++||||+|.++++|++||+.||      +..|.++
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            456789999999999999999999999999999999877     68999999999999999999876      5678999


Q ss_pred             EEEEEEeecCCCC
Q psy2347          75 KLRVEISRGRGRG   87 (207)
Q Consensus        75 ~l~V~~a~~k~~~   87 (207)
                      +|+|++|++|++.
T Consensus        85 ~l~v~~a~~k~~a   97 (98)
T d1x4ha1          85 QLKVDLAVTRDEA   97 (98)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCCcC
Confidence            9999999987653

>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=99.84  E-value=3e-21  Score=138.57  Aligned_cols=77  Identities=23%  Similarity=0.406  Sum_probs=72.0

Q ss_pred             CcEEEEcCCCc-CCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           9 GTRVYVGGLTE-TVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         9 ~~~lfV~nLp~-~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      +++|||+|||+ .+||++|+++|++||+|++|+|++++++||||+|+++++|++||+.||+..|.+++|+|++++.+.
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~~~~   79 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN   79 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            57999999965 599999999999999999999999988999999999999999999999999999999999987553

>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=99.84  E-value=5.8e-21  Score=132.20  Aligned_cols=80  Identities=20%  Similarity=0.339  Sum_probs=73.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCcee-CCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDL-MGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i-~g~~l~V~~a~   82 (207)
                      ..+|+++|||+|||+++|+++|+++|++|+.|+++.++.+ .+++|||+|+++++|++|++.||+..| ++++|+|++++
T Consensus         6 ~~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           6 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            4578899999999999999999999999999998877765 688999999999999999999999988 58999999997


Q ss_pred             cC
Q psy2347          83 GR   84 (207)
Q Consensus        83 ~k   84 (207)
                      ++
T Consensus        86 ~~   87 (88)
T d2adca2          86 ST   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.84  E-value=2.3e-21  Score=133.52  Aligned_cols=75  Identities=28%  Similarity=0.582  Sum_probs=69.3

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVE   79 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~   79 (207)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++|     +++||||+|+++++|++|++.||+..|.+  ++|+|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            45678999999999999999999999999999999987     56899999999999999999999999987  569998


Q ss_pred             Ee
Q psy2347          80 IS   81 (207)
Q Consensus        80 ~a   81 (207)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.84  E-value=3.4e-21  Score=132.63  Aligned_cols=75  Identities=27%  Similarity=0.484  Sum_probs=69.7

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEE
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVE   79 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~   79 (207)
                      .+.++|||+|||+++||++|+++|++||+|++|+|+++     +++||||+|+++++|++||+.||+..+.+  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            35678999999999999999999999999999999987     57899999999999999999999999976  889999


Q ss_pred             Ee
Q psy2347          80 IS   81 (207)
Q Consensus        80 ~a   81 (207)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.84  E-value=7.6e-21  Score=134.05  Aligned_cols=81  Identities=28%  Similarity=0.512  Sum_probs=74.2

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCC--cEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMG--SKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g--~~l~V~~a~   82 (207)
                      ...++++|||+|||+++|+++|+++|++|++|+.|+|+++ +.||||+|+++++|++|++.||+.+|.+  ++|+|++|+
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            3467899999999999999999999999999999999887 8899999999999999999999999976  589999998


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      +.+.
T Consensus        92 ~~~~   95 (97)
T d1whya_          92 SGPS   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.84  E-value=2.5e-21  Score=133.68  Aligned_cols=77  Identities=23%  Similarity=0.357  Sum_probs=70.1

Q ss_pred             CCcEEEEcCCCcCCc-HHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           8 RGTRVYVGGLTETVK-KEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         8 ~~~~lfV~nLp~~~t-e~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      +.++|||.|||+++| |++|+++|++||+|++|+|+.+      +++||||+|+++++|++||+ ||++.|.+++|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            578999999999876 5679999999999999998764      68899999999999999995 999999999999999


Q ss_pred             eecCC
Q psy2347          81 SRGRG   85 (207)
Q Consensus        81 a~~k~   85 (207)
                      |++|+
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            99875

>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=1.8e-21  Score=132.66  Aligned_cols=77  Identities=25%  Similarity=0.398  Sum_probs=70.9

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCc-eeCCcEEEEEEeecCCCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQ-DLMGSKLRVEISRGRGRG   87 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~-~i~g~~l~V~~a~~k~~~   87 (207)
                      .+|||+|||+++||++|+++|++|+.|..++++++ ++||||+|.++++|++||+.||+. +|.+++|+|++|.|+.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~r   79 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKLR   79 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE-TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc-cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCcC
Confidence            47999999999999999999999999988877775 899999999999999999999985 699999999999987654

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=1.3e-21  Score=132.57  Aligned_cols=71  Identities=23%  Similarity=0.482  Sum_probs=67.8

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      |+|||+|||+++||++|+++|++||+|++|+|++|     +++||||+|+++++|++||+ ++.+.|++++|+|++|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            68999999999999999999999999999999987     78999999999999999997 6999999999999986

>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=99.83  E-value=3.5e-21  Score=138.54  Aligned_cols=79  Identities=19%  Similarity=0.190  Sum_probs=72.7

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      ....++|||+|||+++|+++|+++|++||+|+.|.|... ++||||+|+++++|++||+.||++.|.+++|.|+++....
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~-kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~~   85 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGV   85 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSS-SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeecc-CceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCCc
Confidence            345679999999999999999999999999999988765 8999999999999999999999999999999999997654

>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=99.83  E-value=6.3e-21  Score=131.13  Aligned_cols=75  Identities=24%  Similarity=0.455  Sum_probs=69.9

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++.++|||+|||+++|+++|+++|++||+|++|+|+.|     +++||||+|.++++|++||+ ++++.|++++|+|+.|
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A   82 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRA   82 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEee
Confidence            45579999999999999999999999999999999987     68999999999999999998 5889999999999987


Q ss_pred             e
Q psy2347          82 R   82 (207)
Q Consensus        82 ~   82 (207)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=1.2e-21  Score=136.84  Aligned_cols=80  Identities=19%  Similarity=0.360  Sum_probs=72.3

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ....+..+|||+|||+++|+++|+++|++|++|+.|+|+.+    +++||||+|+++++|++||+ ||+++|.+++|+|+
T Consensus         8 ~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1           8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            34456679999999999999999999999999988877655    78999999999999999996 89999999999999


Q ss_pred             EeecC
Q psy2347          80 ISRGR   84 (207)
Q Consensus        80 ~a~~k   84 (207)
                      +|++|
T Consensus        87 ~ak~k   91 (91)
T d1fjeb1          87 KPKGR   91 (91)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            99875

>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=99.83  E-value=1.1e-20  Score=134.61  Aligned_cols=80  Identities=20%  Similarity=0.352  Sum_probs=70.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      .++.++|||+|||+++||++|+++|++|+ |+++.++.+      +++||||+|+++++|++|+ +||+++|.+++|+|+
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~   89 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEE
Confidence            45678999999999999999999999998 777777665      5789999999999998777 589999999999999


Q ss_pred             EeecCCCC
Q psy2347          80 ISRGRGRG   87 (207)
Q Consensus        80 ~a~~k~~~   87 (207)
                      +|+++...
T Consensus        90 ~a~~~~~~   97 (104)
T d1wi8a_          90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             ECCCCCCC
Confidence            99887554

>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=99.83  E-value=3.2e-21  Score=135.74  Aligned_cols=84  Identities=17%  Similarity=0.280  Sum_probs=74.4

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ....+.++|||+|||+++|+++|+++|++|+.|..+.+...+++||||+|+++++|++||+.||++.|.+++|+|+++++
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            34456789999999999999999999999999877754333789999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy2347          84 RGRG   87 (207)
Q Consensus        84 k~~~   87 (207)
                      +...
T Consensus        91 k~~~   94 (96)
T d1fjca_          91 KGGT   94 (96)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7653

>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=1.3e-20  Score=133.17  Aligned_cols=79  Identities=22%  Similarity=0.220  Sum_probs=73.3

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGR   86 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~   86 (207)
                      .+..+|||.|||+++++++|+++|++|++|+.|+|..  ++||||+|.++++|++||++||+.+|.++.|+|.++++++.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~--~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK--DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET--TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc--cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            4567899999999999999999999999999999875  58999999999999999999999999999999999988765


Q ss_pred             C
Q psy2347          87 G   87 (207)
Q Consensus        87 ~   87 (207)
                      +
T Consensus        91 ~   91 (98)
T d1wg4a_          91 R   91 (98)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.83  E-value=9.7e-21  Score=133.88  Aligned_cols=77  Identities=32%  Similarity=0.539  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCC-cCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecC
Q psy2347           6 MERGTRVYVGGLT-ETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGR   84 (207)
Q Consensus         6 ~~~~~~lfV~nLp-~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k   84 (207)
                      ....++|||+||| ..+++++|+++|++||+|++|+|.   ++||||+|+++++|++||+.||+++|.+++|+|++++++
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~---rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH---KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE---TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe---CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3456789999996 578899999999999999999984   789999999999999999999999999999999999764


Q ss_pred             C
Q psy2347          85 G   85 (207)
Q Consensus        85 ~   85 (207)
                      .
T Consensus        89 ~   89 (98)
T d1wf2a_          89 K   89 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.83  E-value=2.2e-21  Score=137.78  Aligned_cols=83  Identities=25%  Similarity=0.329  Sum_probs=76.1

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..+++++|||+|||.++|+++|+++|++|+.|+.+.++.+     +++||||+|.++++|++||+.||+..|.+++|+|+
T Consensus        14 ~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   93 (102)
T d2cpxa1          14 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE   93 (102)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4567899999999999999999999999999988877654     78999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy2347          80 ISRGRGRG   87 (207)
Q Consensus        80 ~a~~k~~~   87 (207)
                      +|+++..+
T Consensus        94 ~ak~k~~r  101 (102)
T d2cpxa1          94 FGKNKKQR  101 (102)
T ss_dssp             ECCCCSCC
T ss_pred             eCCCcccC
Confidence            99987654

>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=99.83  E-value=4.3e-21  Score=136.86  Aligned_cols=77  Identities=26%  Similarity=0.487  Sum_probs=72.0

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+++|+++|+++|++||+|++|+|+.+     +++||||+|.++++|++||+.||++.|.+++|+|++|.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999886     568999999999999999999999999999999999876


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.82  E-value=7.7e-21  Score=127.91  Aligned_cols=70  Identities=26%  Similarity=0.511  Sum_probs=65.7

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +|||+|||+++||++|+++|++||+|+.|+|+.+     +++||||+|+++++|++||+ ++.+.|++++|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            5999999999999999999999999999999987     78999999999999999997 6999999999999754

>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=99.82  E-value=1.3e-20  Score=133.46  Aligned_cols=82  Identities=28%  Similarity=0.477  Sum_probs=72.4

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE--------EEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeC
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNS--------VWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLM   72 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~--------v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~   72 (207)
                      ..+.++|||+|||+++||++|+++|++||+|..        +.++.+     +++||||+|.++++|++||+.||+..|.
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            456789999999999999999999999998753        444444     5689999999999999999999999999


Q ss_pred             CcEEEEEEeecCCCC
Q psy2347          73 GSKLRVEISRGRGRG   87 (207)
Q Consensus        73 g~~l~V~~a~~k~~~   87 (207)
                      +++|+|++|++++++
T Consensus        85 gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          85 GSKLKVSLARKKPPM   99 (101)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CEEEEEEEcCCCCCC
Confidence            999999999987654

>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=99.82  E-value=3.1e-21  Score=137.04  Aligned_cols=83  Identities=17%  Similarity=0.252  Sum_probs=74.5

Q ss_pred             CCCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEE
Q psy2347           1 MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKL   76 (207)
Q Consensus         1 ms~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l   76 (207)
                      |+.....+.++|||+|||+++|+++|+++|++||+|+.+.++.+    +++||||+|+++++|++||+.||+.+|.+++|
T Consensus        10 ~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          10 MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             hhccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            34455566789999999999999999999999999999998877    57899999999999999999999999999999


Q ss_pred             EEEEeec
Q psy2347          77 RVEISRG   83 (207)
Q Consensus        77 ~V~~a~~   83 (207)
                      .|.+++|
T Consensus        90 ~v~~~~P   96 (101)
T d1x5oa1          90 VSAPTEP   96 (101)
T ss_dssp             SCCCSSC
T ss_pred             ccCCCCC
Confidence            8877765

>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=99.82  E-value=2.5e-20  Score=126.27  Aligned_cols=72  Identities=24%  Similarity=0.462  Sum_probs=67.7

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      .++|||+|||+++|+++|+++|++|+.|+.++++.+     +++||||+|+++++|++|++ |++++|++++|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            479999999999999999999999999999999887     67899999999999999996 7999999999999876

>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=99.82  E-value=3.2e-21  Score=133.39  Aligned_cols=76  Identities=22%  Similarity=0.250  Sum_probs=69.8

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGRG   87 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~~   87 (207)
                      .+|||+|||+++|+++|+++|++||+|++|+|+.+  +||||+|+++++|++||+.||+.+|.++.|+|.+++++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~--g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~~~   76 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG   76 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc--ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCcCC
Confidence            37999999999999999999999999999998764  89999999999999999999999999999999888765443

>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=99.82  E-value=1.9e-20  Score=129.83  Aligned_cols=78  Identities=17%  Similarity=0.230  Sum_probs=68.5

Q ss_pred             CCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCCC
Q psy2347           7 ERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRGR   86 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~~   86 (207)
                      ..+++|||+|||+++|++||+++|++|+ |+.+++.+ +++||||+|+++++|++||+.||+++|.+++|+|++++++..
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~~-~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~~~   80 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDAL   80 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEEG-GGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeeec-cCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            3467899999999999999999999999 44444444 489999999999999999999999999999999999976644

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=1.5e-20  Score=126.04  Aligned_cols=70  Identities=27%  Similarity=0.605  Sum_probs=66.4

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +|||+|||+++||++|+++|++|+.|+.+.++.+     +++||||+|+++++|++||+ ||++.|++++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            5999999999999999999999999999988776     78999999999999999997 8999999999999876

>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=99.81  E-value=1.2e-20  Score=134.12  Aligned_cols=76  Identities=26%  Similarity=0.411  Sum_probs=71.3

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      .++|||+|||+++||++|+++|++||+|++|+|+++     +++||||+|+++++|++||+ ||++.|.++.|+|++|++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999987     78999999999999999995 899999999999999876


Q ss_pred             CC
Q psy2347          84 RG   85 (207)
Q Consensus        84 k~   85 (207)
                      +.
T Consensus        97 ~~   98 (101)
T d2cq4a1          97 EK   98 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.81  E-value=6.9e-21  Score=128.28  Aligned_cols=70  Identities=21%  Similarity=0.492  Sum_probs=65.9

Q ss_pred             EEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          11 RVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        11 ~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +|||+|||+++||++|+++|++||+|++|+|+.|     +++||||+|+++++|++||+. +.++|.++.|+|++|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            6999999999999999999999999999999987     789999999999999999975 778999999999875

>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=1.8e-20  Score=130.61  Aligned_cols=79  Identities=25%  Similarity=0.445  Sum_probs=72.2

Q ss_pred             CCcEEEEcCCCcCCcHHHHHH----HHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           8 RGTRVYVGGLTETVKKEDLEL----EFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~----~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      |+++|||+|||+++|++||++    +|++||+|++|++..+  +++||||+|+++++|++|++.||+++|.+++|+|++|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            678999999999999999864    5799999999988765  7899999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy2347          82 RGRGR   86 (207)
Q Consensus        82 ~~k~~   86 (207)
                      ++++.
T Consensus        82 k~~~~   86 (91)
T d1nu4a_          82 KTDSD   86 (91)
T ss_dssp             SSCCT
T ss_pred             CCCch
Confidence            88653

>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=99.81  E-value=2.2e-19  Score=127.95  Aligned_cols=83  Identities=25%  Similarity=0.213  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc--CCceeCCcEEEEEEe
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM--NDQDLMGSKLRVEIS   81 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l--~g~~i~g~~l~V~~a   81 (207)
                      ...+++++|||.|||+++||++|+++|++||+|++|.|+++ +++|||+|+++++|++||+.|  +...+.+++|+|+++
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s   88 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEc
Confidence            34568899999999999999999999999999999999876 899999999999999999977  456788999999999


Q ss_pred             ecCCCC
Q psy2347          82 RGRGRG   87 (207)
Q Consensus        82 ~~k~~~   87 (207)
                      +.++..
T Consensus        89 ~~~~~~   94 (104)
T d1wexa_          89 TSKRIT   94 (104)
T ss_dssp             SSSSCC
T ss_pred             CCCccC
Confidence            775443

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.1e-20  Score=129.40  Aligned_cols=79  Identities=25%  Similarity=0.388  Sum_probs=70.7

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCC-eeEEEEeeC------CCcEEEEEEcCHHHHHHHHHhcCCc--eeCCcEEEEE
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGK-LNSVWVAFN------PPGFAFVEFSNQIDAEAACDSMNDQ--DLMGSKLRVE   79 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~-V~~v~i~~d------~rG~afV~F~~~e~A~~Al~~l~g~--~i~g~~l~V~   79 (207)
                      +|+|||+|||.++|+++|+++|++|++ |+.|.|+++      +++||||+|+++++|++|++.|+..  .+.+++|+|+
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 899999876      6789999999999999999998754  4579999999


Q ss_pred             EeecCCCC
Q psy2347          80 ISRGRGRG   87 (207)
Q Consensus        80 ~a~~k~~~   87 (207)
                      ||+|+...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99987654

>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=99.80  E-value=8.8e-20  Score=126.18  Aligned_cols=80  Identities=14%  Similarity=0.130  Sum_probs=73.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc--CCceeCCcEEEEEEee
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM--NDQDLMGSKLRVEISR   82 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l--~g~~i~g~~l~V~~a~   82 (207)
                      ..+|+++|||+|||+++|+++|+++|++||.|++|+++.+ +++|||+|+++++|++|++.|  +...|.+++|+|++++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk   82 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN   82 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECC
Confidence            3578999999999999999999999999999999999887 789999999999999999865  5778999999999998


Q ss_pred             cCC
Q psy2347          83 GRG   85 (207)
Q Consensus        83 ~k~   85 (207)
                      .+.
T Consensus        83 ~~~   85 (88)
T d2cq1a1          83 HKE   85 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>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=99.80  E-value=3.9e-20  Score=132.76  Aligned_cols=82  Identities=21%  Similarity=0.252  Sum_probs=73.5

Q ss_pred             CCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCcee--CCcEEEEEEee
Q psy2347           6 MERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDL--MGSKLRVEISR   82 (207)
Q Consensus         6 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i--~g~~l~V~~a~   82 (207)
                      ..+..+|||+|||+++||++|+++|++||+|++|+|+.+ ++++|||+|+++++|++||+.||++.|  .+++|+|.+++
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            356778999999999999999999999999999999877 678999999999999999999999998  57889998887


Q ss_pred             cCCCC
Q psy2347          83 GRGRG   87 (207)
Q Consensus        83 ~k~~~   87 (207)
                      ++...
T Consensus        84 ~~~~~   88 (108)
T d2adba1          84 LTSLN   88 (108)
T ss_dssp             SCSCC
T ss_pred             Ccccc
Confidence            75543

>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=99.80  E-value=7.5e-20  Score=123.03  Aligned_cols=71  Identities=24%  Similarity=0.176  Sum_probs=66.8

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC---CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN---PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d---~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ++|||+|||+++++++|+++|++||+|+.|+|+.+   .+.+|||+|+++++|++||+ ||++.|.+++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999888   56799999999999999995 7999999999999875

>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=3.5e-20  Score=131.73  Aligned_cols=81  Identities=21%  Similarity=0.226  Sum_probs=71.6

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEI   80 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~   80 (207)
                      ...+..+|||.|||+++||++|+++|+.|+ |+.|.++.+    +++||||+|+++++|++||+ ||++.|.++.|+|.+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            445667999999999999999999999997 557777776    67899999999999999986 899999999999999


Q ss_pred             eecCCCC
Q psy2347          81 SRGRGRG   87 (207)
Q Consensus        81 a~~k~~~   87 (207)
                      +++++..
T Consensus        89 s~~~~~~   95 (102)
T d1weza_          89 NSTAGTS   95 (102)
T ss_dssp             ECCCCCC
T ss_pred             cCCCCCC
Confidence            9887654

>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=2.1e-19  Score=128.07  Aligned_cols=83  Identities=19%  Similarity=0.103  Sum_probs=71.9

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ...+..+|||.|||+++||+||+++|++++.|+.+.++.+     ++++|||+|+++++|++||+ ||++.|.++.|+|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            3455668999999999999999999999999887544443     78999999999999999996 89999999999999


Q ss_pred             EeecCCCCC
Q psy2347          80 ISRGRGRGR   88 (207)
Q Consensus        80 ~a~~k~~~~   88 (207)
                      ++++++...
T Consensus        90 ~~~~~~~~~   98 (104)
T d1wg5a_          90 KSSRAEVRT   98 (104)
T ss_dssp             EECTTTSCC
T ss_pred             ECCHHHhcc
Confidence            998876543

>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=99.79  E-value=2.2e-19  Score=123.48  Aligned_cols=74  Identities=18%  Similarity=0.253  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.++|||+|||+++|+++|+++|++||+|+.|+|+.+    +++||||+|+++++|++||+ +++++|.+++|.|++++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            3579999999999999999999999999999999877    57899999999999999996 69999999999999864

>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=99.79  E-value=2.8e-19  Score=120.21  Aligned_cols=72  Identities=24%  Similarity=0.355  Sum_probs=65.8

Q ss_pred             EEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEeecCC
Q psy2347          12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISRGRG   85 (207)
Q Consensus        12 lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~~k~   85 (207)
                      |||+|||+++|+++|+++|++|+ ++.+++.+ ++++|||+|+++++|++|++.||+.+|.+++|+|++++++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~-~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK-YKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEET-TTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecc-cceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999998 66666655 49999999999999999999999999999999999997643

>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=99.78  E-value=1.4e-19  Score=124.55  Aligned_cols=77  Identities=23%  Similarity=0.302  Sum_probs=68.4

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ..+..++|||.|||++++++||+++|+.|+.|.. +.+..+    ++++|||+|+++++|++||++||++.|.+++|+|+
T Consensus         5 g~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~   84 (86)
T d2cqpa1           5 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   84 (86)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456678999999999999999999999999865 455544    67899999999999999999999999999999999


Q ss_pred             Ee
Q psy2347          80 IS   81 (207)
Q Consensus        80 ~a   81 (207)
                      ++
T Consensus        85 l~   86 (86)
T d2cqpa1          85 LG   86 (86)
T ss_dssp             ES
T ss_pred             EC
Confidence            85

>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=99.78  E-value=1.8e-19  Score=127.42  Aligned_cols=80  Identities=20%  Similarity=0.219  Sum_probs=72.2

Q ss_pred             CCCCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHH--hcCCceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACD--SMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~--~l~g~~i~g~~l~V~~a   81 (207)
                      ...++++|||.|||.+ +|+++|+++|++||+|++|.|+.+ +++|||+|+++++|++|++  .++...|.+++|+|++|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s   92 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS   92 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEc
Confidence            3456789999999985 899999999999999999999887 8999999999999999997  56788999999999999


Q ss_pred             ecCC
Q psy2347          82 RGRG   85 (207)
Q Consensus        82 ~~k~   85 (207)
                      +.+.
T Consensus        93 ~~~~   96 (99)
T d1x4fa1          93 EKYK   96 (99)
T ss_dssp             CSCS
T ss_pred             CCcc
Confidence            7654

>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=99.78  E-value=1.3e-19  Score=125.71  Aligned_cols=72  Identities=26%  Similarity=0.425  Sum_probs=66.4

Q ss_pred             CCcEEEEcCCCcCCcHHHH---HHHHHhCCCeeEEEEeeC--------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEE
Q psy2347           8 RGTRVYVGGLTETVKKEDL---ELEFEKFGKLNSVWVAFN--------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKL   76 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L---~~~F~~~G~V~~v~i~~d--------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l   76 (207)
                      +.++|||+|||+++++++|   +++|++||+|++|.|+++        +++||||+|+++++|++||+.||+..|.+++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   678999999999999987        34899999999999999999999999999999


Q ss_pred             EEE
Q psy2347          77 RVE   79 (207)
Q Consensus        77 ~V~   79 (207)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>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=99.77  E-value=7.2e-19  Score=121.96  Aligned_cols=80  Identities=23%  Similarity=0.238  Sum_probs=72.3

Q ss_pred             CCCCCcEEEEcCCCcC-CcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhc--CCceeCCcEEEEEEe
Q psy2347           5 MMERGTRVYVGGLTET-VKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSM--NDQDLMGSKLRVEIS   81 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~-~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l--~g~~i~g~~l~V~~a   81 (207)
                      ..+++++|||+|||.. +|++||.++|++||+|++|.|+.+ +.+|||+|++.++|++|++.|  +...+.+++|+|++|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s   82 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLS   82 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEEC
Confidence            4578899999999986 899999999999999999999887 789999999999999999965  677899999999999


Q ss_pred             ecCC
Q psy2347          82 RGRG   85 (207)
Q Consensus        82 ~~k~   85 (207)
                      ++..
T Consensus        83 ~~~~   86 (89)
T d1x4da1          83 QKYK   86 (89)
T ss_dssp             CCCT
T ss_pred             CCcc
Confidence            7643

>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=99.75  E-value=1.9e-19  Score=119.79  Aligned_cols=66  Identities=21%  Similarity=0.420  Sum_probs=62.5

Q ss_pred             EEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347          12 VYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus        12 lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      |||+|||+++|+++|+++|++||+|..++++.+     ++++|||+|+++++|++|++.||+++|+++.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            899999999999999999999999999999877     789999999999999999999999999998764

>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=7e-19  Score=124.97  Aligned_cols=79  Identities=19%  Similarity=0.178  Sum_probs=69.1

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeE-EEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNS-VWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~-v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      +..+...+|||+|||+++|+++|+++|++|+.|+. +.++.+    ++++|||+|.++++|++||+ ||++.|.++.|.|
T Consensus         3 dv~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V   81 (103)
T d2cpya1           3 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFV   81 (103)
T ss_dssp             SCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEE
T ss_pred             CCCCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEE
Confidence            34455678999999999999999999999999876 444444    78999999999999999996 8999999999999


Q ss_pred             EEeec
Q psy2347          79 EISRG   83 (207)
Q Consensus        79 ~~a~~   83 (207)
                      .++++
T Consensus        82 ~~~~~   86 (103)
T d2cpya1          82 HVVTL   86 (103)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99864

>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=2.4e-18  Score=122.65  Aligned_cols=81  Identities=14%  Similarity=0.188  Sum_probs=72.2

Q ss_pred             CCCcEEEEcCCCcCC-c----HHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347           7 ERGTRVYVGGLTETV-K----KEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~-t----e~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      ..+++|||.||+.++ +    +++|+++|++|++|++|++++. +++|||+|+++++|++||++||+..|.+++|+|.+|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~-~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a   81 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-FKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFA   81 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-TTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC-CCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeec
Confidence            467899999999875 3    3679999999999999999876 889999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy2347          82 RGRGRGR   88 (207)
Q Consensus        82 ~~k~~~~   88 (207)
                      +++....
T Consensus        82 ~~~~~~~   88 (104)
T d1weya_          82 QTLHIGS   88 (104)
T ss_dssp             CCSSCCS
T ss_pred             ccCCCCC
Confidence            8775543

>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=99.70  E-value=2e-18  Score=124.57  Aligned_cols=80  Identities=25%  Similarity=0.285  Sum_probs=69.1

Q ss_pred             CCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEE-eeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEE
Q psy2347           4 GMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWV-AFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRV   78 (207)
Q Consensus         4 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i-~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V   78 (207)
                      .+..+.++|||.|||+++|+++|+++|+.|+.|+.+.+ +.+    ++++|||+|.++++|++||+ ||++.|.++.|.|
T Consensus        13 ~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V   91 (112)
T d1wela1          13 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQV   91 (112)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEE
T ss_pred             CCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEE
Confidence            44566789999999999999999999999999866433 333    67999999999999999996 8999999999999


Q ss_pred             EEeecC
Q psy2347          79 EISRGR   84 (207)
Q Consensus        79 ~~a~~k   84 (207)
                      ..+.++
T Consensus        92 ~~~~~~   97 (112)
T d1wela1          92 HPITKK   97 (112)
T ss_dssp             EEECHH
T ss_pred             EEcChH
Confidence            998654

>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=99.69  E-value=3.3e-17  Score=116.07  Aligned_cols=67  Identities=16%  Similarity=0.298  Sum_probs=61.9

Q ss_pred             CCCCCCcEEEEcC--CCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCcee
Q psy2347           4 GMMERGTRVYVGG--LTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDL   71 (207)
Q Consensus         4 ~~~~~~~~lfV~n--Lp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i   71 (207)
                      ...+++++|+|.|  ||+++||++|+++|++||+|++|.++.+ ++||||+|++.++|++|+++||+++|
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4467788999965  9999999999999999999999999887 88999999999999999999999887

>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=99.69  E-value=2.6e-17  Score=127.18  Aligned_cols=81  Identities=21%  Similarity=0.391  Sum_probs=73.9

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      .....++|||.|||+.+|+++|+++|++||+|+.+.|+++     +++||||+|+++++|++||+ ++.+.|++++|+|+
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEE
Confidence            3456789999999999999999999999999999999987     56899999999999999997 68899999999999


Q ss_pred             EeecCCC
Q psy2347          80 ISRGRGR   86 (207)
Q Consensus        80 ~a~~k~~   86 (207)
                      +|.||.+
T Consensus       172 ~A~~k~e  178 (183)
T d1u1qa_         172 KALSKQE  178 (183)
T ss_dssp             ECCCHHH
T ss_pred             ecCCccc
Confidence            9988754

>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=99.68  E-value=3.6e-19  Score=123.47  Aligned_cols=71  Identities=23%  Similarity=0.328  Sum_probs=62.2

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----------CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEE
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----------PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVE   79 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----------~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~   79 (207)
                      ++|||+|||+++||++|+++|++|+.|..+.++..          +++||||+|+++|+|++|++ ||+++|.+++|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            68999999999999999999999998766544321          68999999999999999985 99999999999996


Q ss_pred             Ee
Q psy2347          80 IS   81 (207)
Q Consensus        80 ~a   81 (207)
                      .+
T Consensus        81 r~   82 (90)
T d1u2fa_          81 RP   82 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>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=99.64  E-value=1.8e-16  Score=114.28  Aligned_cols=73  Identities=16%  Similarity=0.202  Sum_probs=64.7

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCH-HHHHHHHHhcCCceeCCcEEEEEEeec
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQ-IDAEAACDSMNDQDLMGSKLRVEISRG   83 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~-e~A~~Al~~l~g~~i~g~~l~V~~a~~   83 (207)
                      ..+||+|||+++|+++|+++|++||+|..|+|+.+ ++||||+|+++ ++|.+|+..|+...|..+.+.|.++..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34599999999999999999999999999999987 89999999985 789999999999988877777776643

>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=99.63  E-value=5.7e-16  Score=109.14  Aligned_cols=81  Identities=21%  Similarity=0.375  Sum_probs=71.4

Q ss_pred             CCCCcEEEEcCC--CcCCc---------HHHHHHHHHhCCCeeEEEEeeC-CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347           6 MERGTRVYVGGL--TETVK---------KEDLELEFEKFGKLNSVWVAFN-PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus         6 ~~~~~~lfV~nL--p~~~t---------e~~L~~~F~~~G~V~~v~i~~d-~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ...+++|+|.||  |.++.         +++|++.|++||+|+.|+++.+ ++++|||+|+++++|++|++.||+..|++
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~g   84 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG   84 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHHHHHHHHHSTTCEETT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHHHHHHHHHhCCcEECC
Confidence            467889999998  55432         3678899999999999999887 78999999999999999999999999999


Q ss_pred             cEEEEEEeecCCC
Q psy2347          74 SKLRVEISRGRGR   86 (207)
Q Consensus        74 ~~l~V~~a~~k~~   86 (207)
                      ++|+|+++.++..
T Consensus        85 r~i~v~~~~g~~~   97 (99)
T d2dita1          85 RQITAQAWDGTTD   97 (99)
T ss_dssp             EECEEEECCSCCC
T ss_pred             EEEEEEEeCCcCC
Confidence            9999999987653

>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=99.61  E-value=4.2e-17  Score=116.11  Aligned_cols=72  Identities=25%  Similarity=0.298  Sum_probs=66.3

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEe
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEIS   81 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a   81 (207)
                      +.|+|.+++.+++|++|+++|++||+|++|+|+++    ++++|||+|+++++|++|++.||+++|++++|+|+++
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 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34677778888999999999999999999999876    7899999999999999999999999999999999985

>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=99.59  E-value=1.6e-15  Score=103.03  Aligned_cols=73  Identities=16%  Similarity=0.235  Sum_probs=63.7

Q ss_pred             CcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcE-EEEEEeecC
Q psy2347           9 GTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSK-LRVEISRGR   84 (207)
Q Consensus         9 ~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~-l~V~~a~~k   84 (207)
                      .+.|+|.+||++++++.| ++|++||+|+++++..+ ++||||+|+++++|++||+ ||++.|+++. |.|+.+..|
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~-~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT-GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS-SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCH
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC-CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCCh
Confidence            467999999999997666 57999999999998765 8999999999999999996 8999999985 678877665

>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=99.52  E-value=8.2e-15  Score=103.93  Aligned_cols=77  Identities=18%  Similarity=0.260  Sum_probs=67.4

Q ss_pred             CCCcEEEEcCC--CcCC--------cHHHHHHHHHhCCCeeEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCc
Q psy2347           7 ERGTRVYVGGL--TETV--------KKEDLELEFEKFGKLNSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQ   69 (207)
Q Consensus         7 ~~~~~lfV~nL--p~~~--------te~~L~~~F~~~G~V~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~   69 (207)
                      +|++.|.|.||  |.++        ..++|++.|++||.|++|.|+++       ..+++||+|+++++|++|++.||+.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            47889999999  5443        23578999999999999999865       3589999999999999999999999


Q ss_pred             eeCCcEEEEEEeec
Q psy2347          70 DLMGSKLRVEISRG   83 (207)
Q Consensus        70 ~i~g~~l~V~~a~~   83 (207)
                      .+++|+|.|.++.+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999865

>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=99.52  E-value=1.1e-14  Score=112.17  Aligned_cols=78  Identities=23%  Similarity=0.447  Sum_probs=68.7

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-----CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-----PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-----~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      ..++|||+|||+++|+++|+++|++||+|++|.|+++     ++++|||+|.++++|++|++. +...+..+.+.+....
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhh
Confidence            3479999999999999999999999999999999876     578999999999999999985 6777888888888776


Q ss_pred             cCCC
Q psy2347          83 GRGR   86 (207)
Q Consensus        83 ~k~~   86 (207)
                      ++..
T Consensus        84 ~~~~   87 (183)
T d1u1qa_          84 SRED   87 (183)
T ss_dssp             CTTG
T ss_pred             hccc
Confidence            5543

>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=98.38  E-value=3.6e-07  Score=61.38  Aligned_cols=72  Identities=15%  Similarity=0.228  Sum_probs=57.6

Q ss_pred             CCCcEEEEcCCCcCC------cH---HHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEE
Q psy2347           7 ERGTRVYVGGLTETV------KK---EDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLR   77 (207)
Q Consensus         7 ~~~~~lfV~nLp~~~------te---~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~   77 (207)
                      ++.-+|.|.=+.++.      +|   ++|.+.|.+||+|.-|+++.+   ...|+|.+-++|.+|++ |++.++.++.|+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d---~mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG---QMLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT---EEEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC---eEEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            456677775443222      22   467788999999999999977   89999999999999998 699999999999


Q ss_pred             EEEee
Q psy2347          78 VEISR   82 (207)
Q Consensus        78 V~~a~   82 (207)
                      |....
T Consensus        89 It~~~   93 (95)
T d1ufwa_          89 ISGPS   93 (95)
T ss_dssp             EECCC
T ss_pred             EecCC
Confidence            97654

>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=98.14  E-value=3.4e-06  Score=53.88  Aligned_cols=59  Identities=25%  Similarity=0.273  Sum_probs=52.2

Q ss_pred             HHHHHHHHhCCCeeEEEEeeC--CCcEEEEEEcCHHHHHHHHHhcCCceeCCcEEEEEEee
Q psy2347          24 EDLELEFEKFGKLNSVWVAFN--PPGFAFVEFSNQIDAEAACDSMNDQDLMGSKLRVEISR   82 (207)
Q Consensus        24 ~~L~~~F~~~G~V~~v~i~~d--~rG~afV~F~~~e~A~~Al~~l~g~~i~g~~l~V~~a~   82 (207)
                      +.|.++|++++.|.++.|...  -.-.|-|...+.++|..|+..|+..+|..++|.|.+++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            456678899999999998655  45689999999999999999999999999999999875

>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=98.00  E-value=7.8e-06  Score=55.21  Aligned_cols=64  Identities=20%  Similarity=0.222  Sum_probs=55.4

Q ss_pred             cEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeC-------CCcEEEEEEcCHHHHHHHHHhcCCceeCC
Q psy2347          10 TRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFN-------PPGFAFVEFSNQIDAEAACDSMNDQDLMG   73 (207)
Q Consensus        10 ~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d-------~rG~afV~F~~~e~A~~Al~~l~g~~i~g   73 (207)
                      ++|.|..||+.+||+++.+.+...+++.....+.-       .-.-|+|.|.+.+++....+.++++.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            58999999999999999999999888887766543       23579999999999999999999998743

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.97  E-value=0.0011  Score=44.66  Aligned_cols=60  Identities=22%  Similarity=0.344  Sum_probs=48.0

Q ss_pred             CCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEcCHHHHHHHHHhcC
Q psy2347           5 MMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFSNQIDAEAACDSMN   67 (207)
Q Consensus         5 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~~~e~A~~Al~~l~   67 (207)
                      +.+....||.-.+|.++...||.++|+.||.|.--.| .|  --|||...+.|+|+.+++.++
T Consensus        11 ~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd--TSa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          11 LQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD--TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET--TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC--ceEEEEecCHHHHHHHHHHhc
Confidence            3455567788789999999999999999998764444 33  379999999999998887544

>d1kvja_ d.58.17.1 (A:) Menkes copper-transporting ATPase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: HMA, heavy metal-associated domain
family: HMA, heavy metal-associated domain
domain: Menkes copper-transporting ATPase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.42  E-value=0.44  Score=29.76  Aligned_cols=65  Identities=18%  Similarity=0.194  Sum_probs=51.0

Q ss_pred             CCCCCCCCCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEc----CHHHHHHHHHhc
Q psy2347           1 MSDGMMERGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFS----NQIDAEAACDSM   66 (207)
Q Consensus         1 ms~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~----~~e~A~~Al~~l   66 (207)
                      |+.......-+|.|.++.-..=...|++.|++.-.|.++++... ...+-|+|+    +.++..++|+.+
T Consensus         1 m~~~~~~~~~~l~V~gm~C~~C~~~ie~~l~~~~gv~~v~v~~~-~~~v~v~~d~~~~~~~~i~~~i~~~   69 (79)
T d1kvja_           1 MDPSMGVNSVTISVEGMTCNSCVWTIEQQIGKVNGVHHIKVSLE-EKNATIIYDPKLQTPKTLQEAIDDM   69 (79)
T ss_dssp             CCSSTTCEEEEEEEESCCSTHHHHHHHHHHHTTTTCSEEEEETT-TTEEEEEECTTTCCHHHHHHHHHHH
T ss_pred             CCCCCCceEEEEEECCeecHHHHHHHHHHHhcCCCceEEEEECC-CCEEEEEECCCCCCHHHHHHHHHhc
Confidence            44455555668999999877777889999999988999988776 668889985    667777777764

>d2aw0a_ d.58.17.1 (A:) Menkes copper-transporting ATPase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: HMA, heavy metal-associated domain
family: HMA, heavy metal-associated domain
domain: Menkes copper-transporting ATPase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.88  E-value=1.6  Score=26.31  Aligned_cols=58  Identities=19%  Similarity=0.215  Sum_probs=45.1

Q ss_pred             CCcEEEEcCCCcCCcHHHHHHHHHhCCCeeEEEEeeCCCcEEEEEEc----CHHHHHHHHHhc
Q psy2347           8 RGTRVYVGGLTETVKKEDLELEFEKFGKLNSVWVAFNPPGFAFVEFS----NQIDAEAACDSM   66 (207)
Q Consensus         8 ~~~~lfV~nLp~~~te~~L~~~F~~~G~V~~v~i~~d~rG~afV~F~----~~e~A~~Al~~l   66 (207)
                      +..+|-|.++.-..=...|++.+.+.--|.++++... ...+.|+|+    +.++..++|+.+
T Consensus         3 ~~~~l~V~GM~C~~C~~~Ie~~l~~~~GV~~v~v~~~-~~~v~v~~d~~~~~~~~i~~~i~~~   64 (72)
T d2aw0a_           3 QETVINIDGMTCNSCVQSIEGVISKKPGVKSIRVSLA-NSNGTVEYDPLLTSPETLRGAIEDM   64 (72)
T ss_dssp             EEEEEEEECCCSHHHHHHHHHHHHTSTTCCCEEEETT-TTEEEEEECTTTCCHHHHHHHHHHH
T ss_pred             EEEEEEECCcccHHHHHHHHHHHhcCCCcEEEEEECC-CCEEEEEECCCCCCHHHHHHHHHhh
Confidence            3456778888776667889999999888998888765 678999994    567777777764