Psyllid ID: psy7847

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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
Protein Sequence
MLGLRPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccEEEccccccccHHHHHHHHccccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEcccccccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEcccHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHHHcccccEEEcccEEEEEEcccc
Coil and Loop (DISEMBL)
mlglrpgpisswiKKTCEDENDFRLFcgdlgndvtdELLIRTFSKYPSFLKAKVVRdkrtnktkgfgfvsfkdpqDFIRANKEMNDDFRLFCgdlgndvtdELLIRTFSKYPSFLKAKVVRdkrtnktkgfgfvsfkdpqDFIRAnkemnefphlfvgdlktrssitlkg
Flexible Loop (DISEMBL)
mlglrpgpissWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFskypsflkakvvrdkrtnktkgfgfvsfkdpqDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFskypsflkakvvrdkrtnktkgfgfvsfkdpQDFIRANKEmnefphlfvgdlktrssitlkg
Low Complexity Region (SEG)
MLGLRPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG
Disordered region (IsUnstruct)
*********SSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL**********
Disordered Region (DISOPRED)
************************LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS******
Disordered Region (DISEMBL)
MLGLRPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG
Disordered Region (DISPRO)
*LG**P*************ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLGLRPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG
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	170	2.2.26 [Sep-21-2011]
Q6DRG1	402	RNA-binding protein 42 OS	yes	N/A	0.388	0.164	0.757	6e-26
A2VDB3	392	RNA-binding protein 42 OS	N/A	N/A	0.382	0.165	0.738	1e-25
Q9BTD8	480	RNA-binding protein 42 OS	yes	N/A	0.464	0.164	0.629	1e-25
Q0P5L0	448	RNA-binding protein 42 OS	yes	N/A	0.464	0.176	0.629	1e-25
Q6AXT7	474	RNA-binding protein 42 OS	yes	N/A	0.464	0.166	0.629	1e-25
Q91V81	474	RNA-binding protein 42 OS	yes	N/A	0.464	0.166	0.629	1e-25
Q66KL9	392	RNA-binding protein 42 OS	yes	N/A	0.388	0.168	0.727	1e-25
Q9SAB3	405	Polyadenylate-binding pro	no	N/A	0.976	0.409	0.306	7e-19
Q10355	219	Uncharacterized RNA-bindi	yes	N/A	0.405	0.315	0.6	1e-16
Q9LEB3	428	Polyadenylate-binding pro	N/A	N/A	0.8	0.317	0.329	6e-16

>sp|Q6DRG1|RBM42_DANRE RNA-binding protein 42 OS=Danio rerio GN=rbm42 PE=2 SV=2

 Score =  116 bits (291), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 50/66 (75%), Positives = 59/66 (89%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
            DDFR+FCGDLGN+V D++L R FS+YPSFLKAKVVRDKRT KTKG+GFVSFKDP D++R
Sbjct: 300 TDDFRIFCGDLGNEVNDDILARAFSRYPSFLKAKVVRDKRTGKTKGYGFVSFKDPNDYVR 359

Query: 145 ANKEMN 150
           A +EMN
Sbjct: 360 AMREMN 365

May bind RNA.
Danio rerio (taxid: 7955)

>sp|A2VDB3|RBM42_XENLA RNA-binding protein 42 OS=Xenopus laevis GN=rbm42 PE=2 SV=1

 Score =  115 bits (289), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 48/65 (73%), Positives = 59/65 (90%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           DDFR+FCGDLGN+V D++L R FS+YPSFL+AKV+RDKRT KTKG+GFVSFKDP D++RA
Sbjct: 291 DDFRIFCGDLGNEVNDDILARAFSRYPSFLRAKVIRDKRTGKTKGYGFVSFKDPNDYVRA 350

Query: 146 NKEMN 150
            +EMN
Sbjct: 351 TREMN 355

May bind RNA.

Xenopus laevis (taxid: 8355)

>sp|Q9BTD8|RBM42_HUMAN RNA-binding protein 42 OS=Homo sapiens GN=RBM42 PE=1 SV=1

 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 65/81 (80%), Gaps = 2/81 (2%)

Query: 10  SSWIKKTC--EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG 67
           SSW   +    D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT KTKG+G
Sbjct: 366 SSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGKTKGYG 425

Query: 68  FVSFKDPQDFIRANKEMNDDF 88
           FVSFKDP D++RA +EMN  +
Sbjct: 426 FVSFKDPSDYVRAMREMNGKY 446

Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA.

Homo sapiens (taxid: 9606)

>sp|Q0P5L0|RBM42_BOVIN RNA-binding protein 42 OS=Bos taurus GN=RBM42 PE=2 SV=1

 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 65/81 (80%), Gaps = 2/81 (2%)

Query: 10  SSWIKKTC--EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG 67
           SSW   +    D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT KTKG+G
Sbjct: 334 SSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGKTKGYG 393

Query: 68  FVSFKDPQDFIRANKEMNDDF 88
           FVSFKDP D++RA +EMN  +
Sbjct: 394 FVSFKDPSDYVRAMREMNGKY 414

Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA.

Bos taurus (taxid: 9913)

>sp|Q6AXT7|RBM42_RAT RNA-binding protein 42 OS=Rattus norvegicus GN=Rbm42 PE=1 SV=1

 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 65/81 (80%), Gaps = 2/81 (2%)

Query: 10  SSWIKKTC--EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG 67
           SSW   +    D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT KTKG+G
Sbjct: 360 SSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGKTKGYG 419

Query: 68  FVSFKDPQDFIRANKEMNDDF 88
           FVSFKDP D++RA +EMN  +
Sbjct: 420 FVSFKDPSDYVRAMREMNGKY 440

Binds (via the RRM domain) to the 3' untranslated region (UTR) of p21 mRNA.

Rattus norvegicus (taxid: 10116)

>sp|Q91V81|RBM42_MOUSE RNA-binding protein 42 OS=Mus musculus GN=Rbm42 PE=1 SV=1

 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 51/81 (62%), Positives = 65/81 (80%), Gaps = 2/81 (2%)

Query: 10  SSWIKKTC--EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG 67
           SSW   +    D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT KTKG+G
Sbjct: 360 SSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTGKTKGYG 419

Query: 68  FVSFKDPQDFIRANKEMNDDF 88
           FVSFKDP D++RA +EMN  +
Sbjct: 420 FVSFKDPSDYVRAMREMNGKY 440

Binds (via the RRM domain) to the 3'-untranslated region (UTR) of CDKN1A mRNA.

Mus musculus (taxid: 10090)

>sp|Q66KL9|RBM42_XENTR RNA-binding protein 42 OS=Xenopus tropicalis GN=rbm42 PE=2 SV=1

 Score =  115 bits (288), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 48/66 (72%), Positives = 60/66 (90%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           +DDFR+FCGDLGN+V D++L R FS+YPSFL+AKV+RDKRT KTKG+GFVSFKDP D++R
Sbjct: 290 SDDFRIFCGDLGNEVNDDILARAFSRYPSFLRAKVIRDKRTGKTKGYGFVSFKDPNDYVR 349

Query: 145 ANKEMN 150
           A +EMN
Sbjct: 350 AMREMN 355

May bind RNA.

Xenopus tropicalis (taxid: 8364)

>sp|Q9SAB3|RB45B_ARATH Polyadenylate-binding protein RBP45B OS=Arabidopsis thaliana GN=RBP45B PE=1 SV=1

 Score = 93.2 bits (230), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 64/209 (30%), Positives = 96/209 (45%), Gaps = 43/209 (20%)

Query: 1   MLGLRPGPISSW---------IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLK 51
           + G  P P   W         ++ T  DE    L+ GDL   + +  L   F+     + 
Sbjct: 32  IAGAAPPPPQMWNPQAAAPPSVQPTTADEIR-TLWIGDLQYWMDENFLYGCFAHTGEMVS 90

Query: 52  AKVVRDKRTNKTKGFGFVSFKD-------------------PQDFIRAN---------KE 83
           AKV+R+K+T + +G+GF+ F                     P    R N         ++
Sbjct: 91  AKVIRNKQTGQVEGYGFIEFASHAAAERVLQTFNNAPIPSFPDQLFRLNWASLSSGDKRD 150

Query: 84  MNDDFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
            + D+ +F GDL  DVTD +L+ TF + YPS   AKVV D+ T +TKG+GFV F D  + 
Sbjct: 151 DSPDYTIFVGDLAADVTDYILLETFRASYPSVKGAKVVIDRVTGRTKGYGFVRFSDESEQ 210

Query: 143 IRANKEMNEFP----HLFVGDLKTRSSIT 167
           IRA  EMN  P     + +G   ++  +T
Sbjct: 211 IRAMTEMNGVPCSTRPMRIGPAASKKGVT 239

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q10355|YDB2_SCHPO Uncharacterized RNA-binding protein C22E12.02 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC22E12.02 PE=4 SV=1

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 42/70 (60%), Positives = 51/70 (72%), Gaps = 1/70 (1%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
          D N FRLF G+LGNDV DE L + FS+YPS +K KVVRD R  KT+GFGFVSFKD   F+
Sbjct: 26 DPNHFRLFVGNLGNDVNDESLYQAFSEYPSLVKTKVVRD-REGKTRGFGFVSFKDSDQFL 84

Query: 79 RANKEMNDDF 88
          +A +E N  +
Sbjct: 85 KAWREKNGKY 94

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

>sp|Q9LEB3|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1

 Score = 83.6 bits (205), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 55/167 (32%), Positives = 80/167 (47%), Gaps = 31/167 (18%)

Query: 13  IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
           I+ + ED     ++ GDL   + +  L   FS+    +  K++R+K+T +++ +GFV F 
Sbjct: 76  IQSSSEDNKT--IWIGDLQQWMDESYLHSCFSQAGEVISVKIIRNKQTGQSERYGFVEFN 133

Query: 73  ------------------DPQDFIRAN----------KEMNDDFRLFCGDLGNDVTDELL 104
                             + +   R N           E   DF +F GDL +DVTD +L
Sbjct: 134 THAAAEKVLQSYNGTMMPNTEQPFRLNWAGFSTGEKRAETGSDFSIFVGDLASDVTDTML 193

Query: 105 IRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
             TF S+YPS   AKVV D  T  +KG+GFV F D  +  RA  EMN
Sbjct: 194 RDTFASRYPSLKGAKVVVDANTGHSKGYGFVRFGDESERSRAMTEMN 240

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.

Nicotiana plumbaginifolia (taxid: 4092)

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	170
345483765	325	PREDICTED: hypothetical protein LOC10011	0.411	0.215	0.828	9e-28
383860233	326	PREDICTED: uncharacterized protein LOC10	0.411	0.214	0.828	1e-27
307187756	325	RNA-binding protein 42 [Camponotus flori	0.411	0.215	0.828	1e-27
340718038	326	PREDICTED: hypothetical protein LOC10064	0.411	0.214	0.828	1e-27
322791811	291	hypothetical protein SINV_08146 [Solenop	0.394	0.230	0.865	1e-27
66501574	326	PREDICTED: hypothetical protein LOC40862	0.411	0.214	0.828	1e-27
307205597	325	RNA-binding protein 42 [Harpegnathos sal	0.411	0.215	0.828	2e-27
332023971	307	RNA-binding protein 42 [Acromyrmex echin	0.4	0.221	0.852	2e-27
291235049	323	PREDICTED: Temporarily Assigned Gene nam	0.411	0.216	0.785	6e-26
242006504	268	rrm-containing protein, putative [Pedicu	0.388	0.246	0.863	2e-25

>gi|345483765|ref|XP_001603091.2| PREDICTED: hypothetical protein LOC100119300 [Nasonia vitripennis]

 Score =  128 bits (321), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 64/70 (91%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 218 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 277

Query: 79  RANKEMNDDF 88
           +A KEMN  +
Sbjct: 278 KAMKEMNGRY 287

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383860233|ref|XP_003705595.1| PREDICTED: uncharacterized protein LOC100882411 [Megachile rotundata]

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 64/70 (91%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 219 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 278

Query: 79  RANKEMNDDF 88
           +A KEMN  +
Sbjct: 279 KAMKEMNGRY 288

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307187756|gb|EFN72728.1| RNA-binding protein 42 [Camponotus floridanus]

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 64/70 (91%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 218 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 277

Query: 79  RANKEMNDDF 88
           +A KEMN  +
Sbjct: 278 KAMKEMNGRY 287

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340718038|ref|XP_003397479.1| PREDICTED: hypothetical protein LOC100647660 [Bombus terrestris] gi|350400127|ref|XP_003485747.1| PREDICTED: hypothetical protein LOC100743172 [Bombus impatiens]

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 64/70 (91%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 219 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 278

Query: 79  RANKEMNDDF 88
           +A KEMN  +
Sbjct: 279 KAMKEMNGRY 288

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322791811|gb|EFZ16028.1| hypothetical protein SINV_08146 [Solenopsis invicta]

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 58/67 (86%), Positives = 63/67 (94%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 225 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 284

Query: 79  RANKEMN 85
           +A KEMN
Sbjct: 285 KAMKEMN 291

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66501574|ref|XP_392161.2| PREDICTED: hypothetical protein LOC408620 isoform 1 [Apis mellifera]

 Score =  127 bits (319), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 64/70 (91%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 219 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 278

Query: 79  RANKEMNDDF 88
           +A KEMN  +
Sbjct: 279 KAMKEMNGRY 288

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307205597|gb|EFN83889.1| RNA-binding protein 42 [Harpegnathos saltator]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 58/70 (82%), Positives = 64/70 (91%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 218 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 277

Query: 79  RANKEMNDDF 88
           +A KEMN  +
Sbjct: 278 KAMKEMNGRY 287

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023971|gb|EGI64189.1| RNA-binding protein 42 [Acromyrmex echinatior]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 58/68 (85%), Positives = 64/68 (94%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           DE+DFR+FCGDLGNDVTDE+L+R F KYPSF KAKVVRDKRTNKTKGFGFVSFKDPQDFI
Sbjct: 218 DEDDFRIFCGDLGNDVTDEMLVRVFGKYPSFQKAKVVRDKRTNKTKGFGFVSFKDPQDFI 277

Query: 79  RANKEMND 86
           +A KEMN+
Sbjct: 278 KAMKEMNE 285

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291235049|ref|XP_002737458.1| PREDICTED: Temporarily Assigned Gene name family member (tag-262)-like [Saccoglossus kowalevskii]

 Score =  122 bits (305), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 55/70 (78%), Positives = 61/70 (87%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           D NDFR+FCGDLGN+VTDELL R F KYPSFLKAKVVRDKRTNKTKGFGFVSF+DP DF+
Sbjct: 220 DPNDFRIFCGDLGNEVTDELLTRVFGKYPSFLKAKVVRDKRTNKTKGFGFVSFRDPNDFV 279

Query: 79  RANKEMNDDF 88
            A +EMN  +
Sbjct: 280 AAMREMNGKY 289

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|242006504|ref|XP_002424090.1| rrm-containing protein, putative [Pediculus humanus corporis] gi|212507396|gb|EEB11352.1| rrm-containing protein, putative [Pediculus humanus corporis]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/66 (86%), Positives = 62/66 (93%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           +DDFR+FCGDLGNDVTDE+L R F+KY SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI+
Sbjct: 162 DDDFRIFCGDLGNDVTDEVLTRAFNKYNSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIK 221

Query: 145 ANKEMN 150
           A KEMN
Sbjct: 222 AMKEMN 227

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

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	170
ZFIN|ZDB-GENE-040809-2	402	rbm42 "RNA binding motif prote	0.382	0.161	0.769	4.6e-25
UNIPROTKB|K7EQ03	426	RBM42 "RNA-binding protein 42"	0.5	0.199	0.609	9.5e-25
UNIPROTKB|F1N7X9	448	RBM42 "RNA-binding protein 42"	0.5	0.189	0.609	1.5e-24
UNIPROTKB|Q0P5L0	448	RBM42 "RNA-binding protein 42"	0.5	0.189	0.609	1.5e-24
UNIPROTKB|K7EP90	458	RBM42 "RNA-binding protein 42"	0.5	0.185	0.609	1.7e-24
MGI|MGI:1915285	474	Rbm42 "RNA binding motif prote	0.5	0.179	0.609	2e-24
RGD|1306184	474	Rbm42 "RNA binding motif prote	0.5	0.179	0.609	2e-24
UNIPROTKB|Q6AXT7	474	Rbm42 "RNA-binding protein 42"	0.5	0.179	0.609	2e-24
UNIPROTKB|F1RM56	477	RBM42 "Uncharacterized protein	0.5	0.178	0.609	2.1e-24
UNIPROTKB|Q9BTD8	480	RBM42 "RNA-binding protein 42"	0.5	0.177	0.609	2.2e-24

ZFIN|ZDB-GENE-040809-2 rbm42 "RNA binding motif protein 42" [Danio rerio (taxid:7955)]

 Score = 285 (105.4 bits), Expect = 4.6e-25, P = 4.6e-25
 Identities = 50/65 (76%), Positives = 59/65 (90%)

Query:    86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
             DDFR+FCGDLGN+V D++L R FS+YPSFLKAKVVRDKRT KTKG+GFVSFKDP D++RA
Sbjct:   301 DDFRIFCGDLGNEVNDDILARAFSRYPSFLKAKVVRDKRTGKTKGYGFVSFKDPNDYVRA 360

Query:   146 NKEMN 150
              +EMN
Sbjct:   361 MREMN 365

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0002088 "lens development in camera-type eye" evidence=IMP

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|K7EQ03 RBM42 "RNA-binding protein 42" [Homo sapiens (taxid:9606)]

 Score = 283 (104.7 bits), Expect = 9.5e-25, P = 9.5e-25
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   306 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 365

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   366 KTKGYGFVSFKDPSDYVRAMREMNGKY 392

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1N7X9 RBM42 "RNA-binding protein 42" [Bos taurus (taxid:9913)]

 Score = 283 (104.7 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   328 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 387

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   388 KTKGYGFVSFKDPSDYVRAMREMNGKY 414

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q0P5L0 RBM42 "RNA-binding protein 42" [Bos taurus (taxid:9913)]

 Score = 283 (104.7 bits), Expect = 1.5e-24, P = 1.5e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   328 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 387

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   388 KTKGYGFVSFKDPSDYVRAMREMNGKY 414

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|K7EP90 RBM42 "RNA-binding protein 42" [Homo sapiens (taxid:9606)]

 Score = 283 (104.7 bits), Expect = 1.7e-24, P = 1.7e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   338 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 397

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   398 KTKGYGFVSFKDPSDYVRAMREMNGKY 424

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1915285 Rbm42 "RNA binding motif protein 42" [Mus musculus (taxid:10090)]

 Score = 283 (104.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   354 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 413

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   414 KTKGYGFVSFKDPSDYVRAMREMNGKY 440

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

RGD|1306184 Rbm42 "RNA binding motif protein 42" [Rattus norvegicus (taxid:10116)]

 Score = 283 (104.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   354 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 413

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   414 KTKGYGFVSFKDPSDYVRAMREMNGKY 440

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q6AXT7 Rbm42 "RNA-binding protein 42" [Rattus norvegicus (taxid:10116)]

 Score = 283 (104.7 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   354 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 413

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   414 KTKGYGFVSFKDPSDYVRAMREMNGKY 440

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1RM56 RBM42 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 283 (104.7 bits), Expect = 2.1e-24, P = 2.1e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   357 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 416

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   417 KTKGYGFVSFKDPSDYVRAMREMNGKY 443

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q9BTD8 RBM42 "RNA-binding protein 42" [Homo sapiens (taxid:9606)]

 Score = 283 (104.7 bits), Expect = 2.2e-24, P = 2.2e-24
 Identities = 53/87 (60%), Positives = 68/87 (78%)

Query:     4 LRPGPISSWIKKTC-E-DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 61
             +R    SSW   +  E D +DFR+FCGDLGN+V D++L R FS++PSFLKAKV+RDKRT 
Sbjct:   360 IRTAAGSSWEDPSLLEWDADDFRIFCGDLGNEVNDDILARAFSRFPSFLKAKVIRDKRTG 419

Query:    62 KTKGFGFVSFKDPQDFIRANKEMNDDF 88
             KTKG+GFVSFKDP D++RA +EMN  +
Sbjct:   420 KTKGYGFVSFKDPSDYVRAMREMNGKY 446

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q91V81	RBM42_MOUSE	No assigned EC number	0.6296	0.4647	0.1666	yes	N/A
Q9BTD8	RBM42_HUMAN	No assigned EC number	0.6296	0.4647	0.1645	yes	N/A
Q6AXT7	RBM42_RAT	No assigned EC number	0.6296	0.4647	0.1666	yes	N/A
Q0P5L0	RBM42_BOVIN	No assigned EC number	0.6296	0.4647	0.1763	yes	N/A
Q10355	YDB2_SCHPO	No assigned EC number	0.6	0.4058	0.3150	yes	N/A

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	170
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-40
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-38
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-18
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-17
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	6e-16
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	6e-16
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-15
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-15
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-15
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-15
smart00360	73	smart00360, RRM, RNA recognition motif	3e-14
smart00360	73	smart00360, RRM, RNA recognition motif	4e-14
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	7e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	5e-12
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-11
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	3e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	3e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	8e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	8e-10
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	9e-10
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-09
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	1e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-09
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-09
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	1e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	3e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-09
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	9e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-08
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	3e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-08
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	9e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	9e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	9e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	1e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	5e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-07
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	9e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	9e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	9e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	9e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-06
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-06
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	3e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	4e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	4e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	6e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	6e-06
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-06
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	8e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	9e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	1e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-05
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	3e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	4e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	4e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	4e-05
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	4e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	5e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	5e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	5e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	6e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	6e-05
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	6e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	7e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-04
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-04
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	3e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	3e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	3e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	3e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	3e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	4e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-04
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	5e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	5e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	5e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-04
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-04
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	6e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	7e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	7e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	7e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	9e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.001
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.001
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	0.001
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	0.001
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.001
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.001
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.001
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.002
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.002
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	0.002
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.002
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.002
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.002
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.002
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.002
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.002
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.003
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.003
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.003
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.003
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.003
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.003
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	0.003
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	0.003
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.004
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.004
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.004
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.004
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.004
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.004

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

 Score =  130 bits (328), Expect = 5e-40
 Identities = 50/67 (74%), Positives = 58/67 (86%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           ENDFR+F GDLGN+VTDE+L R FSKYPSF KAKVVRDKRT K+KG+GFVSF DP D++
Sbjct: 3  PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62

Query: 79 RANKEMN 85
          +A KEMN
Sbjct: 63 KAMKEMN 69

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score =  125 bits (316), Expect = 3e-38
 Identities = 48/65 (73%), Positives = 57/65 (87%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           +DFR+F GDLGN+VTDE+L R FSKYPSF KAKVVRDKRT K+KG+GFVSF DP D+++A
Sbjct: 5   NDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKA 64

Query: 146 NKEMN 150
            KEMN
Sbjct: 65  MKEMN 69

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 80.2 bits (198), Expect = 4e-18
 Identities = 44/169 (26%), Positives = 74/169 (43%), Gaps = 45/169 (26%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L+  +L   V ++ L   F+K+     A V++D  + +++GF FV+F+  +D  +A +EM
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 85  ND--------DFRLFCG-----------------------------------DLGNDVTD 101
           N           +L+ G                                   +L + VTD
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           E L   FS+      AKV+ D+    ++GFGFV F +P++  RA  EM+
Sbjct: 300 EKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEMH 347

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

 Score = 78.7 bits (194), Expect = 1e-17
 Identities = 44/174 (25%), Positives = 82/174 (47%), Gaps = 36/174 (20%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           +F  +L   V ++ L  TFSK+ + L  KV  D+   K++G+GFV F+  +    A +++
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 85  N----DDFRLFCG----------------------DLGNDVTDELLIRTFSKYPSFLKAK 118
           N    +D  ++ G                      +L   V ++ L   F+K+     A 
Sbjct: 150 NGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA 209

Query: 119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN--EFPH------LFVGDLKTRS 164
           V++D  + +++GF FV+F+  +D  +A +EMN  +         L+VG  + R+
Sbjct: 210 VMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRA 262

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

 Score = 68.3 bits (167), Expect = 6e-16
 Identities = 27/61 (44%), Positives = 39/61 (63%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F GDL  +VTD  L   FS +PS   A+V+ D ++ +++G+GFVSF+  QD   A  EM
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 85 N 85
          N
Sbjct: 62 N 62

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

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

 Score = 68.3 bits (167), Expect = 6e-16
 Identities = 27/61 (44%), Positives = 39/61 (63%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F GDL  +VTD  L   FS +PS   A+V+ D ++ +++G+GFVSF+  QD   A  EM
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 150 N 150
           N
Sbjct: 62  N 62

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

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

 Score = 67.7 bits (166), Expect = 1e-15
 Identities = 33/65 (50%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 22 DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          D  +F GDL  DVTD +L  TF ++YPS   AKVV D  T ++KG+GFV F D  +  RA
Sbjct: 1  DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 81 NKEMN 85
            EMN
Sbjct: 61 LTEMN 65

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

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

 Score = 67.7 bits (166), Expect = 1e-15
 Identities = 33/65 (50%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 87  DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           D  +F GDL  DVTD +L  TF ++YPS   AKVV D  T ++KG+GFV F D  +  RA
Sbjct: 1   DHSIFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRA 60

Query: 146 NKEMN 150
             EMN
Sbjct: 61  LTEMN 65

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

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

 Score = 71.0 bits (174), Expect = 6e-15
 Identities = 45/149 (30%), Positives = 72/149 (48%), Gaps = 24/149 (16%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L+ GDL  DVT+  L   F  +   L  +V RD  T ++ G+G+V+F++P D  RA + M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 85  NDD------FRL-----------------FCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
           N         R+                 F  +L   V ++ L  TFSK+ + L  KV  
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122

Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           D+   K++G+GFV F+  +    A +++N
Sbjct: 123 DE-NGKSRGYGFVHFEKEESAKAAIQKVN 150

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

 Score = 65.6 bits (161), Expect = 6e-15
 Identities = 24/63 (38%), Positives = 36/63 (57%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+ +V+F++P D  RA   +
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 85 NDD 87
          N D
Sbjct: 62 NFD 64

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

 Score = 65.5 bits (160), Expect = 6e-15
 Identities = 24/61 (39%), Positives = 36/61 (59%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F GDL  ++  E L   F+ +     A+VV+D +T K+KG+GFVSF   +D   A + M
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 85 N 85
          N
Sbjct: 62 N 62

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

 Score = 65.5 bits (160), Expect = 6e-15
 Identities = 24/61 (39%), Positives = 36/61 (59%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F GDL  ++  E L   F+ +     A+VV+D +T K+KG+GFVSF   +D   A + M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 150 N 150
           N
Sbjct: 62  N 62

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|214636 smart00360, RRM, RNA recognition motif

 Score = 63.4 bits (155), Expect = 3e-14
 Identities = 26/65 (40%), Positives = 37/65 (56%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            LF G+L  D T+E L   FSK+      ++VRDK T K+KGF FV F+  +D  +A + 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 149 MNEFP 153
           +N   
Sbjct: 61  LNGKE 65

Length = 73

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

 Score = 63.4 bits (155), Expect = 4e-14
 Identities = 26/62 (41%), Positives = 37/62 (59%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           LF G+L  D T+E L   FSK+      ++VRDK T K+KGF FV F+  +D  +A + 
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 84 MN 85
          +N
Sbjct: 61 LN 62

Length = 73

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

 Score = 62.9 bits (154), Expect = 7e-14
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+ +V+F++P D  RA   +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 150 N 150
           N
Sbjct: 62  N 62

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 58.8 bits (143), Expect = 2e-12
 Identities = 25/63 (39%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF G+L  D T+E L   FSK+      ++VRD+ T ++KGF FV F+D +D  +A + +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 150 NEF 152
           N  
Sbjct: 60  NGK 62

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

>gnl|CDD|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 = 58.8 bits (143), Expect = 2e-12
 Identities = 26/63 (41%), Positives = 38/63 (60%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L N+ TD+ L + F+ + + + AKV  DK T ++K FGFVS+ +P+    A K M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 150 NEF 152
           N F
Sbjct: 61  NGF 63

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

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

 Score = 58.4 bits (142), Expect = 3e-12
 Identities = 25/61 (40%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF G+L  D T+E L   FSK+      ++VRD+ T ++KGF FV F+D +D  +A + +
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 85 N 85
          N
Sbjct: 60 N 60

(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|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 = 58.0 bits (141), Expect = 5e-12
 Identities = 25/61 (40%), Positives = 37/61 (60%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L N+ TD+ L + F+ + + + AKV  DK T ++K FGFVS+ +P+    A K M
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 85 N 85
          N
Sbjct: 61 N 61

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|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 56.2 bits (136), Expect = 3e-11
 Identities = 30/65 (46%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          +F LF GDL  DV D  L   FS +YPS   AKVV D+    ++G+GFV F D  +  RA
Sbjct: 1  EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRA 59

Query: 81 NKEMN 85
            EM 
Sbjct: 60 LTEMQ 64

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 56.2 bits (136), Expect = 3e-11
 Identities = 30/65 (46%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           +F LF GDL  DV D  L   FS +YPS   AKVV D+    ++G+GFV F D  +  RA
Sbjct: 1   EFSLFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQ-NGNSRGYGFVRFSDESEQKRA 59

Query: 146 NKEMN 150
             EM 
Sbjct: 60  LTEMQ 64

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|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 = 55.2 bits (133), Expect = 7e-11
 Identities = 25/62 (40%), Positives = 38/62 (61%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++P D   A   
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 84 MN 85
          MN
Sbjct: 62 MN 63

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|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 = 55.2 bits (133), Expect = 7e-11
 Identities = 25/62 (40%), Positives = 38/62 (61%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++P D   A   
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 149 MN 150
           MN
Sbjct: 62  MN 63

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|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 = 53.8 bits (130), Expect = 2e-10
 Identities = 19/61 (31%), Positives = 35/61 (57%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L    T++ L   FSK+    +  +++D  T +++GFGFV+F+  +D   A +++
Sbjct: 4  LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 85 N 85
          N
Sbjct: 64 N 64

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|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 = 53.8 bits (130), Expect = 2e-10
 Identities = 19/61 (31%), Positives = 35/61 (57%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L    T++ L   FSK+    +  +++D  T +++GFGFV+F+  +D   A +++
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 150 N 150
           N
Sbjct: 64  N 64

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

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

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 24/62 (38%), Positives = 40/62 (64%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L    TD+ L + FS++    +A V+ D++T K++G+GFV+FKD +   RA K+
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 84 MN 85
           N
Sbjct: 62 PN 63

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

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 24/62 (38%), Positives = 40/62 (64%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L    TD+ L + FS++    +A V+ D++T K++G+GFV+FKD +   RA K+
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 149 MN 150
            N
Sbjct: 62  PN 63

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

 Score = 52.3 bits (126), Expect = 8e-10
 Identities = 20/58 (34%), Positives = 29/58 (50%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
           L  D+T E L   F         K+VRD+ T ++ G+GFV + D  D  +A   +N F
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGF 65

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

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

 Score = 52.2 bits (126), Expect = 8e-10
 Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
          LG D+ DE L   F KY     AKV++D    K+KGFGFV+F++ +   +A +E+N 
Sbjct: 9  LGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 55.8 bits (134), Expect = 9e-10
 Identities = 38/140 (27%), Positives = 58/140 (41%), Gaps = 24/140 (17%)

Query: 30  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN---- 85
           L  D+TD  L   F         +++RD +T  + G+ FV F    D  RA K +N    
Sbjct: 115 LPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITV 174

Query: 86  -----------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
                             D  L+  +L   +TD+ L   F KY   ++  ++RDK T   
Sbjct: 175 RNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTP 234

Query: 129 KGFGFVSF---KDPQDFIRA 145
           +G  FV F   ++ Q+ I A
Sbjct: 235 RGVAFVRFNKREEAQEAISA 254

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 4/74 (5%)

Query: 22 DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          ++ +F GDL  +V +  L+  F S++PS   AK++ D  T  ++G+GFV F D  D  RA
Sbjct: 1  EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 81 NKEMNDDFRLFCGD 94
            EM     ++CG 
Sbjct: 61 LIEMQG---VYCGG 71

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

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

 Score = 51.8 bits (124), Expect = 1e-09
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 87  DFRLFCGDLGNDVTDELLIRTF-SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           ++ +F GDL  +V +  L+  F S++PS   AK++ D  T  ++G+GFV F D  D  RA
Sbjct: 1   EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 146 NKEM 149
             EM
Sbjct: 61  LIEM 64

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

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

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+  +L + + DE L   FS + +   AKV+ D++  ++KGFGFV F  P++  +A  EM
Sbjct: 4  LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 85 N 85
          N
Sbjct: 63 N 63

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

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+  +L + + DE L   FS + +   AKV+ D++  ++KGFGFV F  P++  +A  EM
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 150 N 150
           N
Sbjct: 63  N 63

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 23/51 (45%), Positives = 31/51 (60%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          +LF G L  DVT+E L   FS+Y +    ++V DK T K +GF FV+F D 
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY 51

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 23/51 (45%), Positives = 31/51 (60%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           +LF G L  DVT+E L   FS+Y +    ++V DK T K +GF FV+F D 
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDY 51

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

 Score = 55.3 bits (132), Expect = 1e-09
 Identities = 30/97 (30%), Positives = 48/97 (49%)

Query: 57  DKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLK 116
           D     TK F    F+  +      K   ++  LF G+L  DVT+E L   F K+    +
Sbjct: 85  DGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKR 144

Query: 117 AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
            ++VRD+ T K++GF FV F+  +   +A +E+N   
Sbjct: 145 VRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKE 181

Length = 306

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

 Score = 51.4 bits (124), Expect = 2e-09
 Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
           LG D+ DE L   F KY     AKV++D    K+KGFGFV+F++ +   +A +E+N 
Sbjct: 9   LGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEELNG 64

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

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 23/63 (36%), Positives = 39/63 (61%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           LF G+L   V DE L   F K+ + + A+V+ D+ T +++GFG+V F+ P+D  +A + 
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 84 MND 86
          M+ 
Sbjct: 61 MDG 63

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

 Score = 50.8 bits (122), Expect = 2e-09
 Identities = 23/63 (36%), Positives = 39/63 (61%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            LF G+L   V DE L   F K+ + + A+V+ D+ T +++GFG+V F+ P+D  +A + 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 149 MNE 151
           M+ 
Sbjct: 61  MDG 63

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

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 2/72 (2%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF  +L     ++ L + FSK+    +  V  DK++ K+KGF +V F DP+D ++A KE
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 84 MNDDFRLFCGDL 95
          +  D ++F G L
Sbjct: 64 L--DGKVFQGRL 73

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

 Score = 50.7 bits (122), Expect = 2e-09
 Identities = 19/63 (30%), Positives = 37/63 (58%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ G+L  ++T++ L   F  +      ++ RD  T ++KG+GF+ F D +D  +A +++
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 150 NEF 152
           N F
Sbjct: 61  NGF 63

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

 Score = 50.9 bits (122), Expect = 3e-09
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           RLF  +L     ++ L + FSK+    +  V  DK++ K+KGF +V F DP+D ++A KE
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 149 MN 150
           ++
Sbjct: 64  LD 65

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

 Score = 54.2 bits (129), Expect = 4e-09
 Identities = 26/81 (32%), Positives = 42/81 (51%)

Query: 5   RPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 64
                 S   +    E +  LF G+L  DVT+E L   F K+    + ++VRD+ T K++
Sbjct: 98  LFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSR 157

Query: 65  GFGFVSFKDPQDFIRANKEMN 85
           GF FV F+  +   +A +E+N
Sbjct: 158 GFAFVEFESEESAEKAIEELN 178

Length = 306

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

 Score = 50.0 bits (120), Expect = 5e-09
 Identities = 19/56 (33%), Positives = 28/56 (50%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          L  D+T E L   F         K+VRD+ T ++ G+GFV + D  D  +A   +N
Sbjct: 8  LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLN 63

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

 Score = 49.6 bits (119), Expect = 7e-09
 Identities = 18/61 (29%), Positives = 36/61 (59%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+ G+L  ++T++ L   F  +      ++ RD  T ++KG+GF+ F D +D  +A +++
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 85 N 85
          N
Sbjct: 61 N 61

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

 Score = 49.5 bits (119), Expect = 8e-09
 Identities = 19/63 (30%), Positives = 37/63 (58%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+ G+L  +VT+E L   F ++     A+V+ D+ T +++GFGFV  +  ++   A ++
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 84 MND 86
          +N 
Sbjct: 61 LNG 63

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

 Score = 49.1 bits (118), Expect = 9e-09
 Identities = 25/66 (37%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF G L  D T+E L   FSKY   +   +++D  T +++GFGFV+F DP      +K +
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSS---VDKVL 57

Query: 150 NEFPHL 155
              PH+
Sbjct: 58  AAKPHV 63

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 53.0 bits (127), Expect = 1e-08
 Identities = 40/168 (23%), Positives = 70/168 (41%), Gaps = 33/168 (19%)

Query: 18  EDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
           E E D R +F   L     +  L   FSK       + ++D+ + ++KG  +V F D + 
Sbjct: 84  EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVES 143

Query: 77  FIRA------------------NKEMN--------------DDFRLFCGDLGNDVTDELL 104
            I+A                    E N              +  +L+ G+L  ++T++ L
Sbjct: 144 VIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQEL 203

Query: 105 IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
            + F  +      ++ RD  T ++KGFGF+ F D ++   A + MN F
Sbjct: 204 RQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGF 251

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

 Score = 48.4 bits (116), Expect = 2e-08
 Identities = 19/62 (30%), Positives = 37/62 (59%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+ G+L  +VT+E L   F ++     A+V+ D+ T +++GFGFV  +  ++   A ++
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 149 MN 150
           +N
Sbjct: 61  LN 62

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

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF G+L  D T+E L   FSK+      ++VRD +  K+KGF FV F+ P+D  +A + +
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 85 N 85
          N
Sbjct: 60 N 60

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

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 25/61 (40%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF G+L  D T+E L   FSK+      ++VRD +  K+KGF FV F+ P+D  +A + +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 150 N 150
           N
Sbjct: 60  N 60

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|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 = 48.4 bits (116), Expect = 2e-08
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF  +L    T+E L   F  +    +  +  DK T ++KGF FVSF  P+  ++A  E
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 84 MN 85
          ++
Sbjct: 61 LD 62

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|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 = 48.4 bits (116), Expect = 2e-08
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           RLF  +L    T+E L   F  +    +  +  DK T ++KGF FVSF  P+  ++A  E
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 149 MN 150
           ++
Sbjct: 61  LD 62

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

 Score = 51.9 bits (124), Expect = 2e-08
 Identities = 33/119 (27%), Positives = 56/119 (47%), Gaps = 21/119 (17%)

Query: 53  KVVRDKRTNKTKGFGFVSFKDPQDFIRA----------NKEM--------NDDFR---LF 91
           K+VRDK T ++ G+GFV++  P+D  +A          NK +        +D  +   L+
Sbjct: 34  KLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSDSIKGANLY 93

Query: 92  CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
              L   +T   L   FS +   + ++++ D  T  +KG GF+ F    +  RA K +N
Sbjct: 94  VSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLN 152

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

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

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 24/51 (47%), Positives = 34/51 (66%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          +LF G L  + T E L R FS+Y   +   +++DK TN+++GFGFV FKDP
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51

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

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

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 24/51 (47%), Positives = 34/51 (66%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           +LF G L  + T E L R FS+Y   +   +++DK TN+++GFGFV FKDP
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51

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

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

 Score = 48.1 bits (115), Expect = 3e-08
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           D + +F G L  DVT E L   FS++   L+  ++  KR N T  F F+ F+  Q   RA
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARA 59

Query: 146 NKEMNEFPH 154
            +  N    
Sbjct: 60  VESENHSML 68

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

 Score = 47.8 bits (114), Expect = 4e-08
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 3/66 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TD+ L   FS++       V++D  T +++GFGFV+F    +    +  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASE---VDAA 57

Query: 149 MNEFPH 154
           MN  PH
Sbjct: 58  MNARPH 63

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 47.6 bits (114), Expect = 6e-08
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF G L    T+E L   FS+Y    + ++VRD  T  +KG+ FV ++  +D +RA ++ 
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 85 N----DDFRLF 91
          +    D   +F
Sbjct: 66 HKLVIDGSEIF 76

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

 Score = 46.8 bits (112), Expect = 7e-08
 Identities = 22/50 (44%), Positives = 31/50 (62%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          LF G L  D T+E L   FSKY   +   +++D  T +++GFGFV+F DP
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP 50

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 47.2 bits (112), Expect = 8e-08
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          +F G L  + TD+ L   F ++       V+RD  T +++GFGF++FK P+
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPK 51

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

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

 Score = 47.2 bits (112), Expect = 8e-08
 Identities = 18/51 (35%), Positives = 30/51 (58%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           +F G L  + TD+ L   F ++       V+RD  T +++GFGF++FK P+
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPK 51

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

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

 Score = 46.9 bits (111), Expect = 9e-08
 Identities = 26/63 (41%), Positives = 36/63 (57%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  + TD  L +TF  + + + AKV  DK+TN +K FGFVS+ +P     A + M
Sbjct: 7   LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 150 NEF 152
           N F
Sbjct: 67  NGF 69

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

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

 Score = 47.6 bits (113), Expect = 9e-08
 Identities = 26/52 (50%), Positives = 30/52 (57%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
          DF LF  +L  D T+E L   FSK+ S   A  V DK T + KG GFV FKD
Sbjct: 1  DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKD 52

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

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

 Score = 47.6 bits (113), Expect = 9e-08
 Identities = 26/52 (50%), Positives = 30/52 (57%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           DF LF  +L  D T+E L   FSK+ S   A  V DK T + KG GFV FKD
Sbjct: 1   DFTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKD 52

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

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

 Score = 46.9 bits (112), Expect = 1e-07
 Identities = 21/62 (33%), Positives = 36/62 (58%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF G L    T+E L   FS+Y    + ++VRD  T  +KG+ FV ++  +D +RA ++ 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 150 NE 151
           ++
Sbjct: 66  HK 67

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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 46.4 bits (110), Expect = 1e-07
 Identities = 24/63 (38%), Positives = 35/63 (55%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  +  D  L++ F  + + + AKV  D+ TN++K FGFVSF +P     A + M
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 150 NEF 152
           N F
Sbjct: 67  NGF 69

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

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

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 21/65 (32%), Positives = 35/65 (53%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L  D  + LL + FS + +    KV+RD  TNK KG+GFV+  + ++   A   +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 150 NEFPH 154
           N +  
Sbjct: 64  NGYRL 68

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

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

 Score = 46.2 bits (110), Expect = 2e-07
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          +F  +L  D  + LL + FS + +    KV+RD  TNK KG+GFV+  + ++
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEE 55

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

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

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 21/64 (32%), Positives = 30/64 (46%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF  +L   VT E L   FS       A VV D  T +++G+GFV+F   +D   A  ++
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 150 NEFP 153
               
Sbjct: 62  KNKK 65

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|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 = 45.7 bits (109), Expect = 2e-07
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          F G++  D T+E LI  FS+    +  ++V D+ T K KG+GF  F+D +    A + +N
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 86 D 86
           
Sbjct: 62 G 62

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|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          F +F GDL  ++T + +   F+ +     A+VV+D  T K+KG+GFVSF +  D   A +
Sbjct: 2  FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 83 EM 84
          +M
Sbjct: 62 QM 63

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           F +F GDL  ++T + +   F+ +     A+VV+D  T K+KG+GFVSF +  D   A +
Sbjct: 2   FHVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

Query: 148 EM 149
           +M
Sbjct: 62  QM 63

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

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+ GDL   + +  +   F++       K++R+K+T K+ G+GFV F   +   +A + +
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 85 N 85
          N
Sbjct: 62 N 62

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ GDL   + +  +   F++       K++R+K+T K+ G+GFV F   +   +A + +
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSL 61

Query: 150 N 150
           N
Sbjct: 62  N 62

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

 Score = 45.7 bits (109), Expect = 3e-07
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  D T+  L R F +Y    + ++VRDK+T K +G+ F+ F+  +D   A K  
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

Query: 85 ND 86
          + 
Sbjct: 64 DG 65

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

 Score = 45.4 bits (108), Expect = 4e-07
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          + +F G L  DVT E L   FS++   L+  ++  KR N T  F F+ F+  Q   RA +
Sbjct: 4  YSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVE 61

Query: 83 EMN 85
            N
Sbjct: 62 SEN 64

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

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 25/61 (40%), Positives = 35/61 (57%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  + TD  L +TF  + + + AKV  DK+TN +K FGFVS+ +P     A + M
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 85 N 85
          N
Sbjct: 67 N 67

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

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

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 21/62 (33%), Positives = 31/62 (50%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF  +L   VT E L   FS       A VV D  T +++G+GFV+F   +D   A  ++
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 85 ND 86
           +
Sbjct: 62 KN 63

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|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 = 45.3 bits (108), Expect = 4e-07
 Identities = 21/60 (35%), Positives = 34/60 (56%)

Query: 91  FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           F G++  D T+E LI  FS+    +  ++V D+ T K KG+GF  F+D +    A + +N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 21/60 (35%), Positives = 32/60 (53%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  D T+  L R F +Y    + ++VRDK+T K +G+ F+ F+  +D   A K  
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYA 63

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF--IRAN 81
          R+F G +  D T+E L   FS++ S    K++ D R   +KG+GFV+F+  +D   I A 
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 82 KEMN 85
            +N
Sbjct: 63 GNLN 66

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF--IRAN 146
           R+F G +  D T+E L   FS++ S    K++ D R   +KG+GFV+F+  +D   I A 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 147 KEMN 150
             +N
Sbjct: 63  GNLN 66

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

 Score = 44.9 bits (107), Expect = 4e-07
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
          L    T+  L   FS+Y    K +VV D++T +++GFGFV F+  +D   A + +N 
Sbjct: 7  LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

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

 Score = 48.1 bits (114), Expect = 5e-07
 Identities = 30/161 (18%), Positives = 60/161 (37%), Gaps = 32/161 (19%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           R++ G +  ++ ++ + R F  +       +  D  T K KGF FV ++ P+    A ++
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 84  MNDD--------------------------------FRLFCGDLGNDVTDELLIRTFSKY 111
           MN                                   R++   +  D+++  +   F  +
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAF 228

Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
              +K ++ R       KG+GF+ + + Q    A   MN F
Sbjct: 229 GEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLF 269

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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 44.8 bits (106), Expect = 6e-07
 Identities = 23/61 (37%), Positives = 34/61 (55%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  +  D  L++ F  + + + AKV  D+ TN++K FGFVSF +P     A + M
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 85 N 85
          N
Sbjct: 67 N 67

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

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

 Score = 44.5 bits (106), Expect = 6e-07
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          F G+L  D+ +E L + F         ++VRD++T   KGFG+V FK   
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKD 52

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

 Score = 44.5 bits (106), Expect = 6e-07
 Identities = 18/50 (36%), Positives = 27/50 (54%)

Query: 91  FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           F G+L  D+ +E L + F         ++VRD++T   KGFG+V FK   
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKD 52

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

 Score = 44.7 bits (105), Expect = 7e-07
 Identities = 22/54 (40%), Positives = 33/54 (61%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D
Sbjct: 2  FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLD 55

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

 Score = 44.7 bits (105), Expect = 7e-07
 Identities = 22/54 (40%), Positives = 33/54 (61%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D
Sbjct: 2   FHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLD 55

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

 Score = 44.3 bits (105), Expect = 9e-07
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G L  + TD+ L   FS++       V++D  T +++GFGFV+F    +    +  
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASE---VDAA 57

Query: 84 MND 86
          MN 
Sbjct: 58 MNA 60

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 44.2 bits (105), Expect = 9e-07
 Identities = 20/56 (35%), Positives = 32/56 (57%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           L    T+  L   FS+Y    K +VV D++T +++GFGFV F+  +D   A + +N
Sbjct: 7   LSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62

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

 Score = 44.1 bits (104), Expect = 9e-07
 Identities = 22/50 (44%), Positives = 32/50 (64%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
          +LF G L  DV +  L   FS++    KA+V+ DK+T K +GFGFV F++
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN 50

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

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

 Score = 44.1 bits (104), Expect = 9e-07
 Identities = 22/50 (44%), Positives = 32/50 (64%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           +LF G L  DV +  L   FS++    KA+V+ DK+T K +GFGFV F++
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN 50

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

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 44.3 bits (105), Expect = 1e-06
 Identities = 21/58 (36%), Positives = 29/58 (50%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
           L   +TDE     F         K+VRDKRT  + GFGFV ++  +D  RA + +N  
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGL 65

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 21/56 (37%), Positives = 29/56 (51%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          L   +TDE     F         K+VRDKRT  + GFGFV ++  +D  RA + +N
Sbjct: 8  LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLN 63

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 24/63 (38%), Positives = 35/63 (55%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF  +L  D TDE L   FS+     +  VV+DK + K +GFG+V+F   +D  RA +E 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 150 NEF 152
            + 
Sbjct: 62  KKT 64

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

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 24/61 (39%), Positives = 34/61 (55%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF  +L  D TDE L   FS+     +  VV+DK + K +GFG+V+F   +D  RA +E 
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 85 N 85
           
Sbjct: 62 K 62

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

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          ++F G L  DVT+E     FS++   + A++++D  T +++GFGFV+F    
Sbjct: 1  KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSES 52

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

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

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           ++F G L  DVT+E     FS++   + A++++D  T +++GFGFV+F    
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSES 52

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

>gnl|CDD|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 = 43.4 bits (103), Expect = 2e-06
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 6/47 (12%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
          ++ G+L + +T+E L RTFS +        + + R  K KG+ FV F
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPF------GAIEEVRVFKDKGYAFVRF 43

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|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 = 43.4 bits (103), Expect = 2e-06
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 6/47 (12%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
           ++ G+L + +T+E L RTFS +        + + R  K KG+ FV F
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPF------GAIEEVRVFKDKGYAFVRF 43

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

 Score = 43.4 bits (103), Expect = 2e-06
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          ++ G+L   VT+ELL   F +    +   + +D+ T   +G+GFV F   +D   A K M
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 85 NDDFRLF 91
          N   +L+
Sbjct: 61 N-MIKLY 66

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

 Score = 43.0 bits (102), Expect = 2e-06
 Identities = 20/61 (32%), Positives = 32/61 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           ++ G+L   VT+ELL   F +    +   + +D+ T   +G+GFV F   +D   A K M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 150 N 150
           N
Sbjct: 61  N 61

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

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G L     D  L   F+ +   + AKV+ D+ T +++GFGFV+F D      A  E
Sbjct: 36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 84 MN 85
          M+
Sbjct: 96 MD 97

Length = 144

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

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 22/62 (35%), Positives = 33/62 (53%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L     D  L   F+ +   + AKV+ D+ T +++GFGFV+F D      A  E
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 149 MN 150
           M+
Sbjct: 96  MD 97

Length = 144

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 42.9 bits (101), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 36/63 (57%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  +KD +  + A + +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 150 NEF 152
           N +
Sbjct: 61  NGY 63

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

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 19/61 (31%), Positives = 35/61 (57%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  +KD +  + A + +
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 85 N 85
          N
Sbjct: 61 N 61

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

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

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSF 71
          LF G+L  +V ++LL  TFS +   L+  K++RD  T  +KGF F+S+
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51

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

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

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSF 136
           LF G+L  +V ++LL  TFS +   L+  K++RD  T  +KGF F+S+
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISY 51

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

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 24/63 (38%), Positives = 36/63 (57%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P     A + M
Sbjct: 10  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 150 NEF 152
           N F
Sbjct: 70  NGF 72

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 42.7 bits (101), Expect = 4e-06
 Identities = 21/59 (35%), Positives = 31/59 (52%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
           L  + T E L   FSKY + +   + R K T   KGF F+ F+ P++  +A K +N  P
Sbjct: 7   LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNNPP 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 42.5 bits (100), Expect = 4e-06
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          ++ G L +   ++ L + FS++ +    +V R K+T  +K +GF+ F +P+    A K M
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 85 ND 86
          N+
Sbjct: 62 NN 63

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 42.7 bits (100), Expect = 4e-06
 Identities = 21/63 (33%), Positives = 35/63 (55%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +LG D  + +L + F  + +    KV+RD  TNK KGFGFV+  + ++   A   +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 150 NEF 152
           N +
Sbjct: 64  NGY 66

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 42.5 bits (101), Expect = 4e-06
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
           L  D  ++ L   F  +    +  + +DK T +++GF FV+F   +D  RA +++N F
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGF 64

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 42.4 bits (99), Expect = 5e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F  +LG D  + +L + F  + +    KV+RD  TNK KGFGFV+  + ++   A   +
Sbjct: 4  IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 85 N 85
          N
Sbjct: 64 N 64

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 42.1 bits (100), Expect = 5e-06
 Identities = 16/56 (28%), Positives = 30/56 (53%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          L  D  ++ L   F  +    +  + +DK T +++GF FV+F   +D  RA +++N
Sbjct: 7  LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 62

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

 Score = 42.3 bits (100), Expect = 6e-06
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 24 RLF--CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          RLF  CG     VT++ L   F+ +       VV+DK+T ++KG  +V F       RA 
Sbjct: 5  RLFIVCG---KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 82 KEMND 86
          +EMN 
Sbjct: 62 EEMNG 66

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

 Score = 42.3 bits (100), Expect = 6e-06
 Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN----DDFRL 90
          TDE L   FS++      +V+RDK+T  +  + F+ F+  +D   A  +M+    DD R+
Sbjct: 16 TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75

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

 Score = 42.2 bits (100), Expect = 6e-06
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 95  LGNDVTDELLIRTFSKYPSF--LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
           L    T+E +++  S   S      +++RDK T  ++GF FV F   +D  +    +N  
Sbjct: 10  LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69

Query: 153 PHLFVGD 159
               +  
Sbjct: 70  DPFVIDG 76

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

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

 Score = 41.7 bits (98), Expect = 8e-06
 Identities = 18/63 (28%), Positives = 35/63 (55%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           ++ G L +   ++ L + FS++ +    +V R K+T  +K +GF+ F +P+    A K M
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 150 NEF 152
           N +
Sbjct: 62  NNY 64

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

 Score = 41.8 bits (99), Expect = 8e-06
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 7/63 (11%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF  +LG + T+E L + FS+ P F + K+         KG G V F + +D   A + +
Sbjct: 5   LFVANLGPNTTEEELRQLFSRQPGFRRLKMHN-------KGGGPVCFVEFEDVSFATQAL 57

Query: 150 NEF 152
           N  
Sbjct: 58  NSL 60

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

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

 Score = 41.5 bits (98), Expect = 9e-06
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 89  RLF--CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
           RLF  CG     VT++ L   F+ +       VV+DK+T ++KG  +V F       RA 
Sbjct: 5   RLFIVCG---KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAM 61

Query: 147 KEMN 150
           +EMN
Sbjct: 62  EEMN 65

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

 Score = 41.5 bits (98), Expect = 9e-06
 Identities = 16/51 (31%), Positives = 28/51 (54%)

Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           TDE L   FS++      +V+RDK+T  +  + F+ F+  +D   A  +M+
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMD 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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P     A + M
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 85 N 85
          N
Sbjct: 70 N 70

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  D T+E L  +F      + A++V D+ T  +KGFGFV F   +D   A + M
Sbjct: 3  LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 85 ND 86
           D
Sbjct: 60 ED 61

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 20/61 (32%), Positives = 38/61 (62%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          ++ G L  ++T+  ++  FS+Y   +   +VRDK+T K+KGF F++++D +  I A   +
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 85 N 85
          N
Sbjct: 72 N 72

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 20/61 (32%), Positives = 38/61 (62%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           ++ G L  ++T+  ++  FS+Y   +   +VRDK+T K+KGF F++++D +  I A   +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 150 N 150
           N
Sbjct: 72  N 72

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

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 21/50 (42%), Positives = 29/50 (58%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          +F G L    T E L   FSK+    +  V+RD  T +++GFGFV+F DP
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP 50

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 40.9 bits (96), Expect = 1e-05
 Identities = 21/50 (42%), Positives = 29/50 (58%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           +F G L    T E L   FSK+    +  V+RD  T +++GFGFV+F DP
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP 50

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
          L  + T E L   FSKY + +   + R K T   KGF F+ F+ P++  +A K +N+
Sbjct: 7  LPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHLNN 63

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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          T + +   FS        K++RDK T ++ G+GFV++ DP+D  +A   +N
Sbjct: 14 TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLN 64

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

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 17/51 (33%), Positives = 29/51 (56%)

Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           T + +   FS        K++RDK T ++ G+GFV++ DP+D  +A   +N
Sbjct: 14  TQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLN 64

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

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 17/42 (40%), Positives = 24/42 (57%)

Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          TDE L +    +   +  K + DK+TNK KG+GFV F  P+ 
Sbjct: 13 TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54

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

 Score = 40.3 bits (95), Expect = 2e-05
 Identities = 17/42 (40%), Positives = 24/42 (57%)

Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           TDE L +    +   +  K + DK+TNK KG+GFV F  P+ 
Sbjct: 13  TDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 21/65 (32%), Positives = 34/65 (52%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F G++   V+D+ + +   K    L  K V+D  T K K FGF  F+DP+  +RA + 
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 149 MNEFP 153
           +N   
Sbjct: 62  LNGLE 66

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

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

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 3/66 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++    +  
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEE---VDAA 60

Query: 149 MNEFPH 154
           MN  PH
Sbjct: 61  MNARPH 66

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

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

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           +F  +L  D  + +L + F  + +    K++RD  TN+ KG+GFVS  +  +   A   +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 85  N 85
           N
Sbjct: 332 N 332

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

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

 Score = 42.6 bits (100), Expect = 3e-05
 Identities = 18/61 (29%), Positives = 32/61 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L  D  + +L + F  + +    K++RD  TN+ KG+GFVS  +  +   A   +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 150 N 150
           N
Sbjct: 332 N 332

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

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

 Score = 40.3 bits (95), Expect = 3e-05
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 7/61 (11%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF  +LG + T+E L + FS+ P F + K+         KG G V F + +D   A + +
Sbjct: 5  LFVANLGPNTTEEELRQLFSRQPGFRRLKMHN-------KGGGPVCFVEFEDVSFATQAL 57

Query: 85 N 85
          N
Sbjct: 58 N 58

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

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

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 23/62 (37%), Positives = 35/62 (56%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF  +L    T+E L + FSKY    +  +  DK T K KGF FV++  P+  ++A  E
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 84 MN 85
          ++
Sbjct: 64 LD 65

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

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 23/62 (37%), Positives = 35/62 (56%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           RLF  +L    T+E L + FSKY    +  +  DK T K KGF FV++  P+  ++A  E
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 149 MN 150
           ++
Sbjct: 64  LD 65

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
           +F G++   V+D+ + +   K    L  K V+D  T K K FGF  F+DP+  +RA
Sbjct: 2  TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRA 58

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

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

 Score = 40.1 bits (93), Expect = 4e-05
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
          +LF G L  + TD+ L   F K+ +     V+RD +T +++GFGFV++
Sbjct: 4  KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51

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

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

 Score = 40.1 bits (93), Expect = 4e-05
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
           +LF G L  + TD+ L   F K+ +     V+RD +T +++GFGFV++
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 39.9 bits (93), Expect = 4e-05
 Identities = 21/51 (41%), Positives = 29/51 (56%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          +F G+LG +  +E L R F K       ++VRD +TN  KGF +V FKD  
Sbjct: 2  VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDEN 52

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 39.9 bits (93), Expect = 4e-05
 Identities = 21/51 (41%), Positives = 29/51 (56%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           +F G+LG +  +E L R F K       ++VRD +TN  KGF +V FKD  
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDEN 52

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
            T++ L   FS +   L  +V +D +T ++KGFGFV F D +D ++ 
Sbjct: 10 KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57

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

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

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 98  DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
             T++ L   FS +   L  +V +D +T ++KGFGFV F D +D ++ 
Sbjct: 10  KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57

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

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

 Score = 39.5 bits (93), Expect = 4e-05
 Identities = 20/63 (31%), Positives = 32/63 (50%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ G L  +V +++L   F  +      ++  D  T K +GF FV F++P+D   A   M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 150 NEF 152
           NE 
Sbjct: 61  NES 63

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.7 bits (92), Expect = 4e-05
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          L+   L    TD+ L++    Y   +  K + DK TNK KG+GFV F  P
Sbjct: 4  LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 53

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 39.7 bits (92), Expect = 4e-05
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           L+   L    TD+ L++    Y   +  K + DK TNK KG+GFV F  P
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 53

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 7/67 (10%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK------GFGFVSFKDPQDFI 78
          LF  +L    T+E L + F K        + + K+  K        G+GFV FK  +   
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAK-KKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 79 RANKEMN 85
          +A K + 
Sbjct: 62 KALKRLQ 68

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

 Score = 39.9 bits (94), Expect = 4e-05
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 7/67 (10%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK------GFGFVSFKDPQDFI 143
           LF  +L    T+E L + F K        + + K+  K        G+GFV FK  +   
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAK-KKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 144 RANKEMN 150
           +A K + 
Sbjct: 62  KALKRLQ 68

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

 Score = 39.6 bits (92), Expect = 5e-05
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  D T+E L  +F      + A++V D+ T  +KGFGFV F   +D   A + M
Sbjct: 3   LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 150 NE 151
            +
Sbjct: 60  ED 61

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 39.7 bits (92), Expect = 5e-05
 Identities = 20/63 (31%), Positives = 33/63 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L  D  + +L + F  + +    KV+RD  TNK KGFGFV+  +  +   A   +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 150 NEF 152
           N +
Sbjct: 66  NGY 68

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.8 bits (92), Expect = 5e-05
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          L+   L  + TD+ L++    Y   +  K + DK TNK KG+GFV F  P
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 59

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 39.8 bits (92), Expect = 5e-05
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           L+   L  + TD+ L++    Y   +  K + DK TNK KG+GFV F  P
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSP 59

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 39.5 bits (93), Expect = 6e-05
 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 30 LGNDVTDELLIRTFSKYPSF--LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD 87
          L    T+E +++  S   S      +++RDK T  ++GF FV F   +D  +    +N+ 
Sbjct: 10 LDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNL 69

Query: 88 FRLF 91
              
Sbjct: 70 DPFV 73

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

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

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          LF G+L  + T++ L   F +     + +++  + + K KGF FV F++ +
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51

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

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

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           LF G+L  + T++ L   F +     + +++  + + K KGF FV F++ +
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE 51

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.4 bits (91), Expect = 6e-05
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          L+   L    TD+ LI+    Y   +  K + DK TN+ KG+GFV F  P
Sbjct: 7  LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSP 56

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.4 bits (91), Expect = 6e-05
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           L+   L    TD+ LI+    Y   +  K + DK TN+ KG+GFV F  P
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSP 56

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 99  VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN--EFP 153
           VT E L R F   P      + RD  T K+KGF +V++ +P   I A +++N  E+P
Sbjct: 11  VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFEYP 67

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

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

 Score = 38.7 bits (91), Expect = 7e-05
 Identities = 19/62 (30%), Positives = 32/62 (51%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+ G L  +V +++L   F  +      ++  D  T K +GF FV F++P+D   A   M
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 85 ND 86
          N+
Sbjct: 61 NE 62

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

 Score = 39.3 bits (91), Expect = 7e-05
 Identities = 20/61 (32%), Positives = 32/61 (52%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F  +L  D  + +L + F  + +    KV+RD  TNK KGFGFV+  +  +   A   +
Sbjct: 6  IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 85 N 85
          N
Sbjct: 66 N 66

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 39.3 bits (91), Expect = 7e-05
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          ++F G L    + + L   FSK+    +  V+RD  T +++GFGFV+F DP
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 39.3 bits (91), Expect = 7e-05
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           ++F G L    + + L   FSK+    +  V+RD  T +++GFGFV+F DP
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADP 51

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
          +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++
Sbjct: 4  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 51

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

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          ++F G L  + T+E +   F K+ + ++ ++  DK+TNK +GF F++F   +
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52

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

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           ++F G L  + T+E +   F K+ + ++ ++  DK+TNK +GF F++F   +
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEE 52

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 40.4 bits (94), Expect = 2e-04
 Identities = 21/76 (27%), Positives = 36/76 (47%)

Query: 11  SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
           S+ +   E   D  L+  +L   +TD+ L   F KY   ++  ++RDK T   +G  FV 
Sbjct: 182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVR 241

Query: 71  FKDPQDFIRANKEMND 86
           F   ++   A   +N+
Sbjct: 242 FNKREEAQEAISALNN 257

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). Length = 346

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

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F  +L   + ++ L  TFS + + L  KV  D+    +KG+GFV F+  +  +RA +++
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 85 N 85
          N
Sbjct: 64 N 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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 37.9 bits (89), Expect = 2e-04
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L   + ++ L  TFS + + L  KV  D+    +KG+GFV F+  +  +RA +++
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 150 N 150
           N
Sbjct: 64  N 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          R+F G +     +  L + FS+Y +  + K+V D R   +KG+GFV+F+  +D  +  +E
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

Query: 84 MN 85
           N
Sbjct: 63 AN 64

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           R+F G +     +  L + FS+Y +  + K+V D R   +KG+GFV+F+  +D  +  +E
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

Query: 149 MN 150
            N
Sbjct: 63  AN 64

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          LF G+L   VT+E+L   F +       K+ +D    K K F FV+FK  
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHE 52

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           LF G+L   VT+E+L   F +       K+ +D    K K F FV+FK  
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHE 52

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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 15/55 (27%), Positives = 25/55 (45%)

Query: 26 FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          F   L   V +  L   FSK       +++RD+ + ++KG  +V F D +    A
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 15/55 (27%), Positives = 25/55 (45%)

Query: 91  FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           F   L   V +  L   FSK       +++RD+ + ++KG  +V F D +    A
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

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

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+  +L   +T++ L + F  Y + ++  ++RDK T   +G  FV +   ++   A   +
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 150 N-EFPH 154
           N   P 
Sbjct: 63  NGTIPP 68

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 37.6 bits (88), Expect = 3e-04
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +++ G+LG   T   L   F KY       V R        GF FV F+DP+D   A + 
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 84 MNDDFRLFCGD 94
          +  D R  CG+
Sbjct: 56 L--DGRRICGN 64

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
          ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMD 51

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G+L   V  + L   FS++       V  DK T  +KG+GFVSF            
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGL---ENA 57

Query: 149 MNEFPHLFVG 158
           + +  H+  G
Sbjct: 58  LQKQKHILEG 67

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

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          L+ GDL   + +  + R F+    + L  K++R+K T    G+ FV F D     R   +
Sbjct: 2  LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 84 MN 85
          +N
Sbjct: 62 LN 63

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           L+ GDL   + +  + R F+    + L  K++R+K T    G+ FV F D     R   +
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 149 MN 150
           +N
Sbjct: 62  LN 63

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 37.8 bits (87), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 33/63 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L  +  + +L + F  + +    KV+RD  TNK KGFGFV+  +  +   A   +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 150 NEF 152
           N +
Sbjct: 64  NGY 66

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 20/52 (38%), Positives = 31/52 (59%)

Query: 35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
          T+  L + FSKY   +K  +V+DK T K+KG  F+ F D +D  +  K +N+
Sbjct: 14 TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNN 65

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

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          D  LF G+L   V +E+L   F +     K  + +DK   K K FGFV FK  +    A 
Sbjct: 1  DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 82 KEMN 85
            +N
Sbjct: 60 ALLN 63

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

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

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
           D  LF G+L   V +E+L   F +     K  + +DK   K K FGFV FK  +    A 
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 147 KEMN 150
             +N
Sbjct: 60  ALLN 63

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

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

 Score = 37.2 bits (86), Expect = 4e-04
 Identities = 15/64 (23%), Positives = 31/64 (48%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+  +L   +T++ L + F  Y + ++  ++RDK T   +G  FV +   ++   A   +
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 85 NDDF 88
          N   
Sbjct: 63 NGTI 66

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 19/61 (31%), Positives = 32/61 (52%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F  +L  +  + +L + F  + +    KV+RD  TNK KGFGFV+  +  +   A   +
Sbjct: 4  IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 85 N 85
          N
Sbjct: 64 N 64

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 20/51 (39%), Positives = 30/51 (58%)

Query: 100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           T+  L + FSKY   +K  +V+DK T K+KG  F+ F D +D  +  K +N
Sbjct: 14  TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALN 64

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

 Score = 37.5 bits (87), Expect = 4e-04
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L    +D  L R F++Y    +  V+ D  T +++GFGF++F    +   A++ 
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADE---ADEA 60

Query: 149 MNEFPH 154
           M   PH
Sbjct: 61  MEAQPH 66

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

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          D T+E L   FS++     A++V+DK T  +KG  FV FK  + 
Sbjct: 11 DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKES 54

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

 Score = 37.2 bits (87), Expect = 4e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 98  DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           D T+E L   FS++     A++V+DK T  +KG  FV FK  + 
Sbjct: 11  DATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKES 54

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

 Score = 37.3 bits (87), Expect = 4e-04
 Identities = 15/64 (23%), Positives = 31/64 (48%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L  G+L  + TDE      S + +  +  +V  + T ++KG+GFV +      ++A  ++
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 150 NEFP 153
           +   
Sbjct: 62  DGKQ 65

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

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 6/54 (11%)

Query: 24 RLFCGDLGNDVTDE---LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          ++F G L N ++++    L+ +F K  +F    +V+D  T  +KG+ F  + DP
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAF---NLVKDSATGLSKGYAFCEYLDP 52

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 6/54 (11%)

Query: 89  RLFCGDLGNDVTDE---LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           ++F G L N ++++    L+ +F K  +F    +V+D  T  +KG+ F  + DP
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAF---NLVKDSATGLSKGYAFCEYLDP 52

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          L  ++T E L   F         K+VRDK T ++ G+GFV++ DP+D  +A   +N
Sbjct: 12 LPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 67

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           L  ++T E L   F         K+VRDK T ++ G+GFV++ DP+D  +A   +N
Sbjct: 12  LPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 67

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 20/63 (31%), Positives = 33/63 (52%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L  D  + +L + F  + +    KV+RD  TNK KGFGFV+  +  +   A   +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 150 NEF 152
           N +
Sbjct: 66  NGY 68

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 34 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          VT E L R F   P      + RD  T K+KGF +V++ +P   I A +++N
Sbjct: 11 VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLN 62

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

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

 Score = 36.4 bits (85), Expect = 5e-04
 Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +++ G+LG   T   L   F KY       V R        GF FV F+DP+D   A + 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 149 MN 150
           ++
Sbjct: 56  LD 57

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

 Score = 36.9 bits (86), Expect = 5e-04
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G+L   V  + L   FS++       V  DK T  +KG+GFVSF        A ++
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

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

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

 Score = 37.0 bits (85), Expect = 5e-04
 Identities = 20/61 (32%), Positives = 32/61 (52%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F  +L  D  + +L + F  + +    KV+RD  TNK KGFGFV+  +  +   A   +
Sbjct: 6  IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 85 N 85
          N
Sbjct: 66 N 66

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 36.5 bits (85), Expect = 6e-04
 Identities = 15/61 (24%), Positives = 31/61 (50%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L  G+L  + TDE      S + +  +  +V  + T ++KG+GFV +      ++A  ++
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 85 N 85
          +
Sbjct: 62 D 62

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

 Score = 36.6 bits (85), Expect = 6e-04
 Identities = 15/63 (23%), Positives = 27/63 (42%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF G+L  D  ++ +   F +Y      ++  D  + + KGFG+V F   +    A   +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 150 NEF 152
              
Sbjct: 61  GGT 63

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 18/62 (29%), Positives = 34/62 (54%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G L    T+E +   F +Y +  +  ++RDK T ++KG  FV F   ++  +A + 
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 84 MN 85
          ++
Sbjct: 61 LH 62

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

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 18/62 (29%), Positives = 34/62 (54%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L    T+E +   F +Y +  +  ++RDK T ++KG  FV F   ++  +A + 
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 149 MN 150
           ++
Sbjct: 61  LH 62

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

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          RLF G L   VT+  L   FS++ +    ++++ K     +GF ++  +  + 
Sbjct: 1  RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA 53

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           RLF G L   VT+  L   FS++ +    ++++ K     +GF ++  +  + 
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA 53

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 36.4 bits (84), Expect = 7e-04
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
          D  LF G+L   VT+EL+   F +    +K K+ +DK   K K F FV+FK
Sbjct: 1  DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFK 50

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 36.4 bits (84), Expect = 7e-04
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
           D  LF G+L   VT+EL+   F +    +K K+ +DK   K K F FV+FK
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFK 50

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 36.5 bits (84), Expect = 7e-04
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+   L   +T + L + FS+Y   + ++++RD+ T  ++G GF+ F    +   A K +
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 85 N 85
          N
Sbjct: 63 N 63

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

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

 Score = 36.5 bits (84), Expect = 7e-04
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+   L   +T + L + FS+Y   + ++++RD+ T  ++G GF+ F    +   A K +
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 150 N 150
           N
Sbjct: 63  N 63

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

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

 Score = 36.3 bits (84), Expect = 9e-04
 Identities = 17/48 (35%), Positives = 28/48 (58%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
          +LF G L    +D  L R F++Y    +  V+ D  T +++GFGF++F
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITF 51

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

 Score = 38.5 bits (89), Expect = 0.001
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 6/74 (8%)

Query: 23  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
            R++   +  D+++  +   F  +   +K ++ R       KG+GF+ + + Q    A  
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264

Query: 83  EMNDDFRLFCGDLG 96
            MN    LF  DLG
Sbjct: 265 SMN----LF--DLG 272

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

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF  +L   VT+E+L ++FS++           +R  K K + FV F++    +RA  EM
Sbjct: 4  LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEERDAAVRAMDEM 55

Query: 85 N 85
          N
Sbjct: 56 N 56

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

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF  +L   VT+E+L ++FS++           +R  K K + FV F++    +RA  EM
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKL--------ERVKKLKDYAFVHFEERDAAVRAMDEM 55

Query: 150 N 150
           N
Sbjct: 56  N 56

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

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
          +LF G L  + T+E L   + ++       V+RD  + +++GFGFV+F
Sbjct: 4  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
           +LF G L  + T+E L   + ++       V+RD  + +++GFGFV+F
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   +N
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 36.2 bits (83), Expect = 0.001
 Identities = 19/56 (33%), Positives = 30/56 (53%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   +N
Sbjct: 10  LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 38.1 bits (88), Expect = 0.001
 Identities = 38/164 (23%), Positives = 71/164 (43%), Gaps = 36/164 (21%)

Query: 17  CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK--GFGFVSFKDP 74
           C   ++ RLF G +  +   E ++  FSK    +   +V     +K K  GF FV ++  
Sbjct: 133 CISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESH 192

Query: 75  Q-----------------------DFIRANKEMNDDFR-----LFCGDLGNDVTDELLIR 106
           +                       D+    +E+++D       L+  +L    T+E++ +
Sbjct: 193 RAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEK 252

Query: 107 TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           +FS+   F   KV   +R  K + + FV F+D +D ++A  E+N
Sbjct: 253 SFSE---FKPGKV---ERVKKIRDYAFVHFEDREDAVKAMDELN 290

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 17/48 (35%), Positives = 32/48 (66%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
          ++F G L  + T++ + + FS++     A ++ DK+TN+ +GFGFV+F
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 17/48 (35%), Positives = 32/48 (66%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
           ++F G L  + T++ + + FS++     A ++ DK+TN+ +GFGFV+F
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTF 48

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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 16/67 (23%), Positives = 36/67 (53%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G +   +T++ +   F ++ + L+  +++DKRT   +G  FV +    +  RA + 
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 84 MNDDFRL 90
          +++   L
Sbjct: 61 LHNQRTL 67

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 15/63 (23%), Positives = 27/63 (42%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF G+L  D  ++ +   F +Y      ++  D  + + KGFG+V F   +    A   +
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 85 NDD 87
             
Sbjct: 61 GGT 63

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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 15/62 (24%), Positives = 34/62 (54%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G +   +T++ +   F ++ + L+  +++DKRT   +G  FV +    +  RA + 
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 149 MN 150
           ++
Sbjct: 61  LH 62

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          D +++ G+LGN+     L R F  Y       V R+       GF FV F+DP+D   A 
Sbjct: 4  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 58

Query: 82 KEMNDDFRLFCG 93
          +E+  D R  CG
Sbjct: 59 REL--DGRTLCG 68

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
          +LF G +  D  +  L   F +Y      +++ D+++ K +GFGFV+F D
Sbjct: 2  KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51

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

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

 Score = 35.4 bits (81), Expect = 0.002
 Identities = 16/50 (32%), Positives = 28/50 (56%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           +LF G +  D  +  L   F +Y      +++ D+++ K +GFGFV+F D
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51

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

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

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 8/61 (13%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF  +L N VT+E+L + F ++           +R  K K + F+ F +    ++A +EM
Sbjct: 4  LFVRNLANTVTEEILEKAFGQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 55

Query: 85 N 85
          N
Sbjct: 56 N 56

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

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 8/61 (13%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF  +L N VT+E+L + F ++           +R  K K + F+ F +    ++A +EM
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKL--------ERVKKLKDYAFIHFDERDGAVKAMEEM 55

Query: 150 N 150
           N
Sbjct: 56  N 56

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

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ--DFIRAN 81
          ++F G L  D + + L   F+K+       +  D  T +++GFGF+ FKD    + +   
Sbjct: 1  KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 82 KEMNDDFRL 90
          KE   D RL
Sbjct: 61 KEHRLDGRL 69

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND 86
            T+  L + FS +    +  + R K   K KGF FV F    D  +A K +N 
Sbjct: 10 KCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVNG 62

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

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 98  DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
             T+  L + FS +    +  + R K   K KGF FV F    D  +A K +N
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIKGVN 61

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

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 30 LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          L  ++T + L   FS       AK++RDK    + G+GFV++ + +D  RA   +N
Sbjct: 9  LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLN 64

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

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

 Score = 35.1 bits (80), Expect = 0.003
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 95  LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           L  ++T + L   FS       AK++RDK    + G+GFV++ + +D  RA   +N
Sbjct: 9   LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLN 64

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

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 6/46 (13%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
          RLF G+L ND+T+E     FSKY        V +   NK KGFGF+
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGE------VSEVFLNKEKGFGFI 42

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 6/46 (13%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 134
           RLF G+L ND+T+E     FSKY        V +   NK KGFGF+
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGE------VSEVFLNKEKGFGFI 42

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L  G L  +V  + L   FS Y +     +  D+  N  +G+ +V F+ P+D  +A K M
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 85 N 85
          +
Sbjct: 61 D 61

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L  G L  +V  + L   FS Y +     +  D+  N  +G+ +V F+ P+D  +A K M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 150 N 150
           +
Sbjct: 61  D 61

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 6/47 (12%)

Query: 116 KAKVVRDKR------TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF 156
           + K++RD +        K+KG+GFV F + +  ++A + +N  P +F
Sbjct: 38  QVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRALNNNPEIF 84

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 30/132 (22%), Positives = 58/132 (43%), Gaps = 19/132 (14%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           +F G +  D+ ++ L+  F K     + +++ D  + + +G+ FV+F   ++   A K +
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLL 119

Query: 85  N----------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
           N                D+ RLF G +  +   E ++  FSK    +   +V     +K 
Sbjct: 120 NNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKK 179

Query: 129 K--GFGFVSFKD 138
           K  GF FV ++ 
Sbjct: 180 KNRGFAFVEYES 191

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

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 16/49 (32%), Positives = 29/49 (59%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
          ++F G L  +   E + + F ++     A ++ DK TN+ +GFGFV+F+
Sbjct: 5  KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53

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

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

 Score = 34.7 bits (79), Expect = 0.004
 Identities = 16/49 (32%), Positives = 29/49 (59%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
           ++F G L  +   E + + F ++     A ++ DK TN+ +GFGFV+F+
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53

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

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

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           D  +LF G+L +D+T++ L   F ++ + L+ ++       +   FGFV F DP+
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPE 56

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 15/42 (35%), Positives = 23/42 (54%)

Query: 33 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
            T+E L   F ++       +V+DK T ++KGFG+V F  P
Sbjct: 11 SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKP 52

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 15/42 (35%), Positives = 23/42 (54%)

Query: 98  DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
             T+E L   F ++       +V+DK T ++KGFG+V F  P
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKP 52

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	170
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
KOG0144|consensus	510		99.97
KOG0148|consensus	321		99.97
KOG0117|consensus	506		99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.95
KOG0131|consensus	203		99.95
KOG0145|consensus	360		99.95
KOG0145|consensus	360		99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG0127|consensus	678		99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.92
KOG0127|consensus	678		99.91
KOG0124|consensus	544		99.91
KOG0148|consensus	321		99.91
KOG0146|consensus	371		99.89
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.89
KOG0109|consensus	346		99.88
KOG0123|consensus	369		99.87
KOG0144|consensus	510		99.86
KOG0147|consensus	549		99.86
KOG4205|consensus	311		99.84
KOG0110|consensus	725		99.81
KOG0123|consensus	369		99.81
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.79
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.77
KOG4211|consensus	510		99.76
KOG0105|consensus	241		99.71
KOG4212|consensus	608		99.7
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.7
KOG4206|consensus	221		99.69
KOG0147|consensus	549		99.67
KOG0121|consensus	153		99.67
KOG1457|consensus	284		99.67
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.67
KOG0122|consensus	270		99.65
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.63
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.62
KOG0129|consensus	520		99.62
KOG0110|consensus	725		99.6
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.58
KOG0125|consensus	376		99.57
KOG1548|consensus	382		99.56
PLN03120	260	nucleic acid binding protein; Provisional	99.56
smart00362	72	RRM_2 RNA recognition motif.	99.54
KOG0149|consensus	247		99.52
KOG0122|consensus	270		99.52
KOG0113|consensus	335		99.52
KOG0107|consensus	195		99.51
smart00360	71	RRM RNA recognition motif.	99.51
KOG0124|consensus	544		99.5
KOG0131|consensus	203		99.5
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.49
KOG0149|consensus	247		99.49
KOG0106|consensus	216		99.47
KOG0130|consensus	170		99.47
KOG0111|consensus	298		99.46
KOG0126|consensus	219		99.46
KOG0114|consensus	124		99.46
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.46
PLN03213	759	repressor of silencing 3; Provisional	99.46
KOG4207|consensus	256		99.45
KOG4212|consensus	608		99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.44
KOG1365|consensus	508		99.44
KOG0117|consensus	506		99.43
PLN03121	243	nucleic acid binding protein; Provisional	99.42
KOG0108|consensus	435		99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.41
KOG0114|consensus	124		99.41
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.4
PLN03120	260	nucleic acid binding protein; Provisional	99.36
KOG1190|consensus	492		99.36
smart00361	70	RRM_1 RNA recognition motif.	99.34
KOG1190|consensus	492		99.34
KOG0120|consensus	500		99.34
KOG0113|consensus	335		99.34
PLN03121	243	nucleic acid binding protein; Provisional	99.33
KOG4454|consensus	267		99.33
smart00362	72	RRM_2 RNA recognition motif.	99.32
KOG0126|consensus	219		99.31
KOG0415|consensus	479		99.31
KOG0121|consensus	153		99.3
KOG0226|consensus	290		99.29
smart00360	71	RRM RNA recognition motif.	99.28
KOG0125|consensus	376		99.28
KOG0112|consensus	975		99.25
KOG4207|consensus	256		99.24
KOG0105|consensus	241		99.24
KOG0128|consensus	881		99.24
KOG0130|consensus	170		99.23
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.2
KOG1456|consensus	494		99.2
PLN03213	759	repressor of silencing 3; Provisional	99.19
KOG0107|consensus	195		99.19
KOG4211|consensus	510		99.18
KOG0146|consensus	371		99.15
KOG0108|consensus	435		99.11
KOG4208|consensus	214		99.11
KOG4206|consensus	221		99.1
KOG0132|consensus	894		99.08
KOG0111|consensus	298		99.04
KOG4660|consensus	549		99.01
KOG1456|consensus	494		99.0
KOG4208|consensus	214		99.0
KOG0120|consensus	500		99.0
KOG0109|consensus	346		98.97
smart00361	70	RRM_1 RNA recognition motif.	98.94
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.93
KOG0153|consensus	377		98.91
KOG0533|consensus	243		98.9
KOG4210|consensus	285		98.84
KOG0226|consensus	290		98.74
KOG0415|consensus	479		98.72
KOG1365|consensus	508		98.69
KOG2193|consensus	584		98.69
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.68
KOG4661|consensus	940		98.66
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.63
KOG1548|consensus	382		98.58
KOG4307|consensus	944		98.55
KOG4205|consensus	311		98.55
KOG4660|consensus	549		98.54
KOG0116|consensus	419		98.54
KOG0151|consensus	877		98.52
KOG0116|consensus	419		98.52
KOG4307|consensus	944		98.5
KOG0132|consensus	894		98.5
KOG4209|consensus	231		98.5
KOG1457|consensus	284		98.46
KOG0106|consensus	216		98.43
KOG4676|consensus	479		98.4
KOG0533|consensus	243		98.34
KOG4661|consensus	940		98.31
KOG0153|consensus	377		98.26
KOG4454|consensus	267		98.22
KOG0151|consensus	877		98.2
KOG4209|consensus	231		98.15
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.12
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.06
KOG1995|consensus	351		97.92
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.9
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.87
KOG0128|consensus	881		97.69
KOG4849|consensus	498		97.64
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.48
KOG0129|consensus	520		97.46
KOG2314|consensus	698		97.44
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.41
KOG1855|consensus	484		97.33
KOG2314|consensus	698		97.33
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.33
KOG3152|consensus	278		97.28
KOG4849|consensus	498		97.28
KOG1995|consensus	351		97.26
KOG4210|consensus	285		97.21
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.15
KOG1855|consensus	484		97.1
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.91
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.9
KOG1996|consensus	378		96.89
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.87
KOG2202|consensus	260		96.82
KOG4676|consensus	479		96.67
KOG2416|consensus	718		96.47
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.37
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.07
KOG0115|consensus	275		96.03
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.02
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.98
KOG3152|consensus	278		95.96
KOG2068|consensus	327		95.88
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.76
KOG2193|consensus	584		95.71
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.62
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.39
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.31
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.23
KOG0115|consensus	275		94.87
KOG0804|consensus	493		94.72
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.71
KOG0112|consensus	975		94.2
KOG2416|consensus	718		94.18
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.0
KOG2135|consensus	526		93.94
KOG4574|consensus	1007		93.02
KOG2591|consensus	684		92.85
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.72
KOG1996|consensus	378		91.52
KOG2202|consensus	260		91.0
KOG2591|consensus	684		90.68
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	90.19
KOG0804|consensus	493		89.45
KOG2068|consensus	327		88.56
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	87.75
KOG4483|consensus	528		86.44
KOG4285|consensus	350		84.92
KOG2253|consensus	668		82.29

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=8.6e-33  Score=215.46  Aligned_cols=149  Identities=26%  Similarity=0.411  Sum_probs=138.1

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-----------
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-----------   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-----------   86 (170)
                      .....++|||+|||+++++++|+++|+.||+|.+++|++++.++.+++||||+|.++++|.+|++.+++           
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            344678899999999999999999999999999999999988999999999999999999999998875           


Q ss_pred             ----------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccc
Q psy7847          87 ----------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF  156 (170)
Q Consensus        87 ----------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  156 (170)
                                ..+|||+|||..+++++|+++|++||.|..+.+++|+.++.++|+|||+|.+.++|++|++.||+   ..
T Consensus       183 ~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng---~~  259 (346)
T TIGR01659       183 YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNN---VI  259 (346)
T ss_pred             cccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC---Cc
Confidence                      24799999999999999999999999999999999988999999999999999999999999999   76


Q ss_pred             cCC--eeEEEEeecc
Q psy7847         157 VGD--LKTRSSITLK  169 (170)
Q Consensus       157 ~~~--~~i~v~~~~~  169 (170)
                      +.+  ++|+|.++.+
T Consensus       260 ~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       260 PEGGSQPLTVRLAEE  274 (346)
T ss_pred             cCCCceeEEEEECCc
Confidence            654  7999998864

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

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

Probab=100.00  E-value=2.7e-31  Score=217.54  Aligned_cols=147  Identities=21%  Similarity=0.397  Sum_probs=138.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ...++|||+|||+++++++|+++|..||.|.+|++++++.+|+++|||||+|.+.++|.+|++.+++.            
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            45678999999999999999999999999999999999999999999999999999999999877651            


Q ss_pred             --------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHH
Q psy7847          88 --------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK  147 (170)
Q Consensus        88 --------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~  147 (170)
                                          .+|||+|||+++++++|+++|+.||.|..+.+.+|+..+.++|||||+|.+.++|.+|++
T Consensus       185 ~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~  264 (612)
T TIGR01645       185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  264 (612)
T ss_pred             ccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHH
Confidence                                489999999999999999999999999999999998888999999999999999999999


Q ss_pred             HhcCCCccccCCeeEEEEeecc
Q psy7847         148 EMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       148 ~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .||+   ..++|+.|+|.++..
T Consensus       265 amNg---~elgGr~LrV~kAi~  283 (612)
T TIGR01645       265 SMNL---FDLGGQYLRVGKCVT  283 (612)
T ss_pred             HhCC---CeeCCeEEEEEecCC
Confidence            9999   999999999998763

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=2.1e-30  Score=203.72  Aligned_cols=150  Identities=25%  Similarity=0.435  Sum_probs=139.0

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------   87 (170)
                      .+.....+|||+|||.++++++|+++|+.||.+..+.++.+..++.++|||||+|.+.++|..|++.+++.         
T Consensus        84 ~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i  163 (352)
T TIGR01661        84 SDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPI  163 (352)
T ss_pred             ccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeE
Confidence            33445678999999999999999999999999999999998888899999999999999999999876642         


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       164 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  243 (352)
T TIGR01661       164 TVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQR  243 (352)
T ss_pred             EEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccccccccc
Confidence                                                                                            


Q ss_pred             --------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHH
Q psy7847          88 --------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD  141 (170)
Q Consensus        88 --------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~  141 (170)
                                                .+|||+|||+.+++++|+++|++||.|..+++++|+.++.++|||||+|.+.++
T Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~  323 (352)
T TIGR01661       244 ASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDE  323 (352)
T ss_pred             CCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHH
Confidence                                      039999999999999999999999999999999999899999999999999999


Q ss_pred             HHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         142 FIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       142 a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      |.+|+..|||   ..++|++|+|+|+..
T Consensus       324 A~~Ai~~lnG---~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       324 AAMAILSLNG---YTLGNRVLQVSFKTN  348 (352)
T ss_pred             HHHHHHHhCC---CEECCeEEEEEEccC
Confidence            9999999999   999999999999865

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=3.2e-30  Score=202.67  Aligned_cols=145  Identities=25%  Similarity=0.377  Sum_probs=134.5

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------------   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------------   87 (170)
                      +..+|||+|||.++++++|+++|+.||+|.+|++++++.+|.++|||||+|.+.++|.+|++.+++.             
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            3568999999999999999999999999999999999989999999999999999999999988762             


Q ss_pred             --------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          88 --------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        88 --------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                              .+|||+|||..+++++|+++|+.||.+..+.++.+..++.++|||||+|.+.++|.+|++.|||   ..+.+
T Consensus        82 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g---~~~~g  158 (352)
T TIGR01661        82 PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG---TTPSG  158 (352)
T ss_pred             ccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC---CccCC
Confidence                    3799999999999999999999999999999998887888999999999999999999999999   66665


Q ss_pred             --eeEEEEeec
Q psy7847         160 --LKTRSSITL  168 (170)
Q Consensus       160 --~~i~v~~~~  168 (170)
                        .+|+|.++.
T Consensus       159 ~~~~i~v~~a~  169 (352)
T TIGR01661       159 CTEPITVKFAN  169 (352)
T ss_pred             CceeEEEEECC
Confidence              678888874

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

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

Probab=99.97  E-value=2.2e-29  Score=204.16  Aligned_cols=146  Identities=23%  Similarity=0.432  Sum_probs=136.4

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC------------
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND------------   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~------------   86 (170)
                      ....++|||+|||.++++++|+++|+.||.|.+|+++.++.+|.++|||||+|.+.++|.+|+. +++            
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            3457789999999999999999999999999999999999899999999999999999999996 332            


Q ss_pred             ---------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHH
Q psy7847          87 ---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA  145 (170)
Q Consensus        87 ---------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  145 (170)
                                           ..+|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence                                 25899999999999999999999999999999999988889999999999999999999


Q ss_pred             HHHhcCCCccccCCeeEEEEeec
Q psy7847         146 NKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       146 ~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +..|||   ..++|++|+|.|+.
T Consensus       245 ~~~l~g---~~i~g~~i~v~~a~  264 (457)
T TIGR01622       245 LEVMNG---FELAGRPIKVGYAQ  264 (457)
T ss_pred             HHhcCC---cEECCEEEEEEEcc
Confidence            999999   99999999999964

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

>KOG0144|consensus

Probab=99.97  E-value=2.2e-30  Score=199.37  Aligned_cols=149  Identities=21%  Similarity=0.348  Sum_probs=141.0

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ...-++||+.+|..++|.||+++|++||.|.+|.+++|+.++.++|+|||.|.+.++|.+++..+|+.            
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            44567999999999999999999999999999999999999999999999999999999999887752            


Q ss_pred             -------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          88 -------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        88 -------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                                   +.|||+.|+..++|.+++++|++||.|++|.+++|. .+.+||||||.|.+.+-|..|++.|||...
T Consensus       112 k~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~t  190 (510)
T KOG0144|consen  112 KYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQT  190 (510)
T ss_pred             cccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhcccee
Confidence                         488999999999999999999999999999999997 799999999999999999999999999888


Q ss_pred             cccCCeeEEEEeecc
Q psy7847         155 LFVGDLKTRSSITLK  169 (170)
Q Consensus       155 ~~~~~~~i~v~~~~~  169 (170)
                      ...++.+|.|.||+.
T Consensus       191 meGcs~PLVVkFADt  205 (510)
T KOG0144|consen  191 MEGCSQPLVVKFADT  205 (510)
T ss_pred             eccCCCceEEEeccc
Confidence            889999999999986

>KOG0148|consensus

Probab=99.97  E-value=3.1e-29  Score=183.15  Aligned_cols=141  Identities=31%  Similarity=0.578  Sum_probs=133.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      .....+||+.|+++++-++|++.|.+||.|.++++++|..|++++||+||.|.+.++|+.|+..++++            
T Consensus        60 ~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWA  139 (321)
T KOG0148|consen   60 NQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWA  139 (321)
T ss_pred             ccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccc
Confidence            33567999999999999999999999999999999999999999999999999999999999999874            


Q ss_pred             -------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHH
Q psy7847          88 -------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF  142 (170)
Q Consensus        88 -------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a  142 (170)
                                               ++||++|++..+++++|++.|++||.|..|++.++      +||+||.|.+.|+|
T Consensus       140 TRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaA  213 (321)
T KOG0148|consen  140 TRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAA  213 (321)
T ss_pred             ccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhH
Confidence                                     49999999999999999999999999999999888      68999999999999


Q ss_pred             HHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         143 IRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       143 ~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .+||..+|+   ..++|+.||++|-.+
T Consensus       214 ahAIv~mNn---tei~G~~VkCsWGKe  237 (321)
T KOG0148|consen  214 AHAIVQMNN---TEIGGQLVRCSWGKE  237 (321)
T ss_pred             HHHHHHhcC---ceeCceEEEEecccc
Confidence            999999999   999999999999654

>KOG0117|consensus

Probab=99.96  E-value=1.5e-28  Score=189.94  Aligned_cols=152  Identities=24%  Similarity=0.405  Sum_probs=139.0

Q ss_pred             CCCCCCcccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847           5 RPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      ..+|+..|..+..  ...+.|||+.||.++.|++|..+|+..|+|-++++|.|+.+|.++|||||.|.+.+.|+.|++.+
T Consensus        68 ~ggPpP~weg~~p--~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~l  145 (506)
T KOG0117|consen   68 YGGPPPGWEGPPP--PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKEL  145 (506)
T ss_pred             cCCCCCcccCCCC--CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHh
Confidence            3456666655444  56789999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CCC-----------------------------------------------------------------------------
Q psy7847          85 NDD-----------------------------------------------------------------------------   87 (170)
Q Consensus        85 ~~~-----------------------------------------------------------------------------   87 (170)
                      |+.                                                                             
T Consensus       146 nn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aR  225 (506)
T KOG0117|consen  146 NNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMAR  225 (506)
T ss_pred             hCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHH
Confidence            862                                                                             


Q ss_pred             ----------------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEE
Q psy7847          88 ----------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGF  133 (170)
Q Consensus        88 ----------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~af  133 (170)
                                                        ..|||+||+.++|+|.|+++|+.||.++.++.++|        |||
T Consensus       226 rKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaF  297 (506)
T KOG0117|consen  226 RKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAF  297 (506)
T ss_pred             hhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeE
Confidence                                              18999999999999999999999999999988766        899


Q ss_pred             EEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         134 VSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       134 v~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      |.|.++++|.+|++.+||   +.+.|..|.|..|.+
T Consensus       298 VHf~eR~davkAm~~~ng---keldG~~iEvtLAKP  330 (506)
T KOG0117|consen  298 VHFAEREDAVKAMKETNG---KELDGSPIEVTLAKP  330 (506)
T ss_pred             EeecchHHHHHHHHHhcC---ceecCceEEEEecCC
Confidence            999999999999999999   999999999999864

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

Probab=99.96  E-value=6.1e-28  Score=200.21  Aligned_cols=140  Identities=32%  Similarity=0.563  Sum_probs=131.7

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----------------
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----------------   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----------------   87 (170)
                      .|||+|||+++|+++|+++|+.||.|.+|++.+++.+++++|||||+|.+.++|.+|+..+++.                
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            6999999999999999999999999999999999988999999999999999999999988753                


Q ss_pred             -------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          88 -------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        88 -------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                             .+|||+|||.++++++|+++|+.||.|..|.+..+. ++.++|||||+|.+.++|.+|++.+||   ..++++
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng---~~~~~~  157 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNG---MLLNDK  157 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcc---cEecCc
Confidence                   379999999999999999999999999999998875 778899999999999999999999999   999999


Q ss_pred             eEEEEee
Q psy7847         161 KTRSSIT  167 (170)
Q Consensus       161 ~i~v~~~  167 (170)
                      .|.|...
T Consensus       158 ~i~v~~~  164 (562)
T TIGR01628       158 EVYVGRF  164 (562)
T ss_pred             eEEEecc
Confidence            9988653

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

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

Probab=99.96  E-value=2.8e-27  Score=193.58  Aligned_cols=160  Identities=19%  Similarity=0.361  Sum_probs=133.5

Q ss_pred             CCCCCcccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847           6 PGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..|+..|...  .+...++|||+|||.++++++|+++|+.+|.|.+++++++ .+|.++|||||+|.+.++|++|++.++
T Consensus        44 g~Pp~~~~~~--~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~ln  120 (578)
T TIGR01648        44 GGPPPGWSGV--QPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLN  120 (578)
T ss_pred             CCCCCcccCC--CCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcC
Confidence            3455666422  2445789999999999999999999999999999999999 699999999999999999999999987


Q ss_pred             C----------------CceEEecCCCCCCCHHHHHHHhccCCC-eeE-EEEeecCCCCCcccEEEEEecCHHHHHHHHH
Q psy7847          86 D----------------DFRLFCGDLGNDVTDELLIRTFSKYPS-FLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANK  147 (170)
Q Consensus        86 ~----------------~~~l~v~nlp~~~~~~~l~~~f~~~g~-i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~  147 (170)
                      +                .++|||+|||..+++++|.+.|+.++. +.. +.+..+...++++|||||+|.+.++|..|+.
T Consensus       121 g~~i~~Gr~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~Air  200 (578)
T TIGR01648       121 NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARR  200 (578)
T ss_pred             CCeecCCccccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHH
Confidence            5                258999999999999999999999863 333 3333333456789999999999999999999


Q ss_pred             HhcCCCccccCCeeEEEEeecc
Q psy7847         148 EMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       148 ~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .|+.. ...+.++.|.|+|+.+
T Consensus       201 kL~~g-ki~l~Gr~I~VdwA~p  221 (578)
T TIGR01648       201 KLMPG-RIQLWGHVIAVDWAEP  221 (578)
T ss_pred             Hhhcc-ceEecCceEEEEeecc
Confidence            88641 1457899999999875

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.

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

Probab=99.95  E-value=4.2e-27  Score=195.20  Aligned_cols=145  Identities=30%  Similarity=0.526  Sum_probs=134.5

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ...+.|||+|||.++++++|+++|+.||.|.++.++++. +|.++|||||.|.+.++|.+|++.+++.            
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            345679999999999999999999999999999999985 7899999999999999999999876542            


Q ss_pred             -------------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEe
Q psy7847          88 -------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF  136 (170)
Q Consensus        88 -------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f  136 (170)
                                                     .+|||+||+..+++++|+++|+.||.|..+.++.| .++.++|+|||+|
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f  333 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCF  333 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEe
Confidence                                           26999999999999999999999999999999998 4789999999999


Q ss_pred             cCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         137 KDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       137 ~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .+.++|.+|+..|||   ..++|++|.|.++..
T Consensus       334 ~~~~~A~~A~~~~~g---~~~~gk~l~V~~a~~  363 (562)
T TIGR01628       334 SNPEEANRAVTEMHG---RMLGGKPLYVALAQR  363 (562)
T ss_pred             CCHHHHHHHHHHhcC---CeeCCceeEEEeccC
Confidence            999999999999999   999999999999875

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

>KOG0131|consensus

Probab=99.95  E-value=1.9e-27  Score=164.78  Aligned_cols=148  Identities=30%  Similarity=0.508  Sum_probs=137.8

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC------------
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND------------   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~------------   86 (170)
                      -+.+.+|||+||+..++++.|+++|-+.|+|.++.+++++.+....||||++|.++++|+.|++-++.            
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999986663            


Q ss_pred             ----------CceEEecCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcc
Q psy7847          87 ----------DFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL  155 (170)
Q Consensus        87 ----------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  155 (170)
                                ...+||+||.+.+++..|...|+.||.+.. ..+++++.++.++|+||+.|.+.+++.+|+..|||   .
T Consensus        86 as~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ng---q  162 (203)
T KOG0131|consen   86 ASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNG---Q  162 (203)
T ss_pred             cccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhcc---c
Confidence                      248999999999999999999999999876 47889988899999999999999999999999999   9


Q ss_pred             ccCCeeEEEEeecc
Q psy7847         156 FVGDLKTRSSITLK  169 (170)
Q Consensus       156 ~~~~~~i~v~~~~~  169 (170)
                      .++++++.|+|+-+
T Consensus       163 ~l~nr~itv~ya~k  176 (203)
T KOG0131|consen  163 YLCNRPITVSYAFK  176 (203)
T ss_pred             hhcCCceEEEEEEe
Confidence            99999999999865

>KOG0145|consensus

Probab=99.95  E-value=1.2e-26  Score=169.09  Aligned_cols=156  Identities=26%  Similarity=0.448  Sum_probs=145.9

Q ss_pred             cccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---
Q psy7847          11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---   87 (170)
Q Consensus        11 ~~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---   87 (170)
                      +..+|+.+.-.+..|||.+||..||..+|+++|.+||.|..-++..|..+|.++|.+||.|....+|+.|++.+|++   
T Consensus       116 SyARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~  195 (360)
T KOG0145|consen  116 SYARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPS  195 (360)
T ss_pred             EeccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCC
Confidence            44566777777888999999999999999999999999999999999899999999999999999999999988873   


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       196 g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~  275 (360)
T KOG0145|consen  196 GCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGP  275 (360)
T ss_pred             CCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCC
Confidence                                                                                            


Q ss_pred             ---ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          88 ---FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        88 ---~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                         +|+||-||.+++++.-|+++|++||.+..+++++|..+++.+|||||.+.+-.+|..|+..|||   ..++++.+.|
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNG---y~lg~rvLQV  352 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNG---YRLGDRVLQV  352 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcC---ccccceEEEE
Confidence               2999999999999999999999999999999999998899999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      ++.+.
T Consensus       353 sFKtn  357 (360)
T KOG0145|consen  353 SFKTN  357 (360)
T ss_pred             EEecC
Confidence            98764

>KOG0145|consensus

Probab=99.94  E-value=2.6e-26  Score=167.41  Aligned_cols=145  Identities=23%  Similarity=0.342  Sum_probs=132.4

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------------   87 (170)
                      ..|.|.-||.+||+++++.+|...|+|++|++++|+.+|++-||+||.|-++++|++|+..+|+-               
T Consensus        42 TNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPS  121 (360)
T KOG0145|consen   42 TNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPS  121 (360)
T ss_pred             ceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCC
Confidence            34999999999999999999999999999999999999999999999999999999999999873               


Q ss_pred             ------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          88 ------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        88 ------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                            ..|||++||..+++.+|+++|++||.|..-+++.|..++.++|.+||.|..+.+|+.|++.|||. .-..+..+
T Consensus       122 s~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~-~P~g~tep  200 (360)
T KOG0145|consen  122 SDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQ-KPSGCTEP  200 (360)
T ss_pred             hhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCC-CCCCCCCC
Confidence                  39999999999999999999999999998889999999999999999999999999999999993 22334467


Q ss_pred             EEEEeec
Q psy7847         162 TRSSITL  168 (170)
Q Consensus       162 i~v~~~~  168 (170)
                      |.|.++.
T Consensus       201 ItVKFan  207 (360)
T KOG0145|consen  201 ITVKFAN  207 (360)
T ss_pred             eEEEecC
Confidence            7777653

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

Probab=99.94  E-value=1.6e-25  Score=183.69  Aligned_cols=140  Identities=20%  Similarity=0.353  Sum_probs=122.7

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcC------------CCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKY------------PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~------------g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++|||+|||+++|+++|.++|..+            +.|..+.+      +..++||||+|.+.++|..|+. +++
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCC
Confidence            4457899999999999999999999864            23333433      3457899999999999999984 322


Q ss_pred             --------------------------------------------------CceEEecCCCCCCCHHHHHHHhccCCCeeE
Q psy7847          87 --------------------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLK  116 (170)
Q Consensus        87 --------------------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~  116 (170)
                                                                        ..+|||+|||..+++++|.++|+.||.|..
T Consensus       245 ~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~  324 (509)
T TIGR01642       245 IIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKA  324 (509)
T ss_pred             eEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE
Confidence                                                              147999999999999999999999999999


Q ss_pred             EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         117 AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       117 ~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +.++++..++.++|||||+|.+.++|..|+..|||   ..++|+.|+|.++.
T Consensus       325 ~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g---~~~~~~~l~v~~a~  373 (509)
T TIGR01642       325 FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNG---KDTGDNKLHVQRAC  373 (509)
T ss_pred             EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCC---CEECCeEEEEEECc
Confidence            99999988899999999999999999999999999   99999999999874

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

>KOG0127|consensus

Probab=99.93  E-value=6.1e-25  Score=173.75  Aligned_cols=143  Identities=28%  Similarity=0.360  Sum_probs=133.6

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----------------   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----------------   86 (170)
                      .+|||++||++++.++|.++|+.+|+|..+.+..++.++.++||+||.|...+++.+|+....+                
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            7999999999999999999999999999999999988889999999999999999999986554                


Q ss_pred             -------------------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEE
Q psy7847          87 -------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS  135 (170)
Q Consensus        87 -------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~  135 (170)
                                                     ..+|.|+|||+.+.+++|+.+|+.||.+..|.|++.. .+.-+|||||.
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~  164 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQ  164 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEE
Confidence                                           1499999999999999999999999999999999765 56667999999


Q ss_pred             ecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         136 FKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       136 f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      |....+|.+|++.+|+   ..++||+|.|.||..
T Consensus       165 fk~~~dA~~Al~~~N~---~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNG---NKIDGRPVAVDWAVD  195 (678)
T ss_pred             EeeHHHHHHHHHhccC---ceecCceeEEeeecc
Confidence            9999999999999999   999999999999864

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

Probab=99.93  E-value=2.6e-24  Score=175.44  Aligned_cols=136  Identities=13%  Similarity=0.132  Sum_probs=119.1

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc--CC------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM--ND------------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~--~~------------   86 (170)
                      ++++|||+|||.++++++|+++|+.||.|.++.++++      +++|||+|.+.++|.+|+..+  ++            
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4789999999999999999999999999999999864      479999999999999999743  11            


Q ss_pred             ---------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHH
Q psy7847          87 ---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA  145 (170)
Q Consensus        87 ---------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  145 (170)
                                           ..+|+|.||++++++++|+++|+.||.|..+.+.++..    .|+|||+|.+.++|.+|
T Consensus        75 s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A~~A  150 (481)
T TIGR01649        75 STSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSAQHA  150 (481)
T ss_pred             cCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHHHHH
Confidence                                 02689999999999999999999999999999877642    47899999999999999


Q ss_pred             HHHhcCCCccccCC--eeEEEEeecc
Q psy7847         146 NKEMNEFPHLFVGD--LKTRSSITLK  169 (170)
Q Consensus       146 ~~~l~~~~~~~~~~--~~i~v~~~~~  169 (170)
                      ++.|||   ..+.+  +.|+|.|+..
T Consensus       151 ~~~Lng---~~i~~~~~~l~v~~sk~  173 (481)
T TIGR01649       151 KAALNG---ADIYNGCCTLKIEYAKP  173 (481)
T ss_pred             HHHhcC---CcccCCceEEEEEEecC
Confidence            999999   77643  6899998753

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).

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

Probab=99.93  E-value=3.2e-24  Score=176.05  Aligned_cols=147  Identities=18%  Similarity=0.243  Sum_probs=125.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..+++.            
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            34578999999999999999999999999999999999889999999999999999999999887752            


Q ss_pred             -------------------------------------ceEEecCCCCC----------CCHHHHHHHhccCCCeeEEEEe
Q psy7847          88 -------------------------------------FRLFCGDLGND----------VTDELLIRTFSKYPSFLKAKVV  120 (170)
Q Consensus        88 -------------------------------------~~l~v~nlp~~----------~~~~~l~~~f~~~g~i~~~~~~  120 (170)
                                                           .+|++.|+...          ...++|+++|+.||.|..+.++
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence                                                 13455555421          1136799999999999999998


Q ss_pred             ecCC---CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         121 RDKR---TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       121 ~~~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ++..   .+...|+|||+|.+.++|.+|+..|||   ..++|+.|.+.|...
T Consensus       453 ~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG---r~~~gr~v~~~~~~~  501 (509)
T TIGR01642       453 RPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG---RKFNDRVVVAAFYGE  501 (509)
T ss_pred             ccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC---CEECCeEEEEEEeCH
Confidence            7532   345579999999999999999999999   999999999998653

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

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

Probab=99.93  E-value=7e-24  Score=172.91  Aligned_cols=140  Identities=19%  Similarity=0.244  Sum_probs=123.4

Q ss_pred             CCCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-----------
Q psy7847          20 ENDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-----------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-----------   87 (170)
                      .++.+|||+|||+ .+++++|+++|+.||.|.+|++++++     +|+|||+|.+.++|..|+..+|+.           
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            4567999999998 69999999999999999999998863     589999999999999999876641           


Q ss_pred             -----------------------------------------------ceEEecCCCCCCCHHHHHHHhccCCC--eeEEE
Q psy7847          88 -----------------------------------------------FRLFCGDLGNDVTDELLIRTFSKYPS--FLKAK  118 (170)
Q Consensus        88 -----------------------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~--i~~~~  118 (170)
                                                                     .+|||.|||..+++++|+++|+.||.  +..++
T Consensus       348 s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik  427 (481)
T TIGR01649       348 SKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFK  427 (481)
T ss_pred             cccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEE
Confidence                                                           26999999999999999999999998  77787


Q ss_pred             EeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee------EEEEeecc
Q psy7847         119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK------TRSSITLK  169 (170)
Q Consensus       119 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~------i~v~~~~~  169 (170)
                      +....  +..+|+|||+|.+.++|.+|+..||+   ..++++.      |+|+++.+
T Consensus       428 ~~~~~--~~~~~~gfVeF~~~e~A~~Al~~ln~---~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       428 FFPKD--NERSKMGLLEWESVEDAVEALIALNH---HQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             EecCC--CCcceeEEEEcCCHHHHHHHHHHhcC---CccCCCCCCccceEEEEeccC
Confidence            75433  33578999999999999999999999   8998885      99999865

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).

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

Probab=99.92  E-value=8.7e-24  Score=173.19  Aligned_cols=138  Identities=22%  Similarity=0.420  Sum_probs=118.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCC-eeEEEEEec-CCCCCcCCEEEEEeCCHHHHHHHHHHcCC------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRD-KRTNKTKGFGFVSFKDPQDFIRANKEMND------------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~-v~~i~~~~~-~~~~~~~~~afv~f~~~~~a~~~~~~~~~------------   86 (170)
                      ..++|||+|||.++++++|.+.|..++. +.++.++.. ...+++++||||+|.++++|..|+..++.            
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4678999999999999999999999863 444444332 23467899999999999999999876532            


Q ss_pred             ----------------CceEEecCCCCCCCHHHHHHHhccC--CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHH
Q psy7847          87 ----------------DFRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE  148 (170)
Q Consensus        87 ----------------~~~l~v~nlp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  148 (170)
                                      ..+|||+|||.++++++|+++|+.|  |.|+.+.+.        ++||||+|.+.++|.+|++.
T Consensus       217 dwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~  288 (578)
T TIGR01648       217 DWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDE  288 (578)
T ss_pred             EeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHH
Confidence                            2479999999999999999999999  999998764        45999999999999999999


Q ss_pred             hcCCCccccCCeeEEEEeecc
Q psy7847         149 MNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       149 l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ||+   ..++|+.|+|+|+.+
T Consensus       289 lnG---~~i~Gr~I~V~~Akp  306 (578)
T TIGR01648       289 LNG---KELEGSEIEVTLAKP  306 (578)
T ss_pred             hCC---CEECCEEEEEEEccC
Confidence            999   999999999999864

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.

>KOG0127|consensus

Probab=99.91  E-value=2.2e-23  Score=164.96  Aligned_cols=146  Identities=27%  Similarity=0.368  Sum_probs=131.6

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--------------
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--------------   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--------------   87 (170)
                      .++|.|+|||+.+...+|+.+|+.||.|.+|.|++.+ .|.-.|||||.|.+..+|..|++.+|+.              
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            6789999999999999999999999999999999775 5555599999999999999999987762              


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence                                                                                            


Q ss_pred             -----------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc
Q psy7847          88 -----------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        88 -----------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                                       .+|||+|||++++++.|...|++||.+.++.++.++.++.++|.|||.|.+..+|+.||....
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence                             299999999999999999999999999999999999999999999999999999999999772


Q ss_pred             ---CCCccccCCeeEEEEeec
Q psy7847         151 ---EFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       151 ---~~~~~~~~~~~i~v~~~~  168 (170)
                         +--...+.||.|+|..|.
T Consensus       356 pa~e~g~~ll~GR~Lkv~~Av  376 (678)
T KOG0127|consen  356 PASEDGSVLLDGRLLKVTLAV  376 (678)
T ss_pred             ccCCCceEEEeccEEeeeecc
Confidence               211278899999998764

>KOG0124|consensus

Probab=99.91  E-value=6.4e-24  Score=161.36  Aligned_cols=142  Identities=22%  Similarity=0.420  Sum_probs=135.7

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------------   87 (170)
                      ++||||.+++...|+.|+..|..||+|.+|.+.+|..+++.+|||||+|+-++.|.-+++.+|+.               
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999973               


Q ss_pred             -----------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc
Q psy7847          88 -----------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        88 -----------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                                       +++||..+.++.+++||+.+|+.||.|..|.+.+++..+.++||+|++|.+.++...|+..||
T Consensus       194 pQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             cccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence                             499999999999999999999999999999999999888999999999999999999999999


Q ss_pred             CCCccccCCeeEEEEee
Q psy7847         151 EFPHLFVGDLKTRSSIT  167 (170)
Q Consensus       151 ~~~~~~~~~~~i~v~~~  167 (170)
                      -   ..+||..++|...
T Consensus       274 l---FDLGGQyLRVGk~  287 (544)
T KOG0124|consen  274 L---FDLGGQYLRVGKC  287 (544)
T ss_pred             h---hhcccceEecccc
Confidence            9   9999999998643

>KOG0148|consensus

Probab=99.91  E-value=4.2e-24  Score=156.38  Aligned_cols=140  Identities=29%  Similarity=0.500  Sum_probs=117.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCceEEecCCCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGND   98 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~~l~v~nlp~~   98 (170)
                      ....++|||+||+.++||+-|..+|++.|++.+++++.+. -+..       ..+.. ..+....++....+||+.|.+.
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e-~~v~-------wa~~p-~nQsk~t~~~hfhvfvgdls~e   73 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDE-LKVN-------WATAP-GNQSKPTSNQHFHVFVGDLSPE   73 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehhh-hccc-------cccCc-ccCCCCccccceeEEehhcchh
Confidence            3457899999999999999999999999999999999873 1111       11111 1111112222457999999999


Q ss_pred             CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeeccC
Q psy7847          99 VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG  170 (170)
Q Consensus        99 ~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~~  170 (170)
                      ++-++|++.|.+||.|.++++++|..+++++||+||.|.+.++|++||..|||   ..||+|.|+-+||+.+
T Consensus        74 I~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnG---qWlG~R~IRTNWATRK  142 (321)
T KOG0148|consen   74 IDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNG---QWLGRRTIRTNWATRK  142 (321)
T ss_pred             cchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCC---eeeccceeeccccccC
Confidence            99999999999999999999999999999999999999999999999999999   9999999999999763

>KOG0146|consensus

Probab=99.89  E-value=8.6e-23  Score=149.55  Aligned_cols=150  Identities=27%  Similarity=0.429  Sum_probs=138.6

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCc-------
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDF-------   88 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~-------   88 (170)
                      +....++++||||.|...-.|||++.+|..||.+++|.+.+.. +|.++|+|||.|.+..+|..++..+|++.       
T Consensus        13 esrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASS   91 (371)
T KOG0146|consen   13 ESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASS   91 (371)
T ss_pred             ccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCcc
Confidence            3344578999999999999999999999999999999999984 89999999999999999999999888731       


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          89 --------------------------------------------------------------------------------   88 (170)
Q Consensus        89 --------------------------------------------------------------------------------   88 (170)
                                                                                                      
T Consensus        92 SLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~a  171 (371)
T KOG0146|consen   92 SLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNA  171 (371)
T ss_pred             ceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhh
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          89 --------------------------------------------------------------------------------   88 (170)
Q Consensus        89 --------------------------------------------------------------------------------   88 (170)
                                                                                                      
T Consensus       172 ngl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~  251 (371)
T KOG0146|consen  172 NGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQ  251 (371)
T ss_pred             cccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHH
Confidence                                                                                            


Q ss_pred             -----------------------------------eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEE
Q psy7847          89 -----------------------------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGF  133 (170)
Q Consensus        89 -----------------------------------~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~af  133 (170)
                                                         .|||-.||.+..+.+|..+|-.||-|.+.++..|+-++.++.|+|
T Consensus       252 ~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGF  331 (371)
T KOG0146|consen  252 QYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGF  331 (371)
T ss_pred             HHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceee
Confidence                                               999999999999999999999999999999998998999999999


Q ss_pred             EEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         134 VSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       134 v~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      |.|.++.+++.||..|||   ..+|-+++||-...+
T Consensus       332 VSfDNp~SaQaAIqAMNG---FQIGMKRLKVQLKRP  364 (371)
T KOG0146|consen  332 VSFDNPASAQAAIQAMNG---FQIGMKRLKVQLKRP  364 (371)
T ss_pred             EecCCchhHHHHHHHhcc---hhhhhhhhhhhhcCc
Confidence            999999999999999999   999999999876543

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

Probab=99.89  E-value=1.9e-21  Score=157.87  Aligned_cols=140  Identities=21%  Similarity=0.348  Sum_probs=120.5

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--------------
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--------------   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--------------   87 (170)
                      .++|||+|||.++++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..+++.              
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            688999999999999999999999999999999999888899999999999999999999877651              


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             -----------------ceEEecCCCCCCC----------HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHH
Q psy7847          88 -----------------FRLFCGDLGNDVT----------DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ  140 (170)
Q Consensus        88 -----------------~~l~v~nlp~~~~----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~  140 (170)
                                       .+|+|.|+....+          .++|.+.|++||.|..+.+...    ...|++||.|.+.+
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~~e  421 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSSVD  421 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECCHH
Confidence                             1233344422222          3689999999999999988633    35799999999999


Q ss_pred             HHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         141 DFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       141 ~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +|.+|++.|||   ..++|+.|.+.+..
T Consensus       422 ~A~~A~~~lnG---r~f~gr~i~~~~~~  446 (457)
T TIGR01622       422 AALAAFQALNG---RYFGGKMITAAFVV  446 (457)
T ss_pred             HHHHHHHHhcC---cccCCeEEEEEEEc
Confidence            99999999999   99999999999865

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=99.88  E-value=1.8e-22  Score=149.16  Aligned_cols=128  Identities=23%  Similarity=0.476  Sum_probs=119.7

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------------   87 (170)
                      .++||+|||..+++.+|+.+|++||+|.+|+|+++        |+||..++...++.++.+||+-               
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            36999999999999999999999999999999987        6999999999999999988862               


Q ss_pred             ----ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          88 ----FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        88 ----~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                          .+++|+|+.+.++.++|+..|++||.+..|.+.+|        |+||.|...++|..|++.||+   ..+.|++++
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~---~~~~gk~m~  143 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDN---TEFQGKRMH  143 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccc---cccccceee
Confidence                48999999999999999999999999999998765        899999999999999999999   999999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |-++++
T Consensus       144 vq~sts  149 (346)
T KOG0109|consen  144 VQLSTS  149 (346)
T ss_pred             eeeecc
Confidence            988764

>KOG0123|consensus

Probab=99.87  E-value=3.2e-21  Score=151.55  Aligned_cols=132  Identities=31%  Similarity=0.542  Sum_probs=122.8

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----------------
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----------------   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----------------   87 (170)
                      .+|||   +++|+.+|.++|+.+|++.++++.++. +  +-|||||.|.++++|++|+..+|..                
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            58888   999999999999999999999999996 5  9999999999999999999988753                


Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ..+||.||+++++...|..+|+.||.|.+|++.++. .| ++|| ||+|.++++|.+|++.+||   ..++|++|-|...
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng---~ll~~kki~vg~~  150 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNG---MLLNGKKIYVGLF  150 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcC---cccCCCeeEEeec
Confidence            369999999999999999999999999999999986 44 8999 9999999999999999999   9999999988654

>KOG0144|consensus

Probab=99.86  E-value=9.9e-22  Score=151.89  Aligned_cols=77  Identities=35%  Similarity=0.480  Sum_probs=73.1

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      .||+.+||.+.-+.+|-..|..||.|....+..|+.++-++.|+||.|++..+|..||..|||   ..++.++++|-...
T Consensus       426 nlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amng---fQig~KrlkVQlk~  502 (510)
T KOG0144|consen  426 NLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNG---FQIGSKRLKVQLKR  502 (510)
T ss_pred             ceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcc---hhhccccceEEeee
Confidence            999999999999999999999999999999888999999999999999999999999999999   99999999986543

>KOG0147|consensus

Probab=99.86  E-value=9.4e-22  Score=155.88  Aligned_cols=148  Identities=23%  Similarity=0.445  Sum_probs=135.4

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------   87 (170)
                      .++...+++|+-.|+...++-+|.++|+.+|+|.+++++.++.++.++|.|||+|-+.+++..++. |.|+         
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~v  252 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIV  252 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEe
Confidence            334556789999999999999999999999999999999999999999999999999999888873 3322         


Q ss_pred             -------------------------c-eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHH
Q psy7847          88 -------------------------F-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD  141 (170)
Q Consensus        88 -------------------------~-~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~  141 (170)
                                               . .|||+||.+++++++|+.+|.+||.|+.+.+++|..+|.++||||++|.+.++
T Consensus       253 q~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~  332 (549)
T KOG0147|consen  253 QLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKED  332 (549)
T ss_pred             cccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHH
Confidence                                     1 38999999999999999999999999999999998899999999999999999


Q ss_pred             HHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         142 FIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       142 a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      |.+|+..|||   ..+.|+.|+|+..+
T Consensus       333 ar~a~e~lng---felAGr~ikV~~v~  356 (549)
T KOG0147|consen  333 ARKALEQLNG---FELAGRLIKVSVVT  356 (549)
T ss_pred             HHHHHHHhcc---ceecCceEEEEEee
Confidence            9999999999   99999999998754

>KOG4205|consensus

Probab=99.84  E-value=1.5e-20  Score=143.49  Aligned_cols=145  Identities=26%  Similarity=0.430  Sum_probs=131.6

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC--------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND--------------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~--------------   86 (170)
                      +..++||++|+++++++.|++.|.+||.+.++.+++++.++++++|+||+|.+++.+.+++..-+.              
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            678999999999999999999999999999999999999999999999999999998888754221              


Q ss_pred             ------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          87 ------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        87 ------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                                  ...+||+++|..+++++++..|.+||.|..+.++.|.....++|++||.|.++++..+++. .+-   
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f---  160 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKF---  160 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cce---
Confidence                        2389999999999999999999999999999999999999999999999999888888766 455   


Q ss_pred             cccCCeeEEEEeecc
Q psy7847         155 LFVGDLKTRSSITLK  169 (170)
Q Consensus       155 ~~~~~~~i~v~~~~~  169 (170)
                      ..++++.+.|..|.+
T Consensus       161 ~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen  161 HDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeecCceeeEeeccc
Confidence            889999999988865

>KOG0110|consensus

Probab=99.81  E-value=1.4e-19  Score=147.24  Aligned_cols=144  Identities=22%  Similarity=0.342  Sum_probs=128.4

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC---CCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~---~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      .++||.||+++++.+++...|...|.|.++.|...+..   -.+.|||||+|.++++|..|++.|++.            
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            34999999999999999999999999999988665421   246699999999999999999988852            


Q ss_pred             ------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHh
Q psy7847          88 ------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM  149 (170)
Q Consensus        88 ------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  149 (170)
                                        ..|+|+|+|+.++..+++.+|..||.+..++++.....+.++|+|||.|-++.+|.+|+..|
T Consensus       596 ~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al  675 (725)
T KOG0110|consen  596 ENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDAL  675 (725)
T ss_pred             cCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhh
Confidence                              38999999999999999999999999999999877556678999999999999999999999


Q ss_pred             cCCCccccCCeeEEEEeecc
Q psy7847         150 NEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       150 ~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .+   ..+-||++.+.|+..
T Consensus       676 ~S---THlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  676 GS---THLYGRRLVLEWAKS  692 (725)
T ss_pred             cc---cceechhhheehhcc
Confidence            98   999999999999853

>KOG0123|consensus

Probab=99.81  E-value=6.2e-19  Score=138.66  Aligned_cols=138  Identities=32%  Similarity=0.536  Sum_probs=124.7

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----------------
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----------------   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----------------   87 (170)
                      .+||.||+++++..+|.++|+.||.|.+|++..+. .| ++|| ||+|.++++|.++++.+|+.                
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            39999999999999999999999999999999985 56 9999 99999999999999999873                


Q ss_pred             -------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          88 -------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        88 -------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                                   ..+++.+++...+++.|...|+.+|.|....++.+. .+.++||+||.|.+.++|..|+..||+   
T Consensus       155 er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~---  230 (369)
T KOG0123|consen  155 EREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNG---  230 (369)
T ss_pred             hhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccC---
Confidence                         256777888999999999999999999999999886 566999999999999999999999999   


Q ss_pred             cccCCeeEEEEeec
Q psy7847         155 LFVGDLKTRSSITL  168 (170)
Q Consensus       155 ~~~~~~~i~v~~~~  168 (170)
                      ...++..+-|.-+.
T Consensus       231 ~~~~~~~~~V~~aq  244 (369)
T KOG0123|consen  231 KIFGDKELYVGRAQ  244 (369)
T ss_pred             CcCCccceeecccc
Confidence            88887777765544

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

Probab=99.79  E-value=2e-17  Score=136.37  Aligned_cols=66  Identities=20%  Similarity=0.383  Sum_probs=62.2

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++|||+|||+++++++|+++|+.||.|.++++.+++.+|.++|||||+|.+.++|.+|+..+|+
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg  268 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNL  268 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCC
Confidence            457899999999999999999999999999999999988899999999999999999999988774

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.

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

Probab=99.77  E-value=4.3e-18  Score=117.86  Aligned_cols=80  Identities=29%  Similarity=0.450  Sum_probs=76.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+.+++++|+++|++||.|..+.+..|+.++.++|||||+|.+.++|+.|++.||+   ..+++++|+|++
T Consensus        34 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng---~~i~Gr~l~V~~  110 (144)
T PLN03134         34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDG---KELNGRHIRVNP  110 (144)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCC---CEECCEEEEEEe
Confidence            46899999999999999999999999999999999998999999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus       111 a~~  113 (144)
T PLN03134        111 AND  113 (144)
T ss_pred             CCc
Confidence            864

>KOG4211|consensus

Probab=99.76  E-value=3.5e-17  Score=128.72  Aligned_cols=143  Identities=18%  Similarity=0.200  Sum_probs=118.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-----------
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-----------   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-----------   86 (170)
                      +......|.+++||+++|++||.++|+.++ |+++.+.+  .+|+..|-|||+|.+++++.+|++....           
T Consensus         6 e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~   82 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFT   82 (510)
T ss_pred             CCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEc
Confidence            445567899999999999999999999998 77766655  4799999999999999999999974321           


Q ss_pred             --------------------CceEEecCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEecCHHHHHHH
Q psy7847          87 --------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRA  145 (170)
Q Consensus        87 --------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a  145 (170)
                                          ...|.+++||+.++++||.++|+..--+.. |.++.++ .+.+.|-|||+|++.++|++|
T Consensus        83 ~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~A  161 (510)
T KOG4211|consen   83 AGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIA  161 (510)
T ss_pred             cCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHH
Confidence                                248889999999999999999987744444 4455554 667899999999999999999


Q ss_pred             HHHhcCCCccccCCeeEEEEeec
Q psy7847         146 NKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       146 ~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +.. |.   ..++.+-|.|..+.
T Consensus       162 l~r-hr---e~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  162 LGR-HR---ENIGHRYIEVFRSS  180 (510)
T ss_pred             HHH-HH---HhhccceEEeehhH
Confidence            995 55   78888888886543

>KOG0105|consensus

Probab=99.71  E-value=2.6e-16  Score=109.97  Aligned_cols=123  Identities=23%  Similarity=0.355  Sum_probs=108.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-------------   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-------------   86 (170)
                      ..++++||+|||.++-+-+|.++|-+||.|.+|.+..-   .....||||+|+++.+|+.|+..-++             
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            35788999999999999999999999999999988432   23467999999999999999974442             


Q ss_pred             ----------------------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEE
Q psy7847          87 ----------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFG  132 (170)
Q Consensus        87 ----------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~a  132 (170)
                                                        ..++.|++||++.++++|+......|.+.+..+.+|       |++
T Consensus        81 rggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~G  153 (241)
T KOG0105|consen   81 RGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVG  153 (241)
T ss_pred             cCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cce
Confidence                                              249999999999999999999999999999999886       378


Q ss_pred             EEEecCHHHHHHHHHHhcCC
Q psy7847         133 FVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus       133 fv~f~~~~~a~~a~~~l~~~  152 (170)
                      .|+|-..++..-|+.+|+..
T Consensus       154 vV~~~r~eDMkYAvr~ld~~  173 (241)
T KOG0105|consen  154 VVEYLRKEDMKYAVRKLDDQ  173 (241)
T ss_pred             eeeeeehhhHHHHHHhhccc
Confidence            99999999999999999873

>KOG4212|consensus

Probab=99.70  E-value=6.7e-16  Score=120.22  Aligned_cols=140  Identities=19%  Similarity=0.305  Sum_probs=126.3

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhh-cCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------------
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------------   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~-~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------------   87 (170)
                      .+.+||.|+|+++.+++|+++|. +.|.|+.|.+..|. +|+++++|.|+|++++.+++|++.++..             
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            45599999999999999999996 68999999999995 8999999999999999999999977631             


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence                                                                                            


Q ss_pred             -------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          88 -------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        88 -------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                                   ..+||.||.+.+....|.+.|...|.++++.+-.|+ -+.++|+|.++|..+-.|..|+..+++   
T Consensus       203 Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idK-eG~s~G~~vi~y~hpveavqaIsml~~---  278 (608)
T KOG4212|consen  203 FLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDK-EGNSRGFAVIEYDHPVEAVQAISMLDR---  278 (608)
T ss_pred             hhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecc-ccccCCeeEEEecchHHHHHHHHhhcc---
Confidence                         188999999999999999999999999999998887 468899999999999999999999998   


Q ss_pred             cccCCeeEEEEe
Q psy7847         155 LFVGDLKTRSSI  166 (170)
Q Consensus       155 ~~~~~~~i~v~~  166 (170)
                      .-+.+++..+..
T Consensus       279 ~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  279 QGLFDRRMTVRL  290 (608)
T ss_pred             CCCccccceeec
Confidence            777777777665

>PF00076 RRM_1: RNA recognition motif

Probab=99.70  E-value=2e-16  Score=96.04  Aligned_cols=70  Identities=36%  Similarity=0.560  Sum_probs=66.6

Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        90 l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      |||+|||+.+++++|+++|++||.+..+.+..+ .++.++|+|||+|.+.++|.+|++.+||   ..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g---~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNG---KKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTT---EEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCC---CEECccCcC
Confidence            799999999999999999999999999999887 4788999999999999999999999999   999999886

(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 ....

>KOG4206|consensus

Probab=99.69  E-value=1.8e-15  Score=108.84  Aligned_cols=140  Identities=21%  Similarity=0.380  Sum_probs=120.7

Q ss_pred             CCCcEEEEcCCCCCccHHHHHH----HhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIR----TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--------   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~----~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--------   87 (170)
                      ++..++||.||+..+..++|+.    +|++||.|.+|...+   +.+.+|-|||.|.+.+.|..|+..++|-        
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3445999999999999999998    999999999887764   5788999999999999999999877651        


Q ss_pred             ---------------------------------------------------------------ceEEecCCCCCCCHHHH
Q psy7847          88 ---------------------------------------------------------------FRLFCGDLGNDVTDELL  104 (170)
Q Consensus        88 ---------------------------------------------------------------~~l~v~nlp~~~~~~~l  104 (170)
                                                                                     ..+++.|+|..++.+.+
T Consensus        84 iqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l  163 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEML  163 (221)
T ss_pred             eecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHH
Confidence                                                                           26889999999999999


Q ss_pred             HHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         105 IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       105 ~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ..+|.+|+....++++...     .+.|||+|.+.-.+..|.+.+.++.+.  ....++|.++.+
T Consensus       164 ~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it--~~~~m~i~~a~K  221 (221)
T KOG4206|consen  164 SDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKIT--KKNTMQITFAKK  221 (221)
T ss_pred             HHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceec--cCceEEecccCC
Confidence            9999999999999987654     679999999999999999999995322  388899888764

>KOG0147|consensus

Probab=99.67  E-value=5.2e-16  Score=123.53  Aligned_cols=137  Identities=20%  Similarity=0.316  Sum_probs=116.1

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------------   87 (170)
                      +.|||+||-.++++++|+.+|+.||.|+.|.+.++..+|.++||+|++|.+.++|.+|++.+|+-               
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            34999999999999999999999999999999999889999999999999999999999988861               


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       359 ~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~  438 (549)
T KOG0147|consen  359 VDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPA  438 (549)
T ss_pred             cccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccc
Confidence                                                                                            


Q ss_pred             -----ceEEecCC--CCC-----CC---HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCC
Q psy7847          88 -----FRLFCGDL--GND-----VT---DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus        88 -----~~l~v~nl--p~~-----~~---~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  152 (170)
                           .|+.+.|+  |..     |.   .+++.+-|++||.|.-|.+-+.     +-|+.||.|.+.++|..|+.+||| 
T Consensus       439 ~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhg-  512 (549)
T KOG0147|consen  439 FDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHG-  512 (549)
T ss_pred             cCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhh-
Confidence                 03333333  111     11   3788888999999999888332     248999999999999999999999 


Q ss_pred             CccccCCeeEEEEee
Q psy7847         153 PHLFVGDLKTRSSIT  167 (170)
Q Consensus       153 ~~~~~~~~~i~v~~~  167 (170)
                        .++.|+-|++.|-
T Consensus       513 --rWF~gr~Ita~~~  525 (549)
T KOG0147|consen  513 --RWFAGRMITAKYL  525 (549)
T ss_pred             --hhhccceeEEEEe
Confidence              9999999999874

>KOG0121|consensus

Probab=99.67  E-value=2.5e-16  Score=103.79  Aligned_cols=85  Identities=19%  Similarity=0.234  Sum_probs=79.2

Q ss_pred             HHHHcCCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          80 ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        80 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      .++.+..++||||+||++.++||+|.++|+..|.|..|.+-.|+....+.|+|||+|.+.++|..|++.++|   ..+.+
T Consensus        29 ~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisg---trLdd  105 (153)
T KOG0121|consen   29 QLEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISG---TRLDD  105 (153)
T ss_pred             HHHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhcc---Ccccc
Confidence            344556678999999999999999999999999999999999998899999999999999999999999999   99999


Q ss_pred             eeEEEEee
Q psy7847         160 LKTRSSIT  167 (170)
Q Consensus       160 ~~i~v~~~  167 (170)
                      ++|++.|.
T Consensus       106 r~ir~D~D  113 (153)
T KOG0121|consen  106 RPIRIDWD  113 (153)
T ss_pred             cceeeecc
Confidence            99999985

>KOG1457|consensus

Probab=99.67  E-value=1.7e-15  Score=108.72  Aligned_cols=134  Identities=22%  Similarity=0.296  Sum_probs=109.9

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEe-cCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR-DKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~-~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------   87 (170)
                      ...++..-++|||.+||.++...+|..+|..|-..+...+.. ++....++-+||++|.+..+|..++..+||-      
T Consensus        27 ~~~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~  106 (284)
T KOG1457|consen   27 LADEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPET  106 (284)
T ss_pred             ccccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeecccc
Confidence            344455578999999999999999999999987777776643 3222346789999999999999999988861      


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus       107 ~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~  186 (284)
T KOG1457|consen  107 GSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAP  186 (284)
T ss_pred             CceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhh
Confidence                                                                                            


Q ss_pred             ------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHH
Q psy7847          88 ------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI  143 (170)
Q Consensus        88 ------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~  143 (170)
                                              .+|||.||.+++++++|+.+|+.|......++.-.  .|.  -.||++|++.+.|.
T Consensus       187 ~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g~--~vaf~~~~~~~~at  262 (284)
T KOG1457|consen  187 DSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GGM--PVAFADFEEIEQAT  262 (284)
T ss_pred             hhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CCc--ceEeecHHHHHHHH
Confidence                                    19999999999999999999999998887776432  233  37999999999999


Q ss_pred             HHHHHhcCC
Q psy7847         144 RANKEMNEF  152 (170)
Q Consensus       144 ~a~~~l~~~  152 (170)
                      .|+..|+|+
T Consensus       263 ~am~~lqg~  271 (284)
T KOG1457|consen  263 DAMNHLQGN  271 (284)
T ss_pred             HHHHHhhcc
Confidence            999999883

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.67  E-value=4.5e-16  Score=121.82  Aligned_cols=81  Identities=26%  Similarity=0.353  Sum_probs=77.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|+.||.|..+++++|..++.++|||||+|.++++|.+|++.||+   ..+.+++|+|+
T Consensus       106 ~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG---~~l~gr~i~V~  182 (346)
T TIGR01659       106 SGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNG---ITVRNKRLKVS  182 (346)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCC---CccCCceeeee
Confidence            457999999999999999999999999999999999988999999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus       183 ~a~p  186 (346)
T TIGR01659       183 YARP  186 (346)
T ss_pred             cccc
Confidence            8754

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

>KOG0122|consensus

Probab=99.65  E-value=1e-15  Score=111.03  Aligned_cols=81  Identities=25%  Similarity=0.374  Sum_probs=77.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|.|.||+.++++++|+++|.+||.|..+.+.+|+.+|.++|||||.|.++++|.+||..|||   .=..+..|+|.|
T Consensus       189 ~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG---~gyd~LILrvEw  265 (270)
T KOG0122|consen  189 EATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNG---YGYDNLILRVEW  265 (270)
T ss_pred             cceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccC---cccceEEEEEEe
Confidence            45899999999999999999999999999999999999999999999999999999999999999   889999999999


Q ss_pred             eccC
Q psy7847         167 TLKG  170 (170)
Q Consensus       167 ~~~~  170 (170)
                      +.+.
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9864

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

Probab=99.63  E-value=2.3e-15  Score=104.18  Aligned_cols=68  Identities=32%  Similarity=0.539  Sum_probs=63.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+++|||+|||+++++++|+++|++||.|.++.++.++.++.+++||||+|.+.++|+.|++.+++.
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~   99 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK   99 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence            34678999999999999999999999999999999999989999999999999999999999988763

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.62  E-value=5.2e-15  Score=90.08  Aligned_cols=70  Identities=27%  Similarity=0.461  Sum_probs=64.5

Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        90 l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      |+|+|||+++++++|.++|+.+|.|..+.+..++. +.++|+|||+|.+.++|.+|++.+++   ..++|++|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~---~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNG---KEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTT---EEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCC---cEECCEEcC
Confidence            68999999999999999999999999999999875 88999999999999999999999999   999999885

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 ....

>KOG0129|consensus

Probab=99.62  E-value=1.3e-14  Score=114.96  Aligned_cols=130  Identities=22%  Similarity=0.335  Sum_probs=109.5

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecC-CCC--CcCC---EEEEEeCCHHHHHHHHHHcCC-----
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK-RTN--KTKG---FGFVSFKDPQDFIRANKEMND-----   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~-~~~--~~~~---~afv~f~~~~~a~~~~~~~~~-----   86 (170)
                      .+.-+++||||+||++++|++|...|..||.+. +...... ..+  ..+|   |+|+.|+++.++...+..+..     
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccce
Confidence            345578899999999999999999999999653 4444211 112  3466   999999999999988864431     


Q ss_pred             ------------------------------------CceEEecCCCCCCCHHHHHHHhc-cCCCeeEEEEeecCCCCCcc
Q psy7847          87 ------------------------------------DFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTK  129 (170)
Q Consensus        87 ------------------------------------~~~l~v~nlp~~~~~~~l~~~f~-~~g~i~~~~~~~~~~~~~~~  129 (170)
                                                          .+|+||++||..++.++|..+|. -||.|..+-|-.|++-+.++
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPk  413 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPK  413 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCC
Confidence                                                35999999999999999999997 79999999999998899999


Q ss_pred             cEEEEEecCHHHHHHHHHH
Q psy7847         130 GFGFVSFKDPQDFIRANKE  148 (170)
Q Consensus       130 g~afv~f~~~~~a~~a~~~  148 (170)
                      |.|-|+|.+.++..+||.+
T Consensus       414 GaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcceeeecccHHHHHHHhh
Confidence            9999999999999999984

>KOG0110|consensus

Probab=99.60  E-value=1.4e-14  Score=118.33  Aligned_cols=141  Identities=23%  Similarity=0.304  Sum_probs=119.3

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-----------
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-----------   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-----------   87 (170)
                      ......++++|||..+..+++...|..||.+..+.+++   .|.   -++|+|-++.+|.+|...+...           
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~---~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle~  455 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPP---GGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEW  455 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecCc---ccc---eeeeeecCccchHHHHHHhchhhhccCcccccc
Confidence            33456799999999999999999999999999996652   222   3899999999999998755431           


Q ss_pred             ------------------------------------------------------------ceEEecCCCCCCCHHHHHHH
Q psy7847          88 ------------------------------------------------------------FRLFCGDLGNDVTDELLIRT  107 (170)
Q Consensus        88 ------------------------------------------------------------~~l~v~nlp~~~~~~~l~~~  107 (170)
                                                                                  ..||+.||+++++.+++...
T Consensus       456 aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~  535 (725)
T KOG0110|consen  456 APEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDL  535 (725)
T ss_pred             ChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHH
Confidence                                                                        14999999999999999999


Q ss_pred             hccCCCeeEEEEeecCCC---CCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         108 FSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       108 f~~~g~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      |...|.|..+.|...+..   ..+.|||||+|.+.++|+.|++.|+|   ..+.|+.|.+.++.
T Consensus       536 F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqg---tvldGH~l~lk~S~  596 (725)
T KOG0110|consen  536 FSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQG---TVLDGHKLELKISE  596 (725)
T ss_pred             HHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcC---ceecCceEEEEecc
Confidence            999999999877654421   13569999999999999999999999   99999999999986

>PF00076 RRM_1: RNA recognition motif

Probab=99.58  E-value=9.6e-15  Score=88.54  Aligned_cols=61  Identities=38%  Similarity=0.629  Sum_probs=58.4

Q ss_pred             EEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        25 v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      |||+|||+++++++|+++|+.||.+..+.+..+ .++..+++|||+|.+.++|.+|+..+++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g   61 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNG   61 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCC
Confidence            799999999999999999999999999999998 5789999999999999999999999987

(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 ....

>KOG0125|consensus

Probab=99.57  E-value=6.5e-15  Score=110.96  Aligned_cols=79  Identities=25%  Similarity=0.379  Sum_probs=73.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +.++|+|+|+|+...+.||+.+|.+||.|.++.|+.+  ...++|||||+|++.+||++|-.+|||   .++.||+|.|+
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHg---t~VEGRkIEVn  169 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHG---TVVEGRKIEVN  169 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhc---ceeeceEEEEe
Confidence            4579999999999999999999999999999999877  366799999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      .++.
T Consensus       170 ~ATa  173 (376)
T KOG0125|consen  170 NATA  173 (376)
T ss_pred             ccch
Confidence            8763

>KOG1548|consensus

Probab=99.56  E-value=4.7e-13  Score=101.65  Aligned_cols=142  Identities=19%  Similarity=0.214  Sum_probs=117.9

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCee--------EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~--------~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---   87 (170)
                      +.....|||.|||.++|.+++.++|+.+|.|.        .|++.++. .|.-+|=|.+.|...+++.-|+..|++.   
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            33455699999999999999999999999664        37888886 5999999999999999999999866641   


Q ss_pred             --------------------------------------------------------ceEEecCCC----CCCC-------
Q psy7847          88 --------------------------------------------------------FRLFCGDLG----NDVT-------  100 (170)
Q Consensus        88 --------------------------------------------------------~~l~v~nlp----~~~~-------  100 (170)
                                                                              ++|.+.|+=    ...+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence                                                                    277777652    1223       


Q ss_pred             HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         101 DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       101 ~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +++|.+-++.||.+..+.+.-    ..+.|.+-|.|.+.++|..|++.|+|   ..++||.|..++.+
T Consensus       290 kedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~G---R~fdgRql~A~i~D  350 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDG---RWFDGRQLTASIWD  350 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcC---eeecceEEEEEEeC
Confidence            477788899999999997753    34688999999999999999999999   99999999988754

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.56  E-value=2.7e-14  Score=106.12  Aligned_cols=75  Identities=15%  Similarity=0.110  Sum_probs=69.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+.+++++|+++|+.||.|..+.+++++.   ++|+|||+|.++++|..|+. |||   ..++|++|+|..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG---~~l~gr~V~Vt~   76 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSG---ATIVDQSVTITP   76 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcC---CeeCCceEEEEe
Confidence            46899999999999999999999999999999988753   57899999999999999995 999   999999999998


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        77 a~   78 (260)
T PLN03120         77 AE   78 (260)
T ss_pred             cc
Confidence            75

>smart00362 RRM_2 RNA recognition motif

Probab=99.54  E-value=9.5e-14  Score=83.78  Aligned_cols=72  Identities=36%  Similarity=0.544  Sum_probs=66.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +|+|+|+|..+++++|+++|.+||.+..+.+..++  +.++|+|||+|.+.++|..|++.+++   ..+.|++++|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~---~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNG---TKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCC---cEECCEEEeeC
Confidence            58999999999999999999999999999988775  67889999999999999999999999   88899998874

>KOG0149|consensus

Probab=99.52  E-value=3.1e-14  Score=102.98  Aligned_cols=65  Identities=35%  Similarity=0.617  Sum_probs=61.2

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      -.+||||||++.+..+.|+++|++||+|++..++.|+.+|+++||+||+|++.++|.+|++.-+.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~p   76 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNP   76 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCC
Confidence            45699999999999999999999999999999999999999999999999999999999986553

>KOG0122|consensus

Probab=99.52  E-value=8.5e-14  Score=101.19  Aligned_cols=67  Identities=27%  Similarity=0.464  Sum_probs=64.4

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +..+|.|.|||.++++++|.++|.+||.+..+.+.+++.||.++|||||.|.+.++|.+|+..|++-
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~  254 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGY  254 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCc
Confidence            5678999999999999999999999999999999999999999999999999999999999999973

>KOG0113|consensus

Probab=99.52  E-value=6.9e-14  Score=104.25  Aligned_cols=78  Identities=27%  Similarity=0.485  Sum_probs=75.7

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +||||+.|++++++..|++.|+.||.|..|.+++|+.+++++|||||+|.++.+...|.+..+|   ..|.|+.|-|.|.
T Consensus       102 ~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG---~~Idgrri~VDvE  178 (335)
T KOG0113|consen  102 KTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADG---IKIDGRRILVDVE  178 (335)
T ss_pred             ceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccC---ceecCcEEEEEec
Confidence            6999999999999999999999999999999999999999999999999999999999999999   9999999999986


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus       179 R  179 (335)
T KOG0113|consen  179 R  179 (335)
T ss_pred             c
Confidence            3

>KOG0107|consensus

Probab=99.51  E-value=6.4e-14  Score=97.17  Aligned_cols=76  Identities=30%  Similarity=0.516  Sum_probs=70.2

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      +....|||+||+..+++.+|+.+|..||.+..+-|.+.+     .|||||+|+++-+|..|+..|+|   ..++|..|+|
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG---~~~cG~r~rV   79 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDG---KDICGSRIRV   79 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCC---ccccCceEEE
Confidence            456799999999999999999999999999988776654     89999999999999999999999   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      .++.
T Consensus        80 E~S~   83 (195)
T KOG0107|consen   80 ELST   83 (195)
T ss_pred             Eeec
Confidence            9875

>smart00360 RRM RNA recognition motif

Probab=99.51  E-value=1.4e-13  Score=82.64  Aligned_cols=71  Identities=35%  Similarity=0.506  Sum_probs=65.9

Q ss_pred             ecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          92 CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        92 v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      |+|||..+++++|+++|++||.+..+.+..++.++.++|+|||+|.+.++|..|++.+++   ..++|++|+|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~---~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNG---KELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCC---CeeCCcEEEeC
Confidence            579999999999999999999999999988876788999999999999999999999999   88899998874

>KOG0124|consensus

Probab=99.50  E-value=5.9e-13  Score=102.01  Aligned_cols=66  Identities=20%  Similarity=0.409  Sum_probs=60.0

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..-.++||..+-++.+++||++.|+.||+|.+|.+-++...+..+||+|++|.+..+...++..+|
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            345689999999999999999999999999999999998777889999999999999998887665

>KOG0131|consensus

Probab=99.50  E-value=4e-14  Score=98.74  Aligned_cols=83  Identities=28%  Similarity=0.420  Sum_probs=78.8

Q ss_pred             HcCCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        83 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ..++..+|||+||+..++++.|+++|-+.|.+..+.+++|+.++..+||||++|.++++|+-|++.||.   ..+-|++|
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~---VkLYgrpI   81 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNM---VKLYGRPI   81 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHH---HHhcCcee
Confidence            346678999999999999999999999999999999999999999999999999999999999999998   99999999


Q ss_pred             EEEeec
Q psy7847         163 RSSITL  168 (170)
Q Consensus       163 ~v~~~~  168 (170)
                      +|+.+.
T Consensus        82 rv~kas   87 (203)
T KOG0131|consen   82 RVNKAS   87 (203)
T ss_pred             EEEecc
Confidence            999875

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.49  E-value=1.7e-13  Score=83.37  Aligned_cols=61  Identities=28%  Similarity=0.524  Sum_probs=55.7

Q ss_pred             EEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        25 v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      |+|+|||+++++++|.++|+.+|.|..+.+..++. +.++++|||+|.++++|..++..+++
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~   61 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNG   61 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCC
Confidence            79999999999999999999999999999999875 89999999999999999999998873

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 ....

>KOG0149|consensus

Probab=99.49  E-value=6.4e-14  Score=101.37  Aligned_cols=76  Identities=32%  Similarity=0.587  Sum_probs=69.6

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ..+||++|++.+..+.|++.|++||+|....++.|+.+++++|||||+|.+.++|.+|.+.-|    -.|+||+.-++.|
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~----piIdGR~aNcnlA   88 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN----PIIDGRKANCNLA   88 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC----Ccccccccccchh
Confidence            489999999999999999999999999999999999999999999999999999999988655    6788887776655

>KOG0106|consensus

Probab=99.47  E-value=8.5e-14  Score=100.94  Aligned_cols=126  Identities=25%  Similarity=0.387  Sum_probs=109.6

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----------------
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----------------   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----------------   87 (170)
                      .+||++||+.+.+.+|..+|+.||.+.++.+..        +|+||.|.+..+|..++..+++.                
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            689999999999999999999999999887743        57899999999999998766541                


Q ss_pred             -------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHH
Q psy7847          88 -------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF  142 (170)
Q Consensus        88 -------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a  142 (170)
                                               +.+.+.+++..+.+.+|...|.++|.+.....        ..+.+||+|.+.+++
T Consensus        75 ~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da  146 (216)
T KOG0106|consen   75 RGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDA  146 (216)
T ss_pred             cccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhh
Confidence                                     37788899999999999999999999854433        256899999999999


Q ss_pred             HHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         143 IRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       143 ~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      .+|+..+++   ..+.+++|++.+..
T Consensus       147 ~ra~~~l~~---~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  147 KRALEKLDG---KKLNGRRISVEKNS  169 (216)
T ss_pred             hhcchhccc---hhhcCceeeecccC
Confidence            999999999   99999999986543

>KOG0130|consensus

Probab=99.47  E-value=1.5e-13  Score=91.55  Aligned_cols=78  Identities=17%  Similarity=0.279  Sum_probs=75.6

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +.|||.++...++++++...|+.||.|..+.+..|+-+|..+|||+|+|.+.++|+.|+..+||   ..+.+..|+|.|.
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng---~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNG---AELLGQNVSVDWC  149 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccc---hhhhCCceeEEEE
Confidence            6999999999999999999999999999999999998999999999999999999999999999   9999999999997


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus       150 F  150 (170)
T KOG0130|consen  150 F  150 (170)
T ss_pred             E
Confidence            5

>KOG0111|consensus

Probab=99.46  E-value=5e-14  Score=101.10  Aligned_cols=82  Identities=27%  Similarity=0.447  Sum_probs=78.9

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      +.+++|||++|-.++++.-|...|=+||.|.+|+++.|..++++||||||+|...++|..|+..||+   ..+.||.|+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMne---sEL~GrtirV   84 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNE---SELFGRTIRV   84 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCch---hhhcceeEEE
Confidence            4578999999999999999999999999999999999999999999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      ++|.+
T Consensus        85 N~AkP   89 (298)
T KOG0111|consen   85 NLAKP   89 (298)
T ss_pred             eecCC
Confidence            99875

>KOG0126|consensus

Probab=99.46  E-value=8.4e-15  Score=102.14  Aligned_cols=80  Identities=26%  Similarity=0.485  Sum_probs=75.6

Q ss_pred             cCCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        84 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ..++..+||+|||+..|+-||--+|++||.++.|.+++|+.+|+++||||+.|++..+..-|+..|||   .-+.||.|+
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NG---iki~gRtir  108 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNG---IKILGRTIR  108 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCC---ceecceeEE
Confidence            34566899999999999999999999999999999999999999999999999999999999999999   999999999


Q ss_pred             EEe
Q psy7847         164 SSI  166 (170)
Q Consensus       164 v~~  166 (170)
                      |..
T Consensus       109 VDH  111 (219)
T KOG0126|consen  109 VDH  111 (219)
T ss_pred             eee
Confidence            974

>KOG0114|consensus

Probab=99.46  E-value=5.3e-13  Score=85.06  Aligned_cols=76  Identities=20%  Similarity=0.247  Sum_probs=68.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .+.|||+|||+.+|.+++.++|+.||+|..|++--.   ...+|-|||.|++..+|.+|...|+|   ..++++.+.|-|
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~---k~TrGTAFVVYedi~dAk~A~dhlsg---~n~~~ryl~vly   91 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT---KETRGTAFVVYEDIFDAKKACDHLSG---YNVDNRYLVVLY   91 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCc---cCcCceEEEEehHhhhHHHHHHHhcc---cccCCceEEEEe
Confidence            358999999999999999999999999999998443   34589999999999999999999999   999999999876


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      -+
T Consensus        92 yq   93 (124)
T KOG0114|consen   92 YQ   93 (124)
T ss_pred             cC
Confidence            43

>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=99.46  E-value=1.1e-12  Score=79.43  Aligned_cols=74  Identities=39%  Similarity=0.582  Sum_probs=67.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +|+|+|||+.+++++|.+.|+.+|.+..+.+..++. +.++|+|+|+|.+.++|..|++.+++   ..+.|+.+.|++
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~---~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNG---KELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCC---CeECCeEEEEeC
Confidence            478999999999999999999999999999988763 36789999999999999999999999   889999999875

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).

>PLN03213 repressor of silencing 3; Provisional

Probab=99.46  E-value=3.3e-13  Score=106.90  Aligned_cols=76  Identities=20%  Similarity=0.323  Sum_probs=70.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCH--HHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP--QDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~--~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..+|||+||++.+++++|..+|+.||.|..+.+++.  +|  +|||||+|.+.  .++.+|+..|||   ..++|+.|+|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNG---AEWKGR~LKV   82 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNG---CVWKGGRLRL   82 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcC---CeecCceeEE
Confidence            468999999999999999999999999999999855  45  99999999987  789999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      ..|.+
T Consensus        83 NKAKP   87 (759)
T PLN03213         83 EKAKE   87 (759)
T ss_pred             eeccH
Confidence            98764

>KOG4207|consensus

Probab=99.45  E-value=1.7e-13  Score=97.55  Aligned_cols=81  Identities=25%  Similarity=0.340  Sum_probs=76.3

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ++-..|.|.||-+.++.++|..+|++||.|-++.|++|+-++.++|||||.|....+|++|+.+|+|   .+++|+-|.|
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG---~~ldgRelrV   87 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDG---AVLDGRELRV   87 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcc---eeeccceeee
Confidence            3456899999999999999999999999999999999999999999999999999999999999999   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      -+|.
T Consensus        88 q~ar   91 (256)
T KOG4207|consen   88 QMAR   91 (256)
T ss_pred             hhhh
Confidence            8763

>KOG4212|consensus

Probab=99.45  E-value=3.7e-12  Score=99.58  Aligned_cols=71  Identities=25%  Similarity=0.304  Sum_probs=65.2

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +++|+|||.++|++.|+..|..+|.+.+..++.   .++++|  .|.|.++++|++|+..|||   ..+.++-|+|.|.
T Consensus       538 qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mng---s~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  538 QIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNG---SRLDGRNIKVTYF  608 (608)
T ss_pred             EEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhcc---CcccCceeeeeeC
Confidence            999999999999999999999999999988843   466776  7999999999999999999   9999999999874

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

Probab=99.44  E-value=3.5e-12  Score=95.78  Aligned_cols=126  Identities=29%  Similarity=0.469  Sum_probs=99.9

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--------------
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--------------   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--------------   87 (170)
                      .++|||+|||.++++++|.++|..||.+..+.+..++.++.++|+|||.|.+.+++..|+..+++.              
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            589999999999999999999999999999999999889999999999999999999999877741              


Q ss_pred             -------------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEe
Q psy7847          88 -------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF  136 (170)
Q Consensus        88 -------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f  136 (170)
                                                     ..+++.+++..++..++...|..+|.+....+.............++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence                                           2666778899999999999999999997666655443333333333333


Q ss_pred             cCHHHHHHHHH
Q psy7847         137 KDPQDFIRANK  147 (170)
Q Consensus       137 ~~~~~a~~a~~  147 (170)
                      .....+.....
T Consensus       275 ~~~~~~~~~~~  285 (306)
T COG0724         275 EASKDALESNS  285 (306)
T ss_pred             hHHHhhhhhhc
Confidence            33333333333

>KOG1365|consensus

Probab=99.44  E-value=1.5e-12  Score=100.22  Aligned_cols=140  Identities=14%  Similarity=0.107  Sum_probs=114.5

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhc---C-CCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSK---Y-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~---~-g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----------   86 (170)
                      ..-.|.+++||+++++.++.++|..   . |..+.+.+++. .+|+..|-||+.|..+++|..++....+          
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHH
Confidence            3456889999999999999999963   2 24566666664 4899999999999999999999864332          


Q ss_pred             -----------------------------------------CceEEecCCCCCCCHHHHHHHhccCCC-eeE--EEEeec
Q psy7847          87 -----------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPS-FLK--AKVVRD  122 (170)
Q Consensus        87 -----------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~-i~~--~~~~~~  122 (170)
                                                               ..++.+++||+..+.|+|-.+|..|-. |..  +.+..+
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N  318 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN  318 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc
Confidence                                                     239999999999999999999988754 333  566665


Q ss_pred             CCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847         123 KRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus       123 ~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      . .|.+.|-|||++.+.++|..|....|.   .....+.|.|-
T Consensus       319 ~-qGrPSGeAFIqm~nae~a~aaaqk~hk---~~mk~RYiEvf  357 (508)
T KOG1365|consen  319 G-QGRPSGEAFIQMRNAERARAAAQKCHK---KLMKSRYIEVF  357 (508)
T ss_pred             C-CCCcChhhhhhhhhhHHHHHHHHHHHH---hhcccceEEEe
Confidence            4 688999999999999999999999998   77778888774

>KOG0117|consensus

Probab=99.43  E-value=2e-12  Score=101.18  Aligned_cols=119  Identities=18%  Similarity=0.300  Sum_probs=93.6

Q ss_pred             cHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCceEEecCCCCCCCHHHHHHHhccCCCe
Q psy7847          35 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSF  114 (170)
Q Consensus        35 t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i  114 (170)
                      .++.|+.+.++-|.-..+..--.++.|.+.+     +.-+        .....+-+||+.||.++.|++|.-+|...|.|
T Consensus        44 ~eaal~al~E~tgy~l~ve~gqrk~ggPpP~-----weg~--------~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I  110 (506)
T KOG0117|consen   44 EEAALKALLERTGYTLVVENGQRKYGGPPPG-----WEGP--------PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKI  110 (506)
T ss_pred             HHHHHHHHHHhcCceEEEeccccccCCCCCc-----ccCC--------CCCCCceEEecCCCccccchhhHHHHHhccce
Confidence            5677778888777555554444444444444     1100        11456799999999999999999999999999


Q ss_pred             eEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         115 LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       115 ~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      -.++++.|+.+|.++|||||.|.+.++|+.|++.||+..  +--|+.|.|+++.
T Consensus       111 ~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~E--ir~GK~igvc~Sv  162 (506)
T KOG0117|consen  111 YELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYE--IRPGKLLGVCVSV  162 (506)
T ss_pred             eeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCcc--ccCCCEeEEEEee
Confidence            999999999999999999999999999999999999953  3367888888764

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.42  E-value=1.4e-12  Score=95.65  Aligned_cols=74  Identities=15%  Similarity=0.187  Sum_probs=67.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|+|+||++.+++++|+++|+.+|.|..|.+++|.   ...|+|||+|.+++++..|+. |+|   ..+.+++|.|.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnG---a~l~d~~I~It   76 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSG---ATIVDQRVCIT   76 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCC---CeeCCceEEEE
Confidence            35799999999999999999999999999999999874   345799999999999999995 999   99999999886


Q ss_pred             e
Q psy7847         166 I  166 (170)
Q Consensus       166 ~  166 (170)
                      -
T Consensus        77 ~   77 (243)
T PLN03121         77 R   77 (243)
T ss_pred             e
Confidence            4

>KOG0108|consensus

Probab=99.42  E-value=6e-13  Score=106.15  Aligned_cols=79  Identities=29%  Similarity=0.442  Sum_probs=76.7

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +.+||+|+|+++++++|..+|+..|.|..+++..|+.+|.++||||++|.+.+++..|++.|||   ..++|++|+|+|+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg---~~~~gr~l~v~~~   95 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNG---AEFNGRKLRVNYA   95 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCC---cccCCceEEeecc
Confidence            7899999999999999999999999999999999999999999999999999999999999999   9999999999997


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      ..
T Consensus        96 ~~   97 (435)
T KOG0108|consen   96 SN   97 (435)
T ss_pred             cc
Confidence            53

>PF13893 RRM_5: RNA recognition motif

Probab=99.41  E-value=2.1e-12  Score=75.19  Aligned_cols=56  Identities=29%  Similarity=0.450  Sum_probs=50.5

Q ss_pred             HHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847         104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus       104 l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      |.++|++||.|..+.+..+.     +++|||+|.+.++|..|++.|||   ..++|++|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~---~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNG---RQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTT---SEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCC---CEECCcEEEEEEC
Confidence            67899999999999986653     68999999999999999999999   9999999999986

(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 ....

>KOG0114|consensus

Probab=99.41  E-value=1.4e-12  Score=83.11  Aligned_cols=70  Identities=23%  Similarity=0.312  Sum_probs=61.4

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..-+++..+.|||+|||+++|.+++.++|+.||+|..|++--   +...+|.|||.|++..+|.+|+.++.+.
T Consensus        11 ~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~---~k~TrGTAFVVYedi~dAk~A~dhlsg~   80 (124)
T KOG0114|consen   11 IRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN---TKETRGTAFVVYEDIFDAKKACDHLSGY   80 (124)
T ss_pred             CCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecC---ccCcCceEEEEehHhhhHHHHHHHhccc
Confidence            344566678899999999999999999999999999998854   3467899999999999999999999873

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

Probab=99.40  E-value=1.8e-12  Score=97.30  Aligned_cols=79  Identities=32%  Similarity=0.481  Sum_probs=75.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||..+++++|.++|..||.+..+.+..++..+.++|+|||.|.+.+++..|+..++|   ..+.|++|+|.+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~---~~~~~~~~~v~~  191 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNG---KELEGRPLRVQK  191 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCC---CeECCceeEeec
Confidence            48999999999999999999999999999999999988899999999999999999999999999   999999999998


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus       192 ~~  193 (306)
T COG0724         192 AQ  193 (306)
T ss_pred             cc
Confidence            64

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.36  E-value=3.7e-12  Score=94.76  Aligned_cols=61  Identities=16%  Similarity=0.175  Sum_probs=55.8

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++|||+|||+++++++|+++|+.||.|.++.+++++   .+++||||+|.+++++..|+. +++
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~---~~~GfAFVtF~d~eaAe~All-LnG   64 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN---ERSQIAYVTFKDPQGAETALL-LSG   64 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC---CCCCEEEEEeCcHHHHHHHHH-hcC
Confidence            5789999999999999999999999999999999875   257899999999999999995 665

>KOG1190|consensus

Probab=99.36  E-value=2.1e-11  Score=94.58  Aligned_cols=139  Identities=18%  Similarity=0.234  Sum_probs=116.1

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----------
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----------   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----------   87 (170)
                      .+..--+++|.|+-+.++-+.|..+|++||.|..|.-...    ...--|.|+|.+.+.|..|...++|.          
T Consensus       146 ~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~K----nn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLr  221 (492)
T KOG1190|consen  146 GPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTK----NNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLR  221 (492)
T ss_pred             CCceeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEec----ccchhhhhhccchhhHHHHHHhccCCcccCceeEEE
Confidence            3444456899999999999999999999999988765443    12234899999999999998877652          


Q ss_pred             ----------------------------------------------------------------------------ceEE
Q psy7847          88 ----------------------------------------------------------------------------FRLF   91 (170)
Q Consensus        88 ----------------------------------------------------------------------------~~l~   91 (170)
                                                                                                  ..|.
T Consensus       222 Id~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vll  301 (492)
T KOG1190|consen  222 IDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLL  301 (492)
T ss_pred             eehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEE
Confidence                                                                                        1466


Q ss_pred             ecCCC-CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          92 CGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        92 v~nlp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      |.||. ..+|.+.|..+|+-||.|.++.++.+++     --|+|+|.+..+|+-|+..|+|   ..+-|++|+|.++.
T Consensus       302 vsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g---~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  302 VSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEG---HKLYGKKLRVTLSK  371 (492)
T ss_pred             EecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhc---ceecCceEEEeecc
Confidence            66764 5799999999999999999999998762     3599999999999999999999   99999999999874

>smart00361 RRM_1 RNA recognition motif

Probab=99.34  E-value=6.5e-12  Score=76.48  Aligned_cols=62  Identities=23%  Similarity=0.350  Sum_probs=54.6

Q ss_pred             HHHHHHHhc----cCCCeeEEE-EeecCCC--CCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847         101 DELLIRTFS----KYPSFLKAK-VVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus       101 ~~~l~~~f~----~~g~i~~~~-~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +++|++.|+    .||.+..+. +..++.+  +.++|+|||+|.+.++|.+|++.|||   ..++|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g---~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNG---RYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCC---CEECCEEEEeC
Confidence            567888888    999999985 6666655  88999999999999999999999999   99999999874

>KOG1190|consensus

Probab=99.34  E-value=3.9e-11  Score=93.13  Aligned_cols=137  Identities=18%  Similarity=0.288  Sum_probs=113.1

Q ss_pred             CcEEEEcCCC-CCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------------
Q psy7847          22 DFRLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------------   87 (170)
Q Consensus        22 ~~~v~v~nLp-~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------------   87 (170)
                      ...|-|.||. ..+|.+.|..+|+-||.|..|+|+.++.     .-|.|++.+...|.-|++.+++.             
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            4567788885 5699999999999999999999998763     46999999999999999987762             


Q ss_pred             -------------------------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCC
Q psy7847          88 -------------------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR  124 (170)
Q Consensus        88 -------------------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~  124 (170)
                                                                 .+++++|+|+++++|+++.+|...|.......-.   
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---  448 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---  448 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---
Confidence                                                       2899999999999999999999888765543211   


Q ss_pred             CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC-eeEEEEeeccC
Q psy7847         125 TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD-LKTRSSITLKG  170 (170)
Q Consensus       125 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~-~~i~v~~~~~~  170 (170)
                       ++.+-+|++++.+.+.|..|+-.+|+   ..++. ..++|+++..+
T Consensus       449 -~kd~kmal~q~~sveeA~~ali~~hn---h~lgen~hlRvSFSks~  491 (492)
T KOG1190|consen  449 -QKDRKMALPQLESVEEAIQALIDLHN---HYLGENHHLRVSFSKST  491 (492)
T ss_pred             -CCCcceeecccCChhHhhhhcccccc---ccCCCCceEEEEeeccc
Confidence             11234899999999999999999998   77666 59999998653

>KOG0120|consensus

Probab=99.34  E-value=1.1e-11  Score=99.77  Aligned_cols=148  Identities=21%  Similarity=0.252  Sum_probs=119.7

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCc----eEEe-
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDF----RLFC-   92 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~----~l~v-   92 (170)
                      .+.....++|++||...+++++.++.+.||++....+..+..+|.++||||-+|-++.....|+..+|+..    .|.| 
T Consensus       285 ~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq  364 (500)
T KOG0120|consen  285 VPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQ  364 (500)
T ss_pred             cccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEee
Confidence            34556789999999999999999999999999999999999889999999999999999999998888631    1110 


Q ss_pred             --------------------cCCCC-----------------CCCH-------------HHHHHHhccCCCeeEEEEeec
Q psy7847          93 --------------------GDLGN-----------------DVTD-------------ELLIRTFSKYPSFLKAKVVRD  122 (170)
Q Consensus        93 --------------------~nlp~-----------------~~~~-------------~~l~~~f~~~g~i~~~~~~~~  122 (170)
                                          -.|+.                 .++.             |+++.-|+.||.|..|.++++
T Consensus       365 ~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~  444 (500)
T KOG0120|consen  365 RAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRP  444 (500)
T ss_pred             hhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCC
Confidence                                01111                 1221             566677889999999999887


Q ss_pred             CC---CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         123 KR---TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       123 ~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      ..   ..-..|-.||+|.+.+++++|...|+|   ..++|+.|..+|=+
T Consensus       445 ~~~~~~~~G~GkVFVefas~ed~qrA~~~L~G---rKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  445 YPDENPVPGTGKVFVEFADTEDSQRAMEELTG---RKFANRTVVASYYD  490 (500)
T ss_pred             CCCCCcCCCcccEEEEecChHHHHHHHHHccC---ceeCCcEEEEEecC
Confidence            22   223466799999999999999999999   99999999988754

>KOG0113|consensus

Probab=99.34  E-value=6.7e-12  Score=93.79  Aligned_cols=67  Identities=31%  Similarity=0.527  Sum_probs=63.5

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +-+||||+-|+++++|+.|+..|..||+|..|.|++++.+|+++|||||+|+++.+...|.+..++.
T Consensus       100 Py~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~  166 (335)
T KOG0113|consen  100 PYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGI  166 (335)
T ss_pred             ccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCc
Confidence            3568999999999999999999999999999999999999999999999999999999999988763

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.33  E-value=7.4e-12  Score=91.89  Aligned_cols=69  Identities=16%  Similarity=0.219  Sum_probs=59.5

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----ceEEec
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----FRLFCG   93 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~~l~v~   93 (170)
                      ..++|+|+||++.+|+++|+++|+.||+|.+|.++++.   .++++|||+|+++++++.|+ .|++.    ..|.|.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It   76 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCIT   76 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEE
Confidence            46899999999999999999999999999999999874   45689999999999999999 56653    355554

>KOG4454|consensus

Probab=99.33  E-value=4.1e-13  Score=96.29  Aligned_cols=133  Identities=24%  Similarity=0.372  Sum_probs=116.5

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--------c
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--------F   88 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--------~   88 (170)
                      ..++.+++|||+|+...++++-|.++|-+.|+|..+.|..++ .+..+ ||||.|+++.++..|++.+++.        .
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~   81 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR   81 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhc
Confidence            345568899999999999999999999999999999998886 55666 9999999999999999999873        5


Q ss_pred             eEEecC----CCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCC
Q psy7847          89 RLFCGD----LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus        89 ~l~v~n----lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  152 (170)
                      +++.++    |...++++.+.+.|+..|.+...++.++. ++.++.++++.+....+.-.++....+.
T Consensus        82 ~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d~rnrn~~~~~~qr~~~~P~~~~~y~~l  148 (267)
T KOG4454|consen   82 TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-DGRNRNFGFVTYQRLCAVPFALDLYQGL  148 (267)
T ss_pred             ccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-cCCccCccchhhhhhhcCcHHhhhhccc
Confidence            888887    88889999999999999999999998877 5778889999998888888888777663

>smart00362 RRM_2 RNA recognition motif

Probab=99.32  E-value=1.4e-11  Score=74.11  Aligned_cols=61  Identities=39%  Similarity=0.626  Sum_probs=56.8

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +|+|+|||..+++++|+++|+.||.+..+.+..++  +.++++|||+|.+.++|..++..+++
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~   61 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNG   61 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCC
Confidence            48999999999999999999999999999998875  77889999999999999999988875

>KOG0126|consensus

Probab=99.31  E-value=1.8e-13  Score=95.54  Aligned_cols=83  Identities=25%  Similarity=0.528  Sum_probs=72.7

Q ss_pred             CcccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC---
Q psy7847          10 SSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---   86 (170)
Q Consensus        10 ~~~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~---   86 (170)
                      .+|+...   .++..|||||||++.||.||.-+|++||.+.+|.+++|+.||.++||||+-|++..+..-|+..+|+   
T Consensus        26 ~SWH~~Y---kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki  102 (219)
T KOG0126|consen   26 KSWHQEY---KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI  102 (219)
T ss_pred             cchhhhc---ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCcee
Confidence            4565443   4477899999999999999999999999999999999999999999999999999999999988887   


Q ss_pred             -CceEEecCC
Q psy7847          87 -DFRLFCGDL   95 (170)
Q Consensus        87 -~~~l~v~nl   95 (170)
                       .++|.|...
T Consensus       103 ~gRtirVDHv  112 (219)
T KOG0126|consen  103 LGRTIRVDHV  112 (219)
T ss_pred             cceeEEeeec
Confidence             467777544

>KOG0415|consensus

Probab=99.31  E-value=4.1e-12  Score=96.99  Aligned_cols=81  Identities=22%  Similarity=0.413  Sum_probs=77.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ....|||..|++-++.++|.-+|+.||.|..|.+++|..+|.+..||||+|.+.+++++|.-+|++   ..+.+++|+|.
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdN---vLIDDrRIHVD  314 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDN---VLIDDRRIHVD  314 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcc---eeeccceEEee
Confidence            357999999999999999999999999999999999999999999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++++
T Consensus       315 FSQS  318 (479)
T KOG0415|consen  315 FSQS  318 (479)
T ss_pred             hhhh
Confidence            8763

>KOG0121|consensus

Probab=99.30  E-value=6.4e-12  Score=83.10  Aligned_cols=71  Identities=20%  Similarity=0.247  Sum_probs=65.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .....+.+|||+||+.-++||+|.++|+.+|+|..|.+-.++.+..+=|||||+|-+.++|..|+.-+++.
T Consensus        31 ~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgt  101 (153)
T KOG0121|consen   31 EALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGT  101 (153)
T ss_pred             HHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccC
Confidence            34566889999999999999999999999999999999999988888899999999999999999988863

>KOG0226|consensus

Probab=99.29  E-value=3.5e-12  Score=93.36  Aligned_cols=140  Identities=49%  Similarity=0.871  Sum_probs=116.1

Q ss_pred             cEEEEcCCCCCccHHH-H--HHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-------------
Q psy7847          23 FRLFCGDLGNDVTDEL-L--IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-------------   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~-l--~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-------------   86 (170)
                      ...+++++-.++..+- |  ...|+.+-.+..-++.+++ .+..++++|+.|+......++...-++             
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~g  175 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAG  175 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccc
Confidence            4566666655555544 3  5667777777777777775 567788999999988877777654333             


Q ss_pred             --------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCC
Q psy7847          87 --------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus        87 --------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  152 (170)
                                    .++||.+.|..+++.+-|.+.|.+|......++.+|+-+++++||+||.|.+..++.+|+..||| 
T Consensus       176 tswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~g-  254 (290)
T KOG0226|consen  176 TSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNG-  254 (290)
T ss_pred             cccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcc-
Confidence                          35999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             CccccCCeeEEEEe
Q psy7847         153 PHLFVGDLKTRSSI  166 (170)
Q Consensus       153 ~~~~~~~~~i~v~~  166 (170)
                        +.+|+++|+..-
T Consensus       255 --kyVgsrpiklRk  266 (290)
T KOG0226|consen  255 --KYVGSRPIKLRK  266 (290)
T ss_pred             --cccccchhHhhh
Confidence              999999998754

>smart00360 RRM RNA recognition motif

Probab=99.28  E-value=2.7e-11  Score=72.54  Aligned_cols=60  Identities=42%  Similarity=0.638  Sum_probs=56.1

Q ss_pred             EcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          27 CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        27 v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      |+|||..+++++|+++|+.||.+..+.+..++.++.++++|||+|.+.++|..++..+++
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~   60 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNG   60 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCC
Confidence            579999999999999999999999999999877789999999999999999999988874

>KOG0125|consensus

Probab=99.28  E-value=1.7e-11  Score=92.77  Aligned_cols=71  Identities=25%  Similarity=0.463  Sum_probs=64.0

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++.+...++|+|.|+|+..-+.||+.+|++||.|.+|.|+.+  ..-+|||+||+|++.+++++|-.++|+.
T Consensus        89 ~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt  159 (376)
T KOG0125|consen   89 NSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGT  159 (376)
T ss_pred             cCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcc
Confidence            3444556788999999999999999999999999999999987  4579999999999999999999999984

>KOG0112|consensus

Probab=99.25  E-value=5.2e-12  Score=105.87  Aligned_cols=156  Identities=17%  Similarity=0.245  Sum_probs=131.6

Q ss_pred             CCCCCCCCcccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHH
Q psy7847           3 GLRPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK   82 (170)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~   82 (170)
                      +.++.+...+.....+....++||++||+..+++.+|+..|..+|.+.+|+|-+-. -+.-..|+||.|.+...+..++.
T Consensus       353 r~r~~rk~t~v~~~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~  431 (975)
T KOG0112|consen  353 RIRPFRKLTHVLKLDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKF  431 (975)
T ss_pred             CCCCcccccccccccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccch
Confidence            34556667777888888889999999999999999999999999999999885542 35566799999999999888876


Q ss_pred             HcCC-------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHH
Q psy7847          83 EMND-------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI  143 (170)
Q Consensus        83 ~~~~-------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~  143 (170)
                      .+.+                   ...+++++|+++.....|.+.|..||.|..|.+...      .-|+++.|.+...++
T Consensus       432 e~s~~~I~~g~~r~glG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq  505 (975)
T KOG0112|consen  432 EESGPLIGNGTHRIGLGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQ  505 (975)
T ss_pred             hhcCCccccCcccccccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccch
Confidence            5543                   258999999999999999999999999999877433      348999999999999


Q ss_pred             HHHHHhcCCCccccCC--eeEEEEeec
Q psy7847         144 RANKEMNEFPHLFVGD--LKTRSSITL  168 (170)
Q Consensus       144 ~a~~~l~~~~~~~~~~--~~i~v~~~~  168 (170)
                      .|...|.|   .-+|+  ++++|+++.
T Consensus       506 ~a~~~~rg---ap~G~P~~r~rvdla~  529 (975)
T KOG0112|consen  506 AATHDMRG---APLGGPPRRLRVDLAS  529 (975)
T ss_pred             hhHHHHhc---CcCCCCCccccccccc
Confidence            99999999   66666  668887765

>KOG4207|consensus

Probab=99.24  E-value=2e-11  Score=87.08  Aligned_cols=71  Identities=28%  Similarity=0.374  Sum_probs=65.9

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++.+.-..|.|.||.+-++.++|+.+|++||.|-+|.|.+|++|+.++|||||.|.+..+|+.|+..+++
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG   77 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDG   77 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcc
Confidence            34445567799999999999999999999999999999999999999999999999999999999999986

>KOG0105|consensus

Probab=99.24  E-value=2.3e-11  Score=85.42  Aligned_cols=78  Identities=21%  Similarity=0.316  Sum_probs=69.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..+++||+|||.++.+.+|+.+|.+||.|..|.+-..   ..+..||||+|++..+|+.|+..-+|   ..+++.+|+|.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdG---Ydydg~rLRVE   78 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDG---YDYDGCRLRVE   78 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccc---cccCcceEEEE
Confidence            4578999999999999999999999999999987432   23456999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        79 fprg   82 (241)
T KOG0105|consen   79 FPRG   82 (241)
T ss_pred             eccC
Confidence            8764

>KOG0128|consensus

Probab=99.24  E-value=5.5e-13  Score=111.11  Aligned_cols=141  Identities=18%  Similarity=0.161  Sum_probs=123.6

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc----CCCceEEecCCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM----NDDFRLFCGDLGN   97 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~----~~~~~l~v~nlp~   97 (170)
                      ..++|++||++.+.+++|...|..+|.+..+++......++.+|.||+.|..++.+.+++...    -++..++|+|.|+
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~g~pf  746 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAISGPPF  746 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhheeCCCC
Confidence            346899999999999999999999998888887655557889999999999999999998643    3578999999999


Q ss_pred             CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        98 ~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..|.+.++.++..+|.+....++..+ .|+++|.|+|.|.++.++.++....+.   ..++-+.+.|.+
T Consensus       747 ~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~---~~~rE~~~~v~v  811 (881)
T KOG0128|consen  747 QGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDV---AGKRENNGEVQV  811 (881)
T ss_pred             CCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchh---hhhhhcCccccc
Confidence            99999999999999999998877766 799999999999999999999988888   666666666655

>KOG0130|consensus

Probab=99.23  E-value=2.9e-11  Score=80.72  Aligned_cols=66  Identities=20%  Similarity=0.387  Sum_probs=63.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.|||.++-+.+++++|.+.|..||+|.++.+-.++.+|..+|||.|+|++..+|.+|+..+|+
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng  136 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNG  136 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccc
Confidence            467899999999999999999999999999999999999999999999999999999999999986

>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=99.20  E-value=1.5e-10  Score=69.82  Aligned_cols=63  Identities=43%  Similarity=0.673  Sum_probs=57.2

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +|+|+|||..+++++|+++|+.+|.+..+.+..++. +..+++|||+|.+.++|..|+..+++.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~-~~~~~~~~v~f~s~~~a~~a~~~~~~~   63 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKD-TKSKGFAFVEFEDEEDAEKALEALNGK   63 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCC-CCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            479999999999999999999999999999998753 477899999999999999999988864

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).

>KOG1456|consensus

Probab=99.20  E-value=3e-09  Score=82.11  Aligned_cols=144  Identities=19%  Similarity=0.213  Sum_probs=114.8

Q ss_pred             CCCCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----------
Q psy7847          19 DENDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----------   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----------   87 (170)
                      ..+...++|.+|.. .++.+.|.++|..||.|+.|++++.+     .|.|.|++.+...+++++..|++.          
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            34567899999985 48999999999999999999999876     478999999999999999988862          


Q ss_pred             ------------------------------------------------ceEEecCCCCCCCHHHHHHHhccCCCe-eEEE
Q psy7847          88 ------------------------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSF-LKAK  118 (170)
Q Consensus        88 ------------------------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i-~~~~  118 (170)
                                                                      ..|+.-|.|..+||+.|..+|..-+.. ..++
T Consensus       359 ~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svk  438 (494)
T KOG1456|consen  359 VSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVK  438 (494)
T ss_pred             eccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEE
Confidence                                                            388888999999999999999766543 3444


Q ss_pred             EeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC---eeEEEEeecc
Q psy7847         119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD---LKTRSSITLK  169 (170)
Q Consensus       119 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~---~~i~v~~~~~  169 (170)
                      +...+ +.+ ...+.++|++.++|..|+..+|.+++..-+|   -.+|..++++
T Consensus       439 vFp~k-ser-SssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts  490 (494)
T KOG1456|consen  439 VFPLK-SER-SSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTS  490 (494)
T ss_pred             eeccc-ccc-cccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccc
Confidence            44333 222 2358899999999999999999977666666   3566666553

>PLN03213 repressor of silencing 3; Provisional

Probab=99.19  E-value=8.2e-11  Score=93.54  Aligned_cols=65  Identities=22%  Similarity=0.402  Sum_probs=58.0

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCH--HHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP--QDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~--~~a~~~~~~~~~~   87 (170)
                      .....+||||||++++++++|...|..||.|.++.|++  .+|  +|||||+|.+.  .++.+|+..|++.
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGA   73 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGC   73 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCC
Confidence            34457899999999999999999999999999999994  466  99999999987  6899999999873

>KOG0107|consensus

Probab=99.19  E-value=5.5e-11  Score=82.72  Aligned_cols=63  Identities=33%  Similarity=0.583  Sum_probs=57.0

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCc
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDF   88 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~   88 (170)
                      -.++|||+||+.++++.||+..|..||++.++-|-+.     ..|||||+|+++.+|+.|+..|++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~   71 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKD   71 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCcc
Confidence            4678999999999999999999999999998877664     46999999999999999999999853

>KOG4211|consensus

Probab=99.18  E-value=8.4e-10  Score=87.61  Aligned_cols=137  Identities=17%  Similarity=0.173  Sum_probs=107.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeE-EEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND------------   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~-i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~------------   86 (170)
                      .....|.+++||+.||++||.++|...-.+.. |.++.+ ..+++.+-|||+|++.+.|+.|+.....            
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehh
Confidence            46788999999999999999999998776555 556666 4678999999999999999999852210            


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          87 --------------------------------------------------------------------------------   86 (170)
Q Consensus        87 --------------------------------------------------------------------------------   86 (170)
                                                                                                      
T Consensus       180 s~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~  259 (510)
T KOG4211|consen  180 SRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNY  259 (510)
T ss_pred             HHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             ---------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHH
Q psy7847          87 ---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA  145 (170)
Q Consensus        87 ---------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  145 (170)
                                           ...++.++||+..++.++...|+..-.+ .+.+-..+ ++...|-|.|+|.+.++|..|
T Consensus       260 ~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~-dGr~TGEAdveF~t~edav~A  337 (510)
T KOG4211|consen  260 PVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGP-DGRATGEADVEFATGEDAVGA  337 (510)
T ss_pred             CCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCC-CCccCCcceeecccchhhHhh
Confidence                                 0167778999999999999999876444 55555454 788899999999999999999


Q ss_pred             HHHhcCCCccccCCeeEE
Q psy7847         146 NKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus       146 ~~~l~~~~~~~~~~~~i~  163 (170)
                      +.+ ++   ..++.+-|.
T Consensus       338 msk-d~---anm~hrYVE  351 (510)
T KOG4211|consen  338 MGK-DG---ANMGHRYVE  351 (510)
T ss_pred             hcc-CC---cccCcceee
Confidence            874 33   444444443

>KOG0146|consensus

Probab=99.15  E-value=9.4e-11  Score=86.71  Aligned_cols=83  Identities=19%  Similarity=0.281  Sum_probs=75.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..+.|||+.|...-.|+|++++|+.||.|..|.+++.+ ++.++|+|||.|.+..+|+.||..|||....-.....+.|.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            35789999999999999999999999999999999987 79999999999999999999999999987666677788888


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      +++.
T Consensus        97 ~ADT  100 (371)
T KOG0146|consen   97 FADT  100 (371)
T ss_pred             eccc
Confidence            7763

>KOG0108|consensus

Probab=99.11  E-value=4.1e-10  Score=90.13  Aligned_cols=71  Identities=31%  Similarity=0.507  Sum_probs=66.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----CceEEec
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----DFRLFCG   93 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----~~~l~v~   93 (170)
                      +.+||||+|+++++++|.++|...|.|.++++..|+.+|..+||+|++|.+.+++..|++.+++    .+.|.|.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~   93 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVN   93 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEee
Confidence            8899999999999999999999999999999999999999999999999999999999999996    3566664

>KOG4208|consensus

Probab=99.11  E-value=3.4e-10  Score=80.71  Aligned_cols=77  Identities=17%  Similarity=0.345  Sum_probs=69.8

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccC-CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .-+++..+|..+.+.++...|.++ |.+...++-+++.+|.++|||||+|.+++.|.-|.+.||+   ..++++.|.+.+
T Consensus        50 g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNN---YLl~e~lL~c~v  126 (214)
T KOG4208|consen   50 GVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNN---YLLMEHLLECHV  126 (214)
T ss_pred             cceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhh---hhhhhheeeeEE
Confidence            367888999999999999999888 6677777879999999999999999999999999999999   999999999887


Q ss_pred             e
Q psy7847         167 T  167 (170)
Q Consensus       167 ~  167 (170)
                      =
T Consensus       127 m  127 (214)
T KOG4208|consen  127 M  127 (214)
T ss_pred             e
Confidence            4

>KOG4206|consensus

Probab=99.10  E-value=3.7e-10  Score=81.64  Aligned_cols=80  Identities=21%  Similarity=0.319  Sum_probs=71.2

Q ss_pred             cCCCceEEecCCCCCCCHHHHHH----HhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          84 MNDDFRLFCGDLGNDVTDELLIR----TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        84 ~~~~~~l~v~nlp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      ++.+.||||.||+..+..++|++    +|++||.|..|...+   +.+.+|-|||.|.+.+.|..|+..|+|   ..+-|
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~g---fpFyg   79 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQG---FPFYG   79 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcC---CcccC
Confidence            34445999999999999998888    999999999998765   456799999999999999999999999   89999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      +++++-||.+
T Consensus        80 K~mriqyA~s   89 (221)
T KOG4206|consen   80 KPMRIQYAKS   89 (221)
T ss_pred             chhheecccC
Confidence            9999999864

>KOG0132|consensus

Probab=99.08  E-value=3.4e-10  Score=93.98  Aligned_cols=74  Identities=18%  Similarity=0.328  Sum_probs=68.9

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ++||||+.|+..+++.+|..+|+.||.|++|.+..      ++|+|||......+|.+|+++|++   .-+.++.|++.|
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n---~kv~~k~Iki~W  491 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSN---VKVADKTIKIAW  491 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhc---ccccceeeEEee
Confidence            36999999999999999999999999999998854      388999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus       492 a~g  494 (894)
T KOG0132|consen  492 AVG  494 (894)
T ss_pred             ecc
Confidence            863

>KOG0111|consensus

Probab=99.04  E-value=3.6e-10  Score=81.44  Aligned_cols=74  Identities=26%  Similarity=0.491  Sum_probs=67.8

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----ceEEe
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----FRLFC   92 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~~l~v   92 (170)
                      ....++|||++|..++++..|...|-+||.|.+|+++.|..+.+.+||+||+|...++|..|+..++..    +++.|
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirV   84 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRV   84 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEE
Confidence            345789999999999999999999999999999999999989999999999999999999999999874    45655

>KOG4660|consensus

Probab=99.01  E-value=5e-09  Score=84.36  Aligned_cols=69  Identities=29%  Similarity=0.378  Sum_probs=59.1

Q ss_pred             cccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        13 ~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+...+.++|+|-|||.++++++|+.+|+.||+|.+++.     +...++.+||+|-|..+|++|++.++.
T Consensus        66 ~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~  134 (549)
T KOG4660|consen   66 DNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNR  134 (549)
T ss_pred             CCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHH
Confidence            556666677899999999999999999999999999998655     344578999999999999999986653

>KOG1456|consensus

Probab=99.00  E-value=2.9e-08  Score=76.74  Aligned_cols=141  Identities=13%  Similarity=0.127  Sum_probs=110.2

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-----------
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-----------   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-----------   86 (170)
                      .+..+-.|+|++|-..+++.+|.+..+.||++..+..+..+      ..|.|+|++.+.|+.++.-.-.           
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al  100 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYIAGQQAL  100 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccccCchhh
Confidence            34556789999999999999999999999999888776553      4699999999998888742110           


Q ss_pred             -------------------CceEEec--CCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHH
Q psy7847          87 -------------------DFRLFCG--DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA  145 (170)
Q Consensus        87 -------------------~~~l~v~--nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a  145 (170)
                                         +..|.+.  |-=+.+|-+-|..++...|.+.+|.+.+.  ++.   -|.|+|++.+.|++|
T Consensus       101 ~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrA  175 (494)
T KOG1456|consen  101 FNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRA  175 (494)
T ss_pred             cccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHH
Confidence                               1233333  44457899999999999999999988765  232   489999999999999


Q ss_pred             HHHhcCCCccccCCeeEEEEeeccC
Q psy7847         146 NKEMNEFPHLFVGDLKTRSSITLKG  170 (170)
Q Consensus       146 ~~~l~~~~~~~~~~~~i~v~~~~~~  170 (170)
                      ...|||..+. -|=..|||.||.++
T Consensus       176 k~alNGADIY-sGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  176 KAALNGADIY-SGCCTLKIEYAKPT  199 (494)
T ss_pred             Hhhccccccc-ccceeEEEEecCcc
Confidence            9999993322 23378999998764

>KOG4208|consensus

Probab=99.00  E-value=3.3e-09  Score=75.77  Aligned_cols=88  Identities=18%  Similarity=0.349  Sum_probs=75.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcC-CCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----CceEEecCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----DFRLFCGDL   95 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~-g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----~~~l~v~nl   95 (170)
                      ...-++++.+|.-..+.++..+|.++ |++...++.|++.||.++|||||+|++++.|.-+.+.||+    ...|.+.-+
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34569999999999999999999887 7888999989999999999999999999999999999997    457777788


Q ss_pred             CCC-CCHHHHHHHh
Q psy7847          96 GND-VTDELLIRTF  108 (170)
Q Consensus        96 p~~-~~~~~l~~~f  108 (170)
                      |+. .-+..+.+.+
T Consensus       128 ppe~~v~~~~~k~~  141 (214)
T KOG4208|consen  128 PPEQKVEKNLKKVS  141 (214)
T ss_pred             Cchhhhhhhhhhhc
Confidence            887 5555555555

>KOG0120|consensus

Probab=99.00  E-value=1.1e-09  Score=88.35  Aligned_cols=140  Identities=21%  Similarity=0.367  Sum_probs=118.0

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcC-----------C-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC--
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKY-----------P-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN--   85 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~-----------g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~--   85 (170)
                      .+++.++++++|+.++++.+-.+|..-           | .+..+.+-      .-+.+||++|.+.++|..++...-  
T Consensus       173 ~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n------~~~nfa~ie~~s~~~at~~~~~~~~~  246 (500)
T KOG0120|consen  173 RQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLN------LEKNFAFIEFRSISEATEAMALDGII  246 (500)
T ss_pred             hhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeec------ccccceeEEecCCCchhhhhcccchh
Confidence            446789999999999999999998642           2 24444442      345799999999999998875221  


Q ss_pred             --C---------------------------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCC
Q psy7847          86 --D---------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR  124 (170)
Q Consensus        86 --~---------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~  124 (170)
                        +                                       ...+++++||...++.++.++...||.+....+..+..
T Consensus       247 f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~  326 (500)
T KOG0120|consen  247 FEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA  326 (500)
T ss_pred             hCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccc
Confidence              0                                       24888999999999999999999999999999999988


Q ss_pred             CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         125 TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       125 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      .+.++||||.+|.+......|+..+||   +.++++.+.|-.|.
T Consensus       327 ~g~skg~af~ey~dpsvtd~A~agLnG---m~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  327 TGNSKGFAFCEYCDPSVTDQAIAGLNG---MQLGDKKLVVQRAI  367 (500)
T ss_pred             cccccceeeeeeeCCcchhhhhcccch---hhhcCceeEeehhh
Confidence            889999999999999999999999999   99999999887664

>KOG0109|consensus

Probab=98.97  E-value=8.8e-10  Score=82.40  Aligned_cols=70  Identities=21%  Similarity=0.436  Sum_probs=64.8

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ..|||+|||..+++.+|+.+|++||.+..|.|+++        ||||..++..++..|+..|||   ..|.|..|.|.-+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhg---YtLhg~nInVeaS   71 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHG---YTLHGVNINVEAS   71 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhccc---ceecceEEEEEec
Confidence            36899999999999999999999999999999875        899999999999999999999   9999998888765


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus        72 k   72 (346)
T KOG0109|consen   72 K   72 (346)
T ss_pred             c
Confidence            4

>smart00361 RRM_1 RNA recognition motif

Probab=98.94  E-value=4e-09  Score=64.07  Aligned_cols=52  Identities=27%  Similarity=0.388  Sum_probs=45.5

Q ss_pred             HHHHHHHhh----cCCCeeEEE-EEecCCC--CCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          36 DELLIRTFS----KYPSFLKAK-VVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        36 ~~~l~~~f~----~~g~v~~i~-~~~~~~~--~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++|+++|+    .||.+.++. +..++.+  +.++|+|||.|.+.++|.+|+..+|+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~   60 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGR   60 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            578888888    999999995 6666656  889999999999999999999999974

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

Probab=98.93  E-value=1.5e-08  Score=65.03  Aligned_cols=81  Identities=21%  Similarity=0.220  Sum_probs=68.4

Q ss_pred             ceEEecCCCCCCCHHHHHHHhcc--CCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC-eeEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSK--YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD-LKTRS  164 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~--~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~-~~i~v  164 (170)
                      .||+++|+|...+.++|.+++..  .|......++-|..++.+.|||||.|.++++|.+-.+.+||..+....+ +...|
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            48999999999999999999844  3667778888898889999999999999999999999999976655544 55577


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      +||.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            7764

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

>KOG0153|consensus

Probab=98.91  E-value=4.8e-09  Score=80.13  Aligned_cols=74  Identities=18%  Similarity=0.339  Sum_probs=66.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+|||++|...+++.+|+..|.+||.|..+.+...      +++|||+|.+.++|+.|..+.-+  ..++.|.+|+|-|.
T Consensus       229 ~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n--~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  229 KTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFN--KLVINGFRLKIKWG  300 (377)
T ss_pred             eEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcc--eeeecceEEEEEeC
Confidence            59999999999999999999999999999988765      56999999999999999875444  49999999999997


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            64

>KOG0533|consensus

Probab=98.90  E-value=9.2e-09  Score=76.37  Aligned_cols=81  Identities=21%  Similarity=0.246  Sum_probs=73.9

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      .+..+|+|.|||+.+.++||+++|..||.+..+.+..++ .+.+.|.|-|.|...++|.+|++.+||   ..+.|+++++
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~g---v~ldG~~mk~  156 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNG---VALDGRPMKI  156 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcC---cccCCceeee
Confidence            345789999999999999999999999988888888886 899999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      ....+
T Consensus       157 ~~i~~  161 (243)
T KOG0533|consen  157 EIISS  161 (243)
T ss_pred             EEecC
Confidence            87643

>KOG4210|consensus

Probab=98.84  E-value=4.4e-09  Score=80.45  Aligned_cols=144  Identities=19%  Similarity=0.218  Sum_probs=123.9

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC--------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND--------------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~--------------   86 (170)
                      ...+.|++++..++.+.+...++...|......+........+++++++.|...+.+..++.....              
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            356799999999999998999999999887777777666788999999999999999988864321              


Q ss_pred             -----------------CceEE-ecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHH
Q psy7847          87 -----------------DFRLF-CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE  148 (170)
Q Consensus        87 -----------------~~~l~-v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  148 (170)
                                       ..+++ +.+++..+++++|+..|..+|.|..++++.++.++..+|+|++.|........++..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence                             12555 999999999999999999999999999999999999999999999999999888886


Q ss_pred             hcCCCccccCCeeEEEEeec
Q psy7847         149 MNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       149 l~~~~~~~~~~~~i~v~~~~  168 (170)
                       ..   ..++++++.+.+..
T Consensus       247 -~~---~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  247 -QT---RSIGGRPLRLEEDE  262 (285)
T ss_pred             -cc---CcccCcccccccCC
Confidence             66   88888888877654

>KOG0226|consensus

Probab=98.74  E-value=2.7e-08  Score=73.25  Aligned_cols=86  Identities=57%  Similarity=1.034  Sum_probs=74.1

Q ss_pred             CCcccccCC--CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847           9 ISSWIKKTC--EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus         9 ~~~~~~~~~--~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+|.++..  -+..+++||++.|.-+++.+.|...|.+|-.....++++++.+|+++||+||.|.++.++.+|+.++++
T Consensus       175 gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~g  254 (290)
T KOG0226|consen  175 GTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNG  254 (290)
T ss_pred             ccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcc
Confidence            345655533  356789999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CceEEecCCCC
Q psy7847          87 DFRLFCGDLGN   97 (170)
Q Consensus        87 ~~~l~v~nlp~   97 (170)
                         -||++=|-
T Consensus       255 ---kyVgsrpi  262 (290)
T KOG0226|consen  255 ---KYVGSRPI  262 (290)
T ss_pred             ---cccccchh
Confidence               45665443

>KOG0415|consensus

Probab=98.72  E-value=2.5e-08  Score=76.61  Aligned_cols=82  Identities=26%  Similarity=0.453  Sum_probs=69.8

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----CceEEecC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----DFRLFCGD   94 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----~~~l~v~n   94 (170)
                      ..+...|||--|.+-++.++|.-+|+.||+|.+|.+++++.+|.+-.||||+|.+.++.++|.-.+.+    .++++| .
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV-D  314 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV-D  314 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe-e
Confidence            44567899999999999999999999999999999999999999999999999999999999987775    345555 3


Q ss_pred             CCCCCCH
Q psy7847          95 LGNDVTD  101 (170)
Q Consensus        95 lp~~~~~  101 (170)
                      +..+++.
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            3333433

>KOG1365|consensus

Probab=98.69  E-value=3.5e-07  Score=71.08  Aligned_cols=137  Identities=17%  Similarity=0.108  Sum_probs=100.9

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC---------------
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---------------   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~---------------   86 (170)
                      ...+..++||+..++.+|..+|+...-..--+.+-....|...+.+.|.|-|++.-+-+++....               
T Consensus        60 ~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge  139 (508)
T KOG1365|consen   60 NVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGE  139 (508)
T ss_pred             ceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCch
Confidence            34578899999999999999998754332222222224577889999999999987777764321               


Q ss_pred             ---------------------CceEEecCCCCCCCHHHHHHHhcc---C-CCeeEEEEeecCCCCCcccEEEEEecCHHH
Q psy7847          87 ---------------------DFRLFCGDLGNDVTDELLIRTFSK---Y-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQD  141 (170)
Q Consensus        87 ---------------------~~~l~v~nlp~~~~~~~l~~~f~~---~-g~i~~~~~~~~~~~~~~~g~afv~f~~~~~  141 (170)
                                           .-.+..++||+++++.++..+|.+   . |..+.+.+.+.+ +|++.|-|||.|..+++
T Consensus       140 ~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~  218 (508)
T KOG1365|consen  140 EFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEED  218 (508)
T ss_pred             hheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHH
Confidence                                 126777899999999999999953   2 244566555544 78999999999999999


Q ss_pred             HHHHHHHhcCCCccccCCeeEE
Q psy7847         142 FIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus       142 a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      |+.|+.+-.    ..+|.|.|.
T Consensus       219 aq~aL~khr----q~iGqRYIE  236 (508)
T KOG1365|consen  219 AQFALRKHR----QNIGQRYIE  236 (508)
T ss_pred             HHHHHHHHH----HHHhHHHHH
Confidence            999998644    445544443

>KOG2193|consensus

Probab=98.69  E-value=2.8e-09  Score=83.40  Aligned_cols=129  Identities=19%  Similarity=0.220  Sum_probs=103.8

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------------
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------------   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------------   87 (170)
                      ++|++||.+.++.+++.++|+..- ....-.++       ..+|+||.+.+...+.++++.++++               
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            689999999999999999997642 12222222       2479999999999999999987763               


Q ss_pred             -----ceEEecCCCCCCCHHHHHHHhccCCCeeEEE-EeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          88 -----FRLFCGDLGNDVTDELLIRTFSKYPSFLKAK-VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        88 -----~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~-~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                           +.+-++|+|+...++.|..+...||.++.|. +..+++.-    ..=|+|.+.+.+..|+..++|   ..+.+..
T Consensus        76 kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~eta----vvnvty~~~~~~~~ai~kl~g---~Q~en~~  148 (584)
T KOG2193|consen   76 KKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETA----VVNVTYSAQQQHRQAIHKLNG---PQLENQH  148 (584)
T ss_pred             HHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHH----HHHHHHHHHHHHHHHHHhhcc---hHhhhhh
Confidence                 4788899999999999999999999999885 34443221    223688999999999999999   9999988


Q ss_pred             EEEEe
Q psy7847         162 TRSSI  166 (170)
Q Consensus       162 i~v~~  166 (170)
                      ++++|
T Consensus       149 ~k~~Y  153 (584)
T KOG2193|consen  149 LKVGY  153 (584)
T ss_pred             hhccc
Confidence            88876

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

Probab=98.68  E-value=1.7e-07  Score=60.21  Aligned_cols=64  Identities=25%  Similarity=0.360  Sum_probs=57.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhc--CCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSK--YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~--~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++|+|+|+|...|.++|.+++..  .|...-+.++.|-.++.+.|||||.|.+++.+.+.....++
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g   67 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNG   67 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcC
Confidence            57999999999999999999864  46777888999988899999999999999999999998886

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

>KOG4661|consensus

Probab=98.66  E-value=7.2e-08  Score=78.28  Aligned_cols=77  Identities=19%  Similarity=0.288  Sum_probs=71.1

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +.|||++|...+...+|+.+|++||.|.-..++.+.-+...+.|+||++.+..+|.+||+.||-   ..+.|+-|+|.-+
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHr---TELHGrmISVEka  482 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHR---TELHGRMISVEKA  482 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhh---hhhcceeeeeeec
Confidence            5999999999999999999999999999999888766666788999999999999999999999   9999999999765

>PF13893 RRM_5: RNA recognition motif

Probab=98.63  E-value=1.5e-07  Score=54.44  Aligned_cols=44  Identities=34%  Similarity=0.610  Sum_probs=38.5

Q ss_pred             HHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          39 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        39 l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      |.++|++||+|.++.+...+     +++|||+|.+.++|..|++.+|+.
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~   44 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGR   44 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTS
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCC
Confidence            67899999999999997653     689999999999999999999874

(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 ....

>KOG1548|consensus

Probab=98.58  E-value=2.7e-07  Score=70.76  Aligned_cols=77  Identities=22%  Similarity=0.215  Sum_probs=70.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      ..|||+|||.++|-+++.++|+.+|.|.        .|.+.++. .|..+|-|++.|-..++..-|++.|++   ..++|
T Consensus       135 t~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe---~~~rg  210 (382)
T KOG1548|consen  135 TSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDE---DELRG  210 (382)
T ss_pred             ceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCc---ccccC
Confidence            4699999999999999999999999874        36788887 599999999999999999999999999   99999


Q ss_pred             eeEEEEeec
Q psy7847         160 LKTRSSITL  168 (170)
Q Consensus       160 ~~i~v~~~~  168 (170)
                      +.|+|..|.
T Consensus       211 ~~~rVerAk  219 (382)
T KOG1548|consen  211 KKLRVERAK  219 (382)
T ss_pred             cEEEEehhh
Confidence            999998763

>KOG4307|consensus

Probab=98.55  E-value=9e-07  Score=73.46  Aligned_cols=75  Identities=20%  Similarity=0.270  Sum_probs=64.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .|-+.|+|+.++-+||-++|..|-.+..-..++-...|.+.|-|-|.|++.++|..|...+++   ..|+++.|++.+
T Consensus       869 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  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDG---QKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhcccc---CcccceeEEEEe
Confidence            577889999999999999999997665433333445899999999999999999999999999   999999998865

>KOG4205|consensus

Probab=98.55  E-value=7.6e-08  Score=74.18  Aligned_cols=78  Identities=26%  Similarity=0.419  Sum_probs=66.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ....|||++|+++++++.|+.-|.+||.+..|.+++|+.++.++|++||+|.+.+....++..-.    ..+.++.|.+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~----h~~dgr~ve~k   80 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNART----HKLDGRSVEPK   80 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccc----cccCCccccce
Confidence            45689999999999999999999999999999999999999999999999999988888877433    45666666554


Q ss_pred             ee
Q psy7847         166 IT  167 (170)
Q Consensus       166 ~~  167 (170)
                      -+
T Consensus        81 ~a   82 (311)
T KOG4205|consen   81 RA   82 (311)
T ss_pred             ec
Confidence            33

>KOG4660|consensus

Probab=98.54  E-value=6.6e-08  Score=78.04  Aligned_cols=71  Identities=24%  Similarity=0.354  Sum_probs=63.6

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ..+.+|+|-|||..+++++|.++|+.||+|..++....     .+|.+||+|.+..+|+.|+++||+   ..+.|+.++
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~---~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNR---REIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHH---HHhhhhhhc
Confidence            44679999999999999999999999999999766443     489999999999999999999999   888888776

>KOG0116|consensus

Probab=98.54  E-value=1.7e-07  Score=74.82  Aligned_cols=71  Identities=20%  Similarity=0.292  Sum_probs=58.1

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC---CCceEEe
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN---DDFRLFC   92 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~---~~~~l~v   92 (170)
                      ..+|||+|||.++++++|+++|..||.|....|......+....||||+|.+.+.+..++....   +.++|.|
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~V  361 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNV  361 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEE
Confidence            3459999999999999999999999999998886654445555999999999999999997552   3445555

>KOG0151|consensus

Probab=98.52  E-value=2.3e-07  Score=76.91  Aligned_cols=78  Identities=24%  Similarity=0.493  Sum_probs=69.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecC---CCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK---RTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~---~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ...|||+||++.+++..|-..|+.||.+..++++-.+   +....+-++||.|-+..++++|++.|+|   ..+.+..++
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg---~iv~~~e~K  250 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQG---IIVMEYEMK  250 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcc---eeeeeeeee
Confidence            4699999999999999999999999999998876443   2344567899999999999999999999   999999999


Q ss_pred             EEee
Q psy7847         164 SSIT  167 (170)
Q Consensus       164 v~~~  167 (170)
                      +-|+
T Consensus       251 ~gWg  254 (877)
T KOG0151|consen  251 LGWG  254 (877)
T ss_pred             eccc
Confidence            9987

>KOG0116|consensus

Probab=98.52  E-value=3.1e-07  Score=73.41  Aligned_cols=77  Identities=21%  Similarity=0.287  Sum_probs=64.3

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+|||.|||.+++..+|++.|..||.|....|......+....||||+|.+..+++.|+.+- -   ..++++++.|.-.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p---~~ig~~kl~Veek  364 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-P---LEIGGRKLNVEEK  364 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-c---cccCCeeEEEEec
Confidence            36999999999999999999999999998776654322333389999999999999999964 4   9999999998754


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus       365 ~  365 (419)
T KOG0116|consen  365 R  365 (419)
T ss_pred             c
Confidence            3

>KOG4307|consensus

Probab=98.50  E-value=3.6e-07  Score=75.71  Aligned_cols=142  Identities=13%  Similarity=0.064  Sum_probs=112.4

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-------------   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-------------   86 (170)
                      .+.+.+-+.+.+.+..+.+++++|...- +....+..+...+...|-++|.|....++.+|++.-+.             
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~~-~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGRN-AQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             chhheeeecccccccccchhhhhcCccc-ccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCC
Confidence            3456678889999999999999996533 33444444544556689999999999999999874331             


Q ss_pred             ----------------------------------------------CceEEecCCCCCCCHHHHHHHhccCCCeeE-EEE
Q psy7847          87 ----------------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKV  119 (170)
Q Consensus        87 ----------------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~  119 (170)
                                                                    ..+|||..||..+++.++-.+|...-.+++ |.+
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~l  467 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIEL  467 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEe
Confidence                                                          139999999999999999999987777776 666


Q ss_pred             eecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847         120 VRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus       120 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .+.+ ++.-++.|||.|..++++..|..--+.   ...|.+.|+|.-
T Consensus       468 t~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k---~y~G~r~irv~s  510 (944)
T KOG4307|consen  468 TRLP-TDLLRPAAFVAFIHPTAPLTASSVKTK---FYPGHRIIRVDS  510 (944)
T ss_pred             ccCC-cccccchhhheeccccccchhhhcccc---cccCceEEEeec
Confidence            5555 677788999999998888888876666   888889998864

>KOG0132|consensus

Probab=98.50  E-value=2.3e-07  Score=77.56  Aligned_cols=59  Identities=19%  Similarity=0.380  Sum_probs=54.7

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++|||||+|+.++++.||.++|+.||.|++|.++..      +++|||.+.+..+|.+|+..+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n  479 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSN  479 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhc
Confidence            689999999999999999999999999999988765      48999999999999999988874

>KOG4209|consensus

Probab=98.50  E-value=2.5e-07  Score=68.73  Aligned_cols=79  Identities=19%  Similarity=0.219  Sum_probs=73.5

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      .+...+|++|+.+.++.++++..|+.+|.+..+.++.|+..+.++|++||+|.+.+.++.++. ||+   ..+-++.++|
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~g---s~i~~~~i~v  174 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDG---SEIPGPAIEV  174 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCC---ccccccccee
Confidence            345699999999999999999999999999999999999888899999999999999999999 999   9999999999


Q ss_pred             Eee
Q psy7847         165 SIT  167 (170)
Q Consensus       165 ~~~  167 (170)
                      ++.
T Consensus       175 t~~  177 (231)
T KOG4209|consen  175 TLK  177 (231)
T ss_pred             eee
Confidence            874

>KOG1457|consensus

Probab=98.46  E-value=1.5e-06  Score=63.18  Aligned_cols=82  Identities=17%  Similarity=0.160  Sum_probs=63.5

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEee-cCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR-DKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~-~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      .+||||++||.++-..+|..+|..|...+.+.+-. ++.....+-+||++|.+.++|..|.+.|||..--.-.+..+++.
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            57999999999999999999999998888776533 33333345689999999999999999999932222234667776


Q ss_pred             eec
Q psy7847         166 ITL  168 (170)
Q Consensus       166 ~~~  168 (170)
                      ++.
T Consensus       114 lAK  116 (284)
T KOG1457|consen  114 LAK  116 (284)
T ss_pred             ehh
Confidence            653

>KOG0106|consensus

Probab=98.43  E-value=1.9e-07  Score=68.05  Aligned_cols=69  Identities=25%  Similarity=0.378  Sum_probs=63.5

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      .+||+++|+.+.+.+|.++|..||.+..+.+.        .||+||.|.+..+|..|+..+|+   ..+++..+.|.|+.
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~---~~l~~e~~vve~~r   71 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDG---KELCGERLVVEHAR   71 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcC---ceecceeeeeeccc
Confidence            58999999999999999999999999998763        46889999999999999999999   99999888888876

>KOG4676|consensus

Probab=98.40  E-value=1.6e-07  Score=73.02  Aligned_cols=124  Identities=11%  Similarity=0.019  Sum_probs=99.7

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC---CCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~---~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ..|.|.||.++++.+++..+|+.+|.|.++.++.....   ......|||.|.|...+..|...-|..            
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            37999999999999999999999999999999774322   345678999999999988876533321            


Q ss_pred             ----------------------------------------------------------------ceEEecCCCCCCCHHH
Q psy7847          88 ----------------------------------------------------------------FRLFCGDLGNDVTDEL  103 (170)
Q Consensus        88 ----------------------------------------------------------------~~l~v~nlp~~~~~~~  103 (170)
                                                                                      .+++|.+|+..+...+
T Consensus        88 ~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e  167 (479)
T KOG4676|consen   88 DEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPE  167 (479)
T ss_pred             CCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchh
Confidence                                                                            2788899999999999


Q ss_pred             HHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847         104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus       104 l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      +.+.|..+|.+.+..+....    ..-+|-+.|....+...|+. ++|
T Consensus       168 ~~e~f~r~Gev~ya~~ask~----~s~~c~~sf~~qts~~halr-~~g  210 (479)
T KOG4676|consen  168 SGESFERKGEVSYAHTASKS----RSSSCSHSFRKQTSSKHALR-SHG  210 (479)
T ss_pred             hhhhhhhcchhhhhhhhccC----CCcchhhhHhhhhhHHHHHH-hcc
Confidence            99999999999988775432    23467789988888888887 455

>KOG0533|consensus

Probab=98.34  E-value=1.9e-06  Score=64.12  Aligned_cols=68  Identities=24%  Similarity=0.312  Sum_probs=61.3

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+....+|+|.|||+.+++++|+++|..||.+..+.+-.++ .|.+.|.|-|.|...++|..+++.+++
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~g  146 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNG  146 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcC
Confidence            33445789999999999999999999999988888888775 899999999999999999999999987

>KOG4661|consensus

Probab=98.31  E-value=1.5e-06  Score=70.81  Aligned_cols=65  Identities=23%  Similarity=0.396  Sum_probs=60.4

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.++|.+|+..+-..+|+++|++||.|...+++.+..+.-.+.|+||++.+.++|.+++++||.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHr  469 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHR  469 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhh
Confidence            46799999999999999999999999999999999887888899999999999999999998874

>KOG0153|consensus

Probab=98.26  E-value=4e-06  Score=64.47  Aligned_cols=60  Identities=20%  Similarity=0.370  Sum_probs=54.0

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+|||++|-..+++.+|++-|.+||.+.++.+...+      +.|||+|.+.++|+.|.+....
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n  286 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFN  286 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcc
Confidence            45679999998899999999999999999999997654      5899999999999999987765

>KOG4454|consensus

Probab=98.22  E-value=6e-07  Score=64.99  Aligned_cols=75  Identities=19%  Similarity=0.255  Sum_probs=66.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|+|.|+...++++-|.++|=+.|.|..+.|..++ .+..+ ||||.|.++-+..-|++.+||   ..+.+..+++..
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng---~~l~~~e~q~~~   83 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENG---DDLEEDEEQRTL   83 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhccc---chhccchhhccc
Confidence            4689999999999999999999999999999888776 56666 999999999999999999999   888887777654

>KOG0151|consensus

Probab=98.20  E-value=5.6e-06  Score=68.98  Aligned_cols=66  Identities=27%  Similarity=0.538  Sum_probs=58.0

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC---CCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~---~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+||+||++.++++.|-..|+.||++.+++++.-+..   ...+-++||.|.+..++++|++.+++.
T Consensus       174 TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~  242 (877)
T KOG0151|consen  174 TTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGI  242 (877)
T ss_pred             ccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcce
Confidence            345999999999999999999999999999999887643   244678999999999999999999984

>KOG4209|consensus

Probab=98.15  E-value=4e-06  Score=62.34  Aligned_cols=68  Identities=21%  Similarity=0.285  Sum_probs=62.2

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+...+||+|+.+.++.+++..-|+.||.+..+.+..++..|.+++|+||+|.+.+.+..++. +++
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~g  164 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDG  164 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCC
Confidence            34557789999999999999999999999999999999999888999999999999999999997 665

>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=98.12  E-value=1.2e-05  Score=52.62  Aligned_cols=72  Identities=21%  Similarity=0.296  Sum_probs=44.1

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCC--CccccCCeeEEEEe
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF--PHLFVGDLKTRSSI  166 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~--~~~~~~~~~i~v~~  166 (170)
                      .|.+.+++..++.++|+..|+.||.|.+|.+.+..      ..|+|.|.+.++|+.|+..+...  ....+.+..+.+.+
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            57888899999999999999999999999886543      25889999999999999877652  12355555555543

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=98.06  E-value=4.8e-05  Score=47.12  Aligned_cols=68  Identities=19%  Similarity=0.132  Sum_probs=46.2

Q ss_pred             ceEEecCCCCCCCHHH----HHHHhccCCC-eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          88 FRLFCGDLGNDVTDEL----LIRTFSKYPS-FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~----l~~~f~~~g~-i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ..|+|.|||-+.+...    |++++..+|. +..+          ..+.|++.|.+.+.|.+|.+.|+|   ...-|++|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmeg---EdVfG~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEG---EDVFGNKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT-----SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcc---cccccceE
Confidence            3689999999888654    5566667765 4443          135799999999999999999999   99999999


Q ss_pred             EEEeec
Q psy7847         163 RSSITL  168 (170)
Q Consensus       163 ~v~~~~  168 (170)
                      .|++..
T Consensus        70 ~v~~~~   75 (90)
T PF11608_consen   70 SVSFSP   75 (90)
T ss_dssp             EEESS-
T ss_pred             EEEEcC
Confidence            999873

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

>KOG1995|consensus

Probab=97.92  E-value=1e-05  Score=62.54  Aligned_cols=82  Identities=21%  Similarity=0.169  Sum_probs=73.2

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccc
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF  156 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  156 (170)
                      ....++||-++|..+++.++...|.+++.|.        .|.+.+|++++.++|-|.|+|.+...|+.|+..+++   +.
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~ag---kd  140 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAG---KD  140 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcc---cc
Confidence            3456999999999999999999999998773        356778888999999999999999999999999999   99


Q ss_pred             cCCeeEEEEeecc
Q psy7847         157 VGDLKTRSSITLK  169 (170)
Q Consensus       157 ~~~~~i~v~~~~~  169 (170)
                      +++..|+|+.+.+
T Consensus       141 f~gn~ikvs~a~~  153 (351)
T KOG1995|consen  141 FCGNTIKVSLAER  153 (351)
T ss_pred             ccCCCchhhhhhh
Confidence            9999999988754

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.90  E-value=4e-05  Score=59.01  Aligned_cols=78  Identities=15%  Similarity=0.205  Sum_probs=61.9

Q ss_pred             ceEEecCCCCCCCHHH------HHHHhccCCCeeEEEEeecCC-CCCcccE--EEEEecCHHHHHHHHHHhcCCCccccC
Q psy7847          88 FRLFCGDLGNDVTDEL------LIRTFSKYPSFLKAKVVRDKR-TNKTKGF--GFVSFKDPQDFIRANKEMNEFPHLFVG  158 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~------l~~~f~~~g~i~~~~~~~~~~-~~~~~g~--afv~f~~~~~a~~a~~~l~~~~~~~~~  158 (170)
                      .-+||-++|+.+..|+      -.+.|++||.|..|.+.+... .....+.  .+++|.+.++|.+||...+|   ..++
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDg---s~~D  191 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDG---SLLD  191 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcc---cccc
Confidence            4788999998877666      246899999999998865432 1222222  48999999999999999999   9999


Q ss_pred             CeeEEEEeec
Q psy7847         159 DLKTRSSITL  168 (170)
Q Consensus       159 ~~~i~v~~~~  168 (170)
                      |+.|+.+|-+
T Consensus       192 Gr~lkatYGT  201 (480)
T COG5175         192 GRVLKATYGT  201 (480)
T ss_pred             CceEeeecCc
Confidence            9999999864

>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=97.87  E-value=5.2e-05  Score=49.62  Aligned_cols=57  Identities=23%  Similarity=0.350  Sum_probs=37.2

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..|++.+++..++-++|++.|+.||.|..|.+.+..      ..|||.|.+++.|..++..+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHH
Confidence            368899999999999999999999999998886543      368999999999999987554

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

>KOG0128|consensus

Probab=97.69  E-value=1.8e-06  Score=72.97  Aligned_cols=141  Identities=13%  Similarity=0.113  Sum_probs=104.6

Q ss_pred             CCcEEEEcCCCCCccHH-HHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-------------
Q psy7847          21 NDFRLFCGDLGNDVTDE-LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-------------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~-~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-------------   86 (170)
                      ..+...+.++.+..... ..+..|+.+|.++.++....+......-++++++....+++.+..--.+             
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad  649 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLAD  649 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCCC
Confidence            34556777886665554 5688899999999998876332222222677877777777766542211             


Q ss_pred             -----------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHh
Q psy7847          87 -----------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM  149 (170)
Q Consensus        87 -----------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  149 (170)
                                       ..+.|++||++.+.+++|...|..+|.+..+++......+..+|+|++.|..++.+.+|+...
T Consensus       650 ~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~  729 (881)
T KOG0128|consen  650 AEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFR  729 (881)
T ss_pred             chhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhh
Confidence                             138899999999999999999999999888776544446788999999999999999999977


Q ss_pred             cCCCccccCCeeEEE
Q psy7847         150 NEFPHLFVGDLKTRS  164 (170)
Q Consensus       150 ~~~~~~~~~~~~i~v  164 (170)
                      .+   .+++...+-+
T Consensus       730 d~---~~~gK~~v~i  741 (881)
T KOG0128|consen  730 DS---CFFGKISVAI  741 (881)
T ss_pred             hh---hhhhhhhhhe
Confidence            77   6666544443

>KOG4849|consensus

Probab=97.64  E-value=4.8e-05  Score=58.83  Aligned_cols=64  Identities=14%  Similarity=0.303  Sum_probs=57.6

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCC--CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g--~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      .+-+||+||-+.+|++||.+.....|  .+.++++..++.+|+++|||.|...+...+++.++-++
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP  145 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILP  145 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcc
Confidence            45599999999999999999998877  67889999999999999999999999999999987655

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

Probab=97.48  E-value=0.00049  Score=39.23  Aligned_cols=52  Identities=15%  Similarity=0.323  Sum_probs=41.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHH
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN   81 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~   81 (170)
                      +.|-|.|.|++..+..| ..|..||.|.++.+..      ...+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl-~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVL-EHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHH-HHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            57889999988876554 4788899999987752      2358999999999999875

>KOG0129|consensus

Probab=97.46  E-value=0.00046  Score=55.95  Aligned_cols=64  Identities=25%  Similarity=0.341  Sum_probs=58.0

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhh-cCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHH
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK   82 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~-~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~   82 (170)
                      -.+.+|||||+||.-++.++|..+|+ .||.|..+-|=.|..-+..+|.|-|+|.+..+..+|+.
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHh
Confidence            35578999999999999999999998 69999999998886678999999999999999999986

>KOG2314|consensus

Probab=97.44  E-value=0.00039  Score=57.02  Aligned_cols=74  Identities=20%  Similarity=0.188  Sum_probs=57.5

Q ss_pred             CceEEecCCCCC------CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC-C
Q psy7847          87 DFRLFCGDLGND------VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG-D  159 (170)
Q Consensus        87 ~~~l~v~nlp~~------~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-~  159 (170)
                      ..+++|.|.|.-      .-+.-|.++|+++|.+....++.+.. |..+||.|++|.+..+|+.|++.|||   +.+. +
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G---~~ldkn  133 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNG---KRLDKN  133 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhccc---ceeccc
Confidence            357888888853      22355778999999999998887764 55899999999999999999999999   5444 3


Q ss_pred             eeEEE
Q psy7847         160 LKTRS  164 (170)
Q Consensus       160 ~~i~v  164 (170)
                      +...|
T Consensus       134 Htf~v  138 (698)
T KOG2314|consen  134 HTFFV  138 (698)
T ss_pred             ceEEe
Confidence            44333

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

Probab=97.41  E-value=0.0013  Score=40.71  Aligned_cols=60  Identities=10%  Similarity=0.157  Sum_probs=43.7

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      +.|..++..+|+ .|......||.++|+.||.| .|..+.+.       .|||...+.+.+..++..+.
T Consensus         4 ~~P~RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    4 PQPSRDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             ---SGCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             CCCCcceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            445556677776 99999999999999999976 46677663       69999999999998887664

; 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.

>KOG1855|consensus

Probab=97.33  E-value=0.00047  Score=54.75  Aligned_cols=64  Identities=16%  Similarity=0.189  Sum_probs=54.4

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeec---CCCC--Cc--------ccEEEEEecCHHHHHHHHHHhcC
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRD---KRTN--KT--------KGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~---~~~~--~~--------~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      ++|.+.|||.+-.-+.|.++|+.+|.|..|+++..   +.+.  .+        +-+|+|+|...+.|.+|.+.++.
T Consensus       232 rtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  232 RTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             ceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            59999999999999999999999999999999876   3222  22        33699999999999999998865

>KOG2314|consensus

Probab=97.33  E-value=0.00099  Score=54.73  Aligned_cols=75  Identities=23%  Similarity=0.264  Sum_probs=59.1

Q ss_pred             CCCCCcEEEEcCCCCC--ccHH----HHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----
Q psy7847          18 EDENDFRLFCGDLGND--VTDE----LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~--~t~~----~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----   87 (170)
                      ++.-+..|+|.|.|--  .-.+    -|.++|+++|++.++.++.+. .|.++||.|++|.+..+|..|++.+||.    
T Consensus        54 ~eg~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   54 AEGFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             cCCcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            3455667999999852  2233    345779999999999999885 5559999999999999999999999984    


Q ss_pred             -ceEEec
Q psy7847          88 -FRLFCG   93 (170)
Q Consensus        88 -~~l~v~   93 (170)
                       ++++|+
T Consensus       133 nHtf~v~  139 (698)
T KOG2314|consen  133 NHTFFVR  139 (698)
T ss_pred             cceEEee
Confidence             566665

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

Probab=97.33  E-value=0.002  Score=40.07  Aligned_cols=64  Identities=14%  Similarity=0.145  Sum_probs=41.1

Q ss_pred             cEEEEcCCCCCccHHHHH----HHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----ceEEec
Q psy7847          23 FRLFCGDLGNDVTDELLI----RTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----FRLFCG   93 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~----~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~~l~v~   93 (170)
                      ..|+|.|||.+.+...|+    .+++.+| .|.++.          .+.|.|.|.+++.|.+|.+.+++.    ..+.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            358999999998886654    5566776 555541          257999999999999999999974    355555


Q ss_pred             CCC
Q psy7847          94 DLG   96 (170)
Q Consensus        94 nlp   96 (170)
                      -.|
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            443

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

>KOG3152|consensus

Probab=97.28  E-value=0.00018  Score=53.41  Aligned_cols=71  Identities=14%  Similarity=0.141  Sum_probs=58.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCC--------CCccc----EEEEEecCHHHHHHHHHHhcCCCcc
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT--------NKTKG----FGFVSFKDPQDFIRANKEMNEFPHL  155 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~--------~~~~g----~afv~f~~~~~a~~a~~~l~~~~~~  155 (170)
                      -.+|++++|+.++..-|+++++.||.|-.+.+.....+        +.+.+    -|-|+|.+...|..+...||+   .
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn---~  151 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNN---T  151 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCC---C
Confidence            48999999999999999999999999999988655433        11111    166899999999999999999   8


Q ss_pred             ccCCee
Q psy7847         156 FVGDLK  161 (170)
Q Consensus       156 ~~~~~~  161 (170)
                      .+||++
T Consensus       152 ~Iggkk  157 (278)
T KOG3152|consen  152 PIGGKK  157 (278)
T ss_pred             ccCCCC
Confidence            888865

>KOG4849|consensus

Probab=97.28  E-value=0.00022  Score=55.29  Aligned_cols=71  Identities=13%  Similarity=0.260  Sum_probs=59.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      .+.++||+||-+++|++||.+.....|  .+..+++..++.+|.++|||+|...+..+..+.++.|-.   +.+.|
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~---k~iHG  151 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPT---KTIHG  151 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhccc---ceecC
Confidence            356999999999999999999997766  356677777888999999999999999988888887765   65555

>KOG1995|consensus

Probab=97.26  E-value=0.001  Score=51.70  Aligned_cols=71  Identities=21%  Similarity=0.226  Sum_probs=61.7

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCee--------EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~--------~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ......-++||-+||..+++.+|.++|.++|.|.        .|.+.+++.|+..++-|.|.|.+...|+.|+.+..+.
T Consensus        61 ~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agk  139 (351)
T KOG1995|consen   61 ADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGK  139 (351)
T ss_pred             ccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccc
Confidence            3355566899999999999999999999999653        4678888889999999999999999999999988763

>KOG4210|consensus

Probab=97.21  E-value=0.00035  Score=53.71  Aligned_cols=62  Identities=21%  Similarity=0.348  Sum_probs=56.7

Q ss_pred             CcEEE-EcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          22 DFRLF-CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        22 ~~~v~-v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      ..+++ +++|+.++++++|+..|..+|.+..++++.+..++.++++||+.|.+......++..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            44555 999999999999999999999999999999999999999999999999998888864

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

Probab=97.15  E-value=0.0013  Score=37.51  Aligned_cols=52  Identities=13%  Similarity=0.309  Sum_probs=40.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN  146 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~  146 (170)
                      +.+-|.+.+++..+. +...|..||.|..+.+...      ....++.|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            356778888776655 5557888999999887521      337999999999999985

>KOG1855|consensus

Probab=97.10  E-value=0.001  Score=52.91  Aligned_cols=73  Identities=16%  Similarity=0.201  Sum_probs=59.4

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEec---CCC--C--------CcCCEEEEEeCCHHHHHHH
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRD---KRT--N--------KTKGFGFVSFKDPQDFIRA   80 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~---~~~--~--------~~~~~afv~f~~~~~a~~~   80 (170)
                      +...++.++++|.+-|||.+-..+-|.++|+.+|.|..|+|..-   ..+  +        ..+..|+|+|...+.|.+|
T Consensus       223 ~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA  302 (484)
T KOG1855|consen  223 EFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA  302 (484)
T ss_pred             CccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH
Confidence            34445568999999999999999999999999999999998654   111  1        1357899999999999999


Q ss_pred             HHHcCC
Q psy7847          81 NKEMND   86 (170)
Q Consensus        81 ~~~~~~   86 (170)
                      .+.++.
T Consensus       303 ~e~~~~  308 (484)
T KOG1855|consen  303 RELLNP  308 (484)
T ss_pred             HHhhch
Confidence            988754

>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=96.91  E-value=0.0045  Score=40.05  Aligned_cols=75  Identities=13%  Similarity=0.154  Sum_probs=47.8

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEE-EeecC------CCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAK-VVRDK------RTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~-~~~~~------~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      .-|.|-+.|+. ....+-+.|++||.|.... +.++.      .......+..|+|.++.+|.+|++ -||   ..++|.
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG---~i~~g~   81 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNG---TIFSGS   81 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTT---EEETTC
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCC---eEEcCc
Confidence            45777788887 5566888999999987764 11110      011224478899999999999999 688   888875


Q ss_pred             eE-EEEee
Q psy7847         161 KT-RSSIT  167 (170)
Q Consensus       161 ~i-~v~~~  167 (170)
                      .| -|.+.
T Consensus        82 ~mvGV~~~   89 (100)
T PF05172_consen   82 LMVGVKPC   89 (100)
T ss_dssp             EEEEEEE-
T ss_pred             EEEEEEEc
Confidence            44 35443

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

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

Probab=96.90  E-value=0.0015  Score=46.82  Aligned_cols=67  Identities=16%  Similarity=0.298  Sum_probs=42.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhc-CCCeeEEEEEe---cCC-C-CCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVR---DKR-T-NKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~-~g~v~~i~~~~---~~~-~-~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+|.||+||+++|+++..+.++. ++.-..+....   ... . ....+-|||.|.+.+++......+++
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g   77 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDG   77 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCC
Confidence            44568999999999999999997776 66552222222   111 1 22346799999999999999998887

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

>KOG1996|consensus

Probab=96.89  E-value=0.0039  Score=47.45  Aligned_cols=64  Identities=14%  Similarity=0.142  Sum_probs=50.8

Q ss_pred             HHHHHHHhccCCCeeEEEEeecCCCCC-cccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847         101 DELLIRTFSKYPSFLKAKVVRDKRTNK-TKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus       101 ~~~l~~~f~~~g~i~~~~~~~~~~~~~-~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++++.+-+.+||.+..|.+...+.... ..-..||+|...++|.+|+-.|||   .++||+.++..+-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnG---RyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNG---RYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCC---ceecceeeeheec
Confidence            456778899999999887765543221 223489999999999999999999   9999999987653

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

Probab=96.87  E-value=0.011  Score=34.76  Aligned_cols=55  Identities=18%  Similarity=0.235  Sum_probs=44.7

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcC---CCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKY---PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~---g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      ..+|+|+|+ -+++-++|+.+|..|   .....|.++.|.       .|-|.|.+.+.|.+|+..|
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            357999999 558888999999988   135578888874       5999999999999998653

>KOG2202|consensus

Probab=96.82  E-value=0.00061  Score=50.69  Aligned_cols=63  Identities=16%  Similarity=0.246  Sum_probs=50.1

Q ss_pred             HHHHHHhc-cCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847         102 ELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       102 ~~l~~~f~-~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +++...++ +||.|+.+.+..+- ...-.|=++|.|..+++|++|++.||+   ..++|++|...+.-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnn---Rw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNN---RWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcC---ccccCCcceeeecC
Confidence            44444454 89999998776553 233467799999999999999999999   99999999887654

>KOG4676|consensus

Probab=96.67  E-value=0.0025  Score=50.21  Aligned_cols=78  Identities=13%  Similarity=0.109  Sum_probs=60.3

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCC---CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR---TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..|.|.||.++++.++++.+|+..|.|..+.++....   .......|||.|.+...+..|.-.-|-   .+++-..|-+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtnt---vfvdraliv~   84 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNT---VFVDRALIVR   84 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccc---eeeeeeEEEE
Confidence            3688999999999999999999999999998765321   222345799999999998888776565   6666666666


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      -|..
T Consensus        85 p~~~   88 (479)
T KOG4676|consen   85 PYGD   88 (479)
T ss_pred             ecCC
Confidence            5543

>KOG2416|consensus

Probab=96.47  E-value=0.0026  Score=52.67  Aligned_cols=76  Identities=12%  Similarity=0.060  Sum_probs=62.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCC-eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...|+|.||-..+|.-+|+.+++.-|. |+.. ++ |+    -+..|||.|.+.++|.....+|||-.|-.-+.+.|.+.
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHH-HH-HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            359999999999999999999986554 4433 32 22    24579999999999999999999987888888999988


Q ss_pred             eec
Q psy7847         166 ITL  168 (170)
Q Consensus       166 ~~~  168 (170)
                      |..
T Consensus       518 f~~  520 (718)
T KOG2416|consen  518 FVR  520 (718)
T ss_pred             ecc
Confidence            864

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

Probab=96.37  E-value=0.02  Score=39.44  Aligned_cols=56  Identities=20%  Similarity=0.352  Sum_probs=44.0

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       102 ~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .+|-+.|..||.+.-+++.-+        --.|+|.+.+.|.+|++ ++|   ..++|+.|+|+...+
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg---~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDG---IQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCC---SEETTEEEEEEE---
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCC---cEECCEEEEEEeCCc
Confidence            367778889999887777543        35799999999999999 899   999999999987654

; PDB: 1UFW_A 2DNR_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.07  E-value=0.016  Score=45.05  Aligned_cols=65  Identities=18%  Similarity=0.267  Sum_probs=48.3

Q ss_pred             cEEEEcCCCCCccHHHH------HHHhhcCCCeeEEEEEecCCC-CCcCC--EEEEEeCCHHHHHHHHHHcCCC
Q psy7847          23 FRLFCGDLGNDVTDELL------IRTFSKYPSFLKAKVVRDKRT-NKTKG--FGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l------~~~f~~~g~v~~i~~~~~~~~-~~~~~--~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+||-+||+.+..|++      .++|++||.|..|.+-+...+ ....+  -.||+|.+.++|.+++.+.++.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs  188 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGS  188 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccc
Confidence            35899999998877763      478999999988877443212 12222  3499999999999999887763

>KOG0115|consensus

Probab=96.03  E-value=0.009  Score=44.63  Aligned_cols=63  Identities=21%  Similarity=0.332  Sum_probs=55.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      ..|+|.||+..++-+.+.+-|+.||.+....+..|. .+.+.+-++|.|...-.+.+|+..++.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhcc
Confidence            479999999999999999999999999987777665 577778899999999999999987743

>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=96.02  E-value=0.013  Score=41.99  Aligned_cols=65  Identities=17%  Similarity=0.289  Sum_probs=43.2

Q ss_pred             CceEEecCCCCCCCHHHHHHHhcc-CCCe---eEEEEeecCCC--CCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSK-YPSF---LKAKVVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~-~g~i---~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      ...|.|++||+.+|++++.+.++. ++.-   .+.....+...  ......|+|.|.+.+++..-...++|
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g   77 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDG   77 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTT
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCC
Confidence            358999999999999999998877 6654   23331122211  11234599999999999999999999

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.

>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=95.98  E-value=0.14  Score=33.76  Aligned_cols=64  Identities=11%  Similarity=0.127  Sum_probs=45.9

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+.+...|..++.++|..+...+- .+..++++++.  ..++-.+.+.|.+.++|..+....||+
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk   77 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGK   77 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCC
Confidence            33455545555566667765555543 67888898874  235668999999999999999999974

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

>KOG3152|consensus

Probab=95.96  E-value=0.005  Score=45.96  Aligned_cols=66  Identities=12%  Similarity=0.136  Sum_probs=54.1

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC--------CCcC----CEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT--------NKTK----GFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~--------~~~~----~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...||++++|+.+...-|++++..||.|=.|.+-....+        |.+.    .-++|+|.+...|..+...||+.
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~  151 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNT  151 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCC
Confidence            356999999999999999999999999988888655444        2221    34689999999999999999863

>KOG2068|consensus

Probab=95.88  E-value=0.0052  Score=47.54  Aligned_cols=76  Identities=16%  Similarity=0.253  Sum_probs=57.3

Q ss_pred             eEEecCCCCCCCHHHHHH---HhccCCCeeEEEEeecCC----CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          89 RLFCGDLGNDVTDELLIR---TFSKYPSFLKAKVVRDKR----TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~---~f~~~g~i~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                      -+|+.+|+.....+.+-+   -|++||.|..+.+.++..    .+... .++|+|...++|.+|+...+|   ....++.
T Consensus        79 lvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rci~~v~g---~~~dg~~  154 (327)
T KOG2068|consen   79 LVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRCIDDVDG---FVDDGRA  154 (327)
T ss_pred             hhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhHHHHhhh---HHhhhhh
Confidence            366778887665554433   678899999998877651    12222 389999999999999999999   9999988


Q ss_pred             EEEEeec
Q psy7847         162 TRSSITL  168 (170)
Q Consensus       162 i~v~~~~  168 (170)
                      ++.++.+
T Consensus       155 lka~~gt  161 (327)
T KOG2068|consen  155 LKASLGT  161 (327)
T ss_pred             hHHhhCC
Confidence            8877654

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

Probab=95.76  E-value=0.079  Score=32.97  Aligned_cols=54  Identities=9%  Similarity=0.169  Sum_probs=39.2

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      ..++. .|..|-..||.++|+.||.|. |.++-|       ..|||...+++.+..|+..++-
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhcc
Confidence            44444 899999999999999999864 444443       2699999999999998887764

; 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.

>KOG2193|consensus

Probab=95.71  E-value=0.015  Score=46.60  Aligned_cols=72  Identities=18%  Similarity=0.212  Sum_probs=55.1

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      .+|++||.+.++..+|+.+|.....--.-.++.      ..||+||.+.+..-|.+|++.++|.  ..+.|+++.+..+-
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk--~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGK--VELQGKRQEVEHSV   74 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchh--hhhcCceeeccchh
Confidence            589999999999999999997541111111211      2579999999999999999999994  67788888776653

>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=95.62  E-value=0.064  Score=34.71  Aligned_cols=62  Identities=15%  Similarity=0.252  Sum_probs=39.9

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEE-EEecC------CCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAK-VVRDK------RTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~-~~~~~------~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      .++.|.|=+.|+.. ...|.+.|+.||+|.+.. +.++.      .......+..|.|.++.+|.+|+..
T Consensus         5 ~~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~   73 (100)
T PF05172_consen    5 SETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK   73 (100)
T ss_dssp             GCCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT
T ss_pred             CCeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh
Confidence            45668888999884 457778899999987664 11110      0112345899999999999999954

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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.39  E-value=0.093  Score=36.02  Aligned_cols=70  Identities=13%  Similarity=0.114  Sum_probs=49.0

Q ss_pred             eEEecCCCCCC----CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          89 RLFCGDLGNDV----TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        89 ~l~v~nlp~~~----~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ++.|+=|..++    +-..+...++.||+|..+...-       +..|.|.|.+..+|.+|+.+++.    ..-|.-+..
T Consensus        88 TIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s----~~pgtm~qC  156 (166)
T PF15023_consen   88 TIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS----RAPGTMFQC  156 (166)
T ss_pred             eEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC----CCCCceEEe
Confidence            77776444433    3344445567899999986642       33699999999999999999986    334556777


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +|..+
T Consensus       157 sWqqr  161 (166)
T PF15023_consen  157 SWQQR  161 (166)
T ss_pred             ecccc
Confidence            77653

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

Probab=95.31  E-value=0.12  Score=30.28  Aligned_cols=53  Identities=19%  Similarity=0.248  Sum_probs=41.3

Q ss_pred             eEEecCCCCCCCHHHHHHHhccC---CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHh
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKY---PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM  149 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~---g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l  149 (170)
                      .|+++++.. ++-+++...|..|   .....+.++-|.       .|=|.|.+.+.|.+|+.+|
T Consensus         7 avhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            688888855 7788899999887   234567776664       4779999999999999764

>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=95.23  E-value=0.063  Score=38.71  Aligned_cols=61  Identities=16%  Similarity=0.098  Sum_probs=44.5

Q ss_pred             CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc--CCCccccCCeeEEEEeecc
Q psy7847         100 TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN--EFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       100 ~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~~~~~~~i~v~~~~~  169 (170)
                      ....|+++|..++.+.....++.      -+...|.|.+.++|..|...++  +   ..++|..+++.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~---~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDG---TSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--T---SEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccc---cccCCCceEEEEccc
Confidence            45789999999998877766654      3468899999999999999999  8   899999999988753

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=94.87  E-value=0.04  Score=41.30  Aligned_cols=62  Identities=19%  Similarity=0.314  Sum_probs=55.0

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..|+|.||+.-++-+.+.+.|..||+++...+.-| ..++..+-+.|.|...-.+.+|...+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            57999999999999999999999999988777776 367888889999999999999998764

>KOG0804|consensus

Probab=94.72  E-value=0.16  Score=41.16  Aligned_cols=66  Identities=18%  Similarity=0.209  Sum_probs=56.3

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+..|.|-.+|.-++..||..|+..+- .|.+|+++++.  -..+=.+.|.|.+.++|..+.+++||+
T Consensus        72 ~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk  138 (493)
T KOG0804|consen   72 SSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGK  138 (493)
T ss_pred             CCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCC
Confidence            3378899999999999999999998765 68999999963  234457899999999999999999985

>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=94.71  E-value=0.22  Score=29.62  Aligned_cols=54  Identities=20%  Similarity=0.375  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          98 DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        98 ~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      .++-++++..+..|+   +..+..|+     .|| ||.|.+.++|++|....+|   ..+.+..|.
T Consensus        11 ~~~v~d~K~~Lr~y~---~~~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~---~~~f~y~m~   64 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR---WDRIRDDR-----TGF-YIVFNDSKEAERCFRAEDG---TLFFTYRMQ   64 (66)
T ss_pred             CccHHHHHHHHhcCC---cceEEecC-----CEE-EEEECChHHHHHHHHhcCC---CEEEEEEEE
Confidence            577889999998873   34444454     454 7999999999999999999   666665543

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

>KOG0112|consensus

Probab=94.20  E-value=0.061  Score=46.83  Aligned_cols=61  Identities=18%  Similarity=0.309  Sum_probs=52.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....+++++|++++....+...|..||.+..|.+....      .|||+.+++...++.+++.+-+
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq------~yayi~yes~~~aq~a~~~~rg  513 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ------PYAYIQYESPPAAQAATHDMRG  513 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC------cceeeecccCccchhhHHHHhc
Confidence            345679999999999999999999999999998775432      5999999999999999987764

>KOG2416|consensus

Probab=94.18  E-value=0.051  Score=45.31  Aligned_cols=63  Identities=14%  Similarity=0.132  Sum_probs=50.5

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhc-CCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~-~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++.|||.||-.-.|.-+|+.++++ .|.|++. +|.     +-+..|||.|.+.++|....+.||+
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmD-----kIKShCyV~yss~eEA~atr~Alhn  503 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMD-----KIKSHCYVSYSSVEEAAATREALHN  503 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH-HHH-----HhhcceeEecccHHHHHHHHHHHhc
Confidence            3455788999999999999999999985 5556555 332     2356799999999999999998886

>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=94.00  E-value=0.75  Score=30.27  Aligned_cols=63  Identities=13%  Similarity=0.155  Sum_probs=45.3

Q ss_pred             eEEecCCCCCCCHHHHHHHhccC-CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCC
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP  153 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  153 (170)
                      .+.+...|..++.++|..+.+.+ ..|..+++++|.  ..++-.+++.|.+.++|..-...+||.+
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~   78 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKP   78 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCc
Confidence            44444555666667776666555 356778888874  2345569999999999999999999933

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

>KOG2135|consensus

Probab=93.94  E-value=0.033  Score=45.16  Aligned_cols=70  Identities=13%  Similarity=-0.029  Sum_probs=54.0

Q ss_pred             EEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          90 LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        90 l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      |-+.-.|+. -+..+|..-|.+||.|..|++-..      .-.|.|+|.+..+|-+|-. .++   ..++++.|||.|-.
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~---avlnnr~iKl~whn  444 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHG---AVLNNRFIKLFWHN  444 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-ccc---ceecCceeEEEEec
Confidence            333444443 346889999999999999988433      2258999999999977765 688   99999999999965


Q ss_pred             c
Q psy7847         169 K  169 (170)
Q Consensus       169 ~  169 (170)
                      +
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            4

>KOG4574|consensus

Probab=93.02  E-value=0.07  Score=46.28  Aligned_cols=73  Identities=22%  Similarity=0.196  Sum_probs=61.0

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +..+.|.+-..+-..|.-+|+.||.+..+..+++-      ..|.|+|.+.+.|..|+.+++|.+..+.|. +.+|++|.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~-Ps~V~~ak  372 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGA-PSRVSFAK  372 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCC-ceeEEecc
Confidence            55566777788889999999999999999887773      378999999999999999999976666655 68888774

>KOG2591|consensus

Probab=92.85  E-value=0.25  Score=41.09  Aligned_cols=71  Identities=13%  Similarity=0.187  Sum_probs=53.9

Q ss_pred             ceEEecCCCCCCCHHHHHHHhcc--CCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSK--YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~--~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +.+.++.+|..+..|+++.+|..  +..+..|.+..+.    +   =||+|.+..||+.|.+.|.. ..+.+.|++|...
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~----n---WyITfesd~DAQqAykylre-evk~fqgKpImAR  247 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND----N---WYITFESDTDAQQAYKYLRE-EVKTFQGKPIMAR  247 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC----c---eEEEeecchhHHHHHHHHHH-HHHhhcCcchhhh
Confidence            45667899999999999999954  6678888886653    1   37999999999999887765 3455666666544


Q ss_pred             e
Q psy7847         166 I  166 (170)
Q Consensus       166 ~  166 (170)
                      +
T Consensus       248 I  248 (684)
T KOG2591|consen  248 I  248 (684)
T ss_pred             h
Confidence            3

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.72  E-value=0.29  Score=33.68  Aligned_cols=59  Identities=17%  Similarity=0.169  Sum_probs=42.3

Q ss_pred             CCcEEEEcCCCCCccH-HHH---HHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTD-ELL---IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~-~~l---~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +-.+|.|+=|..++.. +|+   ..-++.||+|.++...-       +..|.|+|++..+|-.|+...+.
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s  147 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS  147 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC
Confidence            3456778766665443 344   44567799999986632       34699999999999999987763

>KOG1996|consensus

Probab=91.52  E-value=0.69  Score=35.62  Aligned_cols=50  Identities=16%  Similarity=0.131  Sum_probs=39.8

Q ss_pred             HHHHHHhhcCCCeeEEEEEecCCCCCc-CCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          37 ELLIRTFSKYPSFLKAKVVRDKRTNKT-KGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        37 ~~l~~~f~~~g~v~~i~~~~~~~~~~~-~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +++++-+++||.|..|.|.....-... .--.||+|...+++.+|+-.+|+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnG  351 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNG  351 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCC
Confidence            577888999999999988776432222 23479999999999999999887

>KOG2202|consensus

Probab=91.00  E-value=0.092  Score=39.36  Aligned_cols=50  Identities=20%  Similarity=0.308  Sum_probs=40.0

Q ss_pred             HHHHHHhh-cCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          37 ELLIRTFS-KYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        37 ~~l~~~f~-~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++...+. +||.|+++.+..+. ...-.|=+||.|..+++|++|+..|++-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnR  133 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNR  133 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCc
Confidence            45555555 89999999876653 3456788999999999999999999873

>KOG2591|consensus

Probab=90.68  E-value=1.4  Score=36.94  Aligned_cols=57  Identities=12%  Similarity=0.237  Sum_probs=47.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhc--CCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSK--YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~--~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      +.+.|.|+.+|..+-.|+++-+|+.  +.++.+|.+-.+.       -=||+|++..+|..|.+-+
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykyl  232 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYL  232 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHH
Confidence            3456899999999999999999975  7888899886553       2599999999999998644

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=90.19  E-value=0.39  Score=30.27  Aligned_cols=42  Identities=12%  Similarity=0.201  Sum_probs=33.7

Q ss_pred             EEEEeCCHHHHHHHHHHcCC-------------------------------CceEEecCCCCCCCHHHHHHHh
Q psy7847          67 GFVSFKDPQDFIRANKEMND-------------------------------DFRLFCGDLGNDVTDELLIRTF  108 (170)
Q Consensus        67 afv~f~~~~~a~~~~~~~~~-------------------------------~~~l~v~nlp~~~~~~~l~~~f  108 (170)
                      |.|+|.++.-|...+..-..                               .+++.|.|+|...++++|+...
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            67899999999998863221                               3589999999999999998554

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0804|consensus

Probab=89.45  E-value=1.2  Score=36.17  Aligned_cols=68  Identities=18%  Similarity=0.183  Sum_probs=56.2

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccC-CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~-g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      ...|+|-.+|..++-.||-.++..+ ..|..+++++|.  -..+-.+++.|.+.++|..--+.+||   +.++.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNG---k~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNG---KQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCC---CcCCC
Confidence            6789999999999999999999765 568899999964  22344589999999999999999999   55544

>KOG2068|consensus

Probab=88.56  E-value=0.43  Score=37.24  Aligned_cols=65  Identities=15%  Similarity=0.248  Sum_probs=47.5

Q ss_pred             CcEEEEcCCCCCccHHHH---HHHhhcCCCeeEEEEEecCC--CC-CcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELL---IRTFSKYPSFLKAKVVRDKR--TN-KTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l---~~~f~~~g~v~~i~~~~~~~--~~-~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+||-+|+.....+++   .+.|.+||.+..|.+.++..  .+ .....+||+|...++|..++...++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g  147 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDG  147 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhh
Confidence            356888899887665555   36799999999998887651  11 1223499999999999999876554

>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=87.75  E-value=2.9  Score=25.17  Aligned_cols=59  Identities=12%  Similarity=0.157  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHhccCCCe-----eEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          97 NDVTDELLIRTFSKYPSF-----LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        97 ~~~~~~~l~~~f~~~g~i-----~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ..++..+|-.++...+.+     -.|.+..        .|+||+-. .+.+..+++.|++   ..++|++++|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~-~~~a~~v~~~l~~---~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVP-EEVAEKVLEALNG---KKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE--TT-HHHHHHHHTT-----SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEEC-HHHHHHHHHHhcC---CCCCCeeEEEEEC
Confidence            357777888888665443     4555543        27888876 4578899999999   9999999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG4483|consensus

Probab=86.44  E-value=4.9  Score=32.47  Aligned_cols=79  Identities=19%  Similarity=0.153  Sum_probs=61.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCceEEecCCCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGND   98 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~~l~v~nlp~~   98 (170)
                      .-.+.|-|.++|.....+||...|+.|+ ..-+|.++.+.       .||..|.+...|..++..-|.  -|.++.|...
T Consensus       389 dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~kh~--~lKiRpLaqa  459 (528)
T KOG4483|consen  389 DLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTLKHD--WLKIRPLAQA  459 (528)
T ss_pred             cccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhccCc--eEEeeehhhc
Confidence            3467899999999888889999999887 45677777775       699999999999999987543  5666777666


Q ss_pred             CCHHHHHHH
Q psy7847          99 VTDELLIRT  107 (170)
Q Consensus        99 ~~~~~l~~~  107 (170)
                      +-...+...
T Consensus       460 tk~sklkAk  468 (528)
T KOG4483|consen  460 TKVSKLKAK  468 (528)
T ss_pred             hhHHHHHhh
Confidence            655555543

>KOG4285|consensus

Probab=84.92  E-value=1.9  Score=33.40  Aligned_cols=61  Identities=8%  Similarity=0.091  Sum_probs=45.0

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      =|.|-++|+.-. ..+-.+|+++|.|.......   ++   .+-+|.|.+..+|++||. .||   .++++-
T Consensus       199 WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~---ng---NwMhirYssr~~A~KALs-kng---~ii~g~  259 (350)
T KOG4285|consen  199 WVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPS---NG---NWMHIRYSSRTHAQKALS-KNG---TIIDGD  259 (350)
T ss_pred             eEEEeccCccch-hHHHHHHHhhCeeeeeecCC---CC---ceEEEEecchhHHHHhhh-hcC---eeeccc
Confidence            455557777543 45778899999998876541   22   367899999999999999 577   777764

>KOG2253|consensus

Probab=82.29  E-value=1.7  Score=37.06  Aligned_cols=57  Identities=21%  Similarity=0.264  Sum_probs=46.7

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      .+..+|||+|+...+..+-++.+...+|-|-++....         |+|..|..+.....++..+.
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t   94 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLT   94 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhc
Confidence            3467899999999999999999999999887665432         78999999998888876443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	170
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-13
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-13
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-11
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-11
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-08
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-08
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		7e-08
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		6e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		9e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		6e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		6e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		9e-07
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		7e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		6e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		7e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		6e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-06
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		7e-06
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		2e-05
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		2e-05
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		3e-05
2khc_A	118	Bruno Rrm3+ Length = 118		3e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		8e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		3e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		8e-05
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		8e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		8e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		1e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		4e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		2e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		3e-04
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		4e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		5e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		5e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		7e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		9e-04

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 78/166 (46%), Gaps = 29/166 (17%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+ +V+F+ P D  RA   M
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 85  NDDF-----------------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
           N D                         +F  +L   + ++ L  TFS + + L  KVV 
Sbjct: 73  NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 132
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMNEF----PHLFVGDLKTR 163
           D+  N +KG+GFV F+  +   RA ++MN        +FVG  K+R
Sbjct: 133 DE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 78/166 (46%), Gaps = 29/166 (17%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+ +V+F+ P D  RA   M
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 85  NDDF-----------------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
           N D                         +F  +L   + ++ L  TFS + + L  KVV 
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMNEF----PHLFVGDLKTR 163
           D+  N +KG+GFV F+  +   RA ++MN        +FVG  K+R
Sbjct: 138 DE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 64.3 bits (155), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/148 (29%), Positives = 64/148 (43%), Gaps = 24/148 (16%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L+ G+L   +T+++L + F         K++ DK  NK   + FV +    D   A + +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 85  N-----------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
           N                       D F LF GDL  +V DE L   F  +PS+L   V+ 
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           D +T  ++G+GFVSF    D   A   M
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSM 149

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 63.9 bits (154), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/145 (28%), Positives = 72/145 (49%), Gaps = 21/145 (14%)
Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK- 82
           ++F G L  D T++ L   F KY +    K+++D  T +++GFGF+SF+ P       K 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 83  ------------------EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR 124
                             E +   ++F G +G DV  +     FS++ + + A+++ DK 
Sbjct: 65  QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 125 TNKTKGFGFVSF--KDPQDFIRANK 147
           T +++GFGFV++   D  D +  NK
Sbjct: 125 TGQSRGFGFVTYDSADAVDRVCQNK 149

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          F LF GDL  +V DE L   F  +PS+L   V+ D +T  ++G+GFVSF    D   A  
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 83 EM 84
           M
Sbjct: 62 SM 63

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 34/62 (54%)
Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           F LF GDL  +V DE L   F  +PS+L   V+ D +T  ++G+GFVSF    D   A  
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 148 EM 149
            M
Sbjct: 62  SM 63

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 60/147 (40%), Gaps = 21/147 (14%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L    L  D+TD  L   F         +++RD +T  + G+ FV F    D  RA K +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 85  ND---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
           N                      D  L+  +L   +TD+ L   F KY S ++  ++RDK
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 125
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
            T + +G  FV +   ++   A   +N
Sbjct: 126 LTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 51.6 bits (122), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 37/147 (25%), Positives = 64/147 (43%), Gaps = 21/147 (14%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L    L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 85  ND---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
           N                      D  L+   L   +T + L + FS+Y   + ++++ D+
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
            T  ++G GF+ F    +   A K +N
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLN 151

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           N F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D   
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72
Query: 80 ANKEMNDDF 88
          A ++M   +
Sbjct: 73 AIQQMGGQW 81

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 41/68 (60%)
Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           K+ ++ F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69
Query: 142 FIRANKEM 149
              A ++M
Sbjct: 70  AENAIQQM 77

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 50.4 bits (119), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 40/66 (60%)
Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           +D+ +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++  D   
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 145 ANKEMN 150
           A   MN
Sbjct: 70  AMMAMN 75

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 50.1 bits (118), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 58/147 (39%), Gaps = 21/147 (14%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L    L  D TD  L   F         ++ RD +T  + G+ FV F    D  RA K +
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 85  ND---------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
           N                      D  L+  +L   +TD+ L   F KY S ++  ++RDK
Sbjct: 77  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 136
Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
            T + +G  FV +   ++   A   +N
Sbjct: 137 LTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 10  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 69
Query: 78  -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
                 R +K               D  R         +F G +  D  +  L   F +Y
Sbjct: 70  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 129
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 +++ D+ + K +GF FV+F D
Sbjct: 130 GKIEVIEIMTDRGSGKKRGFAFVTFDD 156

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++   A   
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 72
Query: 149 MNEFPH 154
           MN  PH
Sbjct: 73  MNARPH 78

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 8   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 67
Query: 78  -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
                 R +K               D  R         +F G +  D  +  L   F +Y
Sbjct: 68  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 127
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 +++ D+ + K +GF FV+F D
Sbjct: 128 GKIEVIEIMTDRGSGKKRGFAFVTFDD 154

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++   A   
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 70
Query: 149 MNEFPH 154
           MN  PH
Sbjct: 71  MNARPH 76

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 49.7 bits (117), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 78  -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
                 R +K               D  R         +F G +  D  +  L   F +Y
Sbjct: 69  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 +++ D+ + K +GF FV+F D
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDD 155

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++   A   
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 149 MNEFPH 154
           MN  PH
Sbjct: 72  MNARPH 77

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 78  -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
                 R +K               D  R         +F G +  D  +  L   F +Y
Sbjct: 69  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 +++ D+ + K +GF FV+F D
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDD 155

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++   A   
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 71
Query: 149 MNEFPH 154
           MN  PH
Sbjct: 72  MNARPH 77

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 49.3 bits (116), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 7   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 66
Query: 78  -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
                 R +K               D  R         +F G +  D  +  L   F +Y
Sbjct: 67  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 126
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 +++ D+ + K +GF FV+F D
Sbjct: 127 GKIEVIEIMTDRGSGKKRGFAFVTFDD 153

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 43.1 bits (100), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++   A   
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 69
Query: 149 MNEFPH 154
           MN  PH
Sbjct: 70  MNARPH 75

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 63/147 (42%), Gaps = 26/147 (17%)
Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61
Query: 78  -----IRANK------------EMNDDFR---------LFCGDLGNDVTDELLIRTFSKY 111
                 R +K               D  R         +F G +  D  +  L   F +Y
Sbjct: 62  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 +++ D+ + K +GF FV+F D
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDD 148

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++   A   
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA--- 64
Query: 149 MNEFPH 154
           MN  PH
Sbjct: 65  MNARPH 70

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 37/69 (53%)
Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           N F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D   
Sbjct: 13 SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAEN 72
Query: 80 ANKEMNDDF 88
          A   M   +
Sbjct: 73 AIVHMGGQW 81

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           K+ ++ F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLD 69
Query: 142 FIRANKEMN 150
              A   M 
Sbjct: 70  AENAIVHMG 78

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 51/105 (48%), Gaps = 21/105 (20%)
Query: 53  KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---------------------DFRLF 91
           K+VRDK T ++ G+GFV++ DP D  +A   +N                      D  L+
Sbjct: 35  KLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPSSASIRDANLY 94
Query: 92  CGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
              L   ++ + + + FS+Y   + ++++ D+ T  ++G GF+ F
Sbjct: 95  VSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 139

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 74
          +LF G L    T E L   FS+Y   +   +++DK TN+++GFGFV FKDP
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           +LF G L    T E L   FS+Y   +   +++DK TN+++GFGFV FKDP
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 33/161 (20%), Positives = 63/161 (39%), Gaps = 32/161 (19%)
Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           R++ G +  ++ ++ + + F+ +       +  D  T K KGF FV ++ P+    A ++
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 84  MNDDF--------------------------------RLFCGDLGNDVTDELLIRTFSKY 111
           MN                                   R++   +  D++D+ +   F  +
Sbjct: 90  MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 149
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
                A + RD  T K KG+GF+ ++  Q    A   MN F
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
           E ++  +LF G L  +  +++L   F K+    +  +++D RT+K++GF F++F++P D
Sbjct: 2  VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPAD 60
Query: 77 FIRANKEMN 85
             A K+MN
Sbjct: 61 AKNAAKDMN 69

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
           E +   +LF G L  +  +++L   F K+    +  +++D RT+K++GF F++F++P D 
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61
Query: 143 IRANKEMN 150
             A K+MN
Sbjct: 62  KNAAKDMN 69

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/161 (19%), Positives = 62/161 (38%), Gaps = 32/161 (19%)
Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           R++ G +  ++ ++ + + F+ +       +  D  T K KGF FV ++ P+    A ++
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 84  MNDDF--------------------------------RLFCGDLGNDVTDELLIRTFSKY 111
           MN                                   R++   +  D++D+ +   F  +
Sbjct: 75  MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 134
Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
                  + RD  T K KG+GF+ ++  Q    A   MN F
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 175

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 40/73 (54%)
Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           + KE  +   LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P
Sbjct: 18  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 77
Query: 140 QDFIRANKEMNEF 152
                A + MN F
Sbjct: 78  VSAQAAIQSMNGF 90

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/70 (42%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 22 DFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          ++ LF GDL  DV D +L   F K YPS    KVV D +T  +KG+GFV F D  +  RA
Sbjct: 9  EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRA 67
Query: 81 NKEMNDDFRL 90
            E      L
Sbjct: 68 LTECQGAVGL 77

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 38/72 (52%), Gaps = 2/72 (2%)
Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           ++     ++ LF GDL  DV D +L   F K YPS    KVV D +T  +KG+GFV F D
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTD 60
Query: 139 PQDFIRANKEMN 150
             +  RA  E  
Sbjct: 61  ELEQKRALTECQ 72

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 37/70 (52%)
Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
           E  +   LF   L  + TD  L  TF  + + + AKV  DK+T+ +K FGFVSF +P   
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 143 IRANKEMNEF 152
             A K MN F
Sbjct: 96  QVAIKAMNGF 105

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  D T+E L  +F      ++A++V D+ T  +KGFGFV F   +D   A + M
Sbjct: 18 LFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 85 ND 86
           D
Sbjct: 75 ED 76

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  D T+E L  +F      ++A++V D+ T  +KGFGFV F   +D   A + M
Sbjct: 18  LFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 150 NE 151
            +
Sbjct: 75  ED 76

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+  +L + + DE L + FS + +   AKV+ +    ++KGFGFV F  P++  +A  EM
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 85 N 85
          N
Sbjct: 76 N 76

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+  +L + + DE L + FS + +   AKV+ +    ++KGFGFV F  P++  +A  EM
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 150 N 150
           N
Sbjct: 76  N 76

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 56/128 (43%), Gaps = 22/128 (17%)
Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           RLF G+L  D+T+E   R F +Y    +  + RD      +GFGF+  +       A  E
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAE 77
Query: 84  MNDDF---------------RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 128
           ++                   L   +L   V++ELL + FS++    KA VV D R   T
Sbjct: 78  LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT 137
Query: 129 KGFGFVSF 136
            G GFV F
Sbjct: 138 -GKGFVEF 144

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/133 (22%), Positives = 57/133 (42%), Gaps = 21/133 (15%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD-------- 76
           L    L  ++T + L   FS       AK++RDK    + G+GFV++   +D        
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 77  -------------FIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
                        + R + E+  D  L+   L   +T + +   FS++   + ++V+ D+
Sbjct: 65  NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 124 RTNKTKGFGFVSF 136
            T  ++G  F+ F
Sbjct: 125 TTGLSRGVAFIRF 137

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/133 (22%), Positives = 57/133 (42%), Gaps = 21/133 (15%)
Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD-------- 76
           L    L  ++T + L   FS       AK++RDK    + G+GFV++   +D        
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 77  -------------FIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
                        + R + E+  D  L+   L   +T + +   FS++   + ++V+ D+
Sbjct: 65  NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 124 RTNKTKGFGFVSF 136
            T  ++G  F+ F
Sbjct: 125 TTGLSRGVAFIRF 137

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 38/65 (58%)
Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
            RL+ G L  ++T+++L   F  +      +++ D  T ++KG+GF++F D +   +A +
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
Query: 148 EMNEF 152
           ++N F
Sbjct: 87  QLNGF 91

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 38/76 (50%)
Query: 11 SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
          S+ +   E   D  L+  +L   +TD+ L   F KY S ++  ++RDK T + +G  FV 
Sbjct: 2  SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 71 FKDPQDFIRANKEMND 86
          +   ++   A   +N+
Sbjct: 62 YNKREEAQEAISALNN 77

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 77  FIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 136
           + R   E   D  L+  +L   +TD+ L   F KY S ++  ++RDK T + +G  FV +
Sbjct: 3   YARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 62
Query: 137 KDPQDFIRANKEMN 150
              ++   A   +N
Sbjct: 63  NKREEAQEAISALN 76

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 22  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
           D +++ G+LGN+     L R F  Y       V R+       GF FV F+DP+D   A 
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 82  KEMNDDFRLFCG 93
           +E+  D R  CG
Sbjct: 128 REL--DGRTLCG 137

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L   + ++ L  TFS + + L  KVV D+  N +KG+GFV F+  +   RA ++M
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 150 NEF----PHLFVGDLKTR 163
           N        +FVG  K+R
Sbjct: 72  NGMLLNDRKVFVGRFKSR 89

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L   + ++ L  TFS + + L  KVV D+  N +KG+GFV F+  +   RA ++M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 150 NEF----PHLFVGDLKTR 163
           N        +FVG  K+R
Sbjct: 66  NGMLLNDRKVFVGRFKSR 83

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          ++E D  +F G+L   V +E+L   F +     K  + +D R  K K FGFV FK P+  
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESV 70
Query: 78 IRANKEMNDDFRLF 91
            A   +N   RL+
Sbjct: 71 SYAIALLN-GIRLY 83

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L    TD  L + F  +    +A V+ D++T K++G+GFV+  D     RA K+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 84 MN 85
           N
Sbjct: 79 PN 80

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 34/62 (54%)
Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L    TD  L + F  +    +A V+ D++T K++G+GFV+  D     RA K+
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 149 MN 150
            N
Sbjct: 79  PN 80

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  ++D +  + A + +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 85 NDDFRLFCG 93
          N   R F G
Sbjct: 71 NG--REFSG 77

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  ++D +  + A + +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 150 N 150
           N
Sbjct: 71  N 71

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 22  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
           D +++ G+LGN+     L R F  Y       V R+       GF FV F+DP+D   A 
Sbjct: 73  DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAV 127
Query: 82  KEMNDDFRLFCG 93
           +++  D R  CG
Sbjct: 128 RDL--DGRTLCG 137

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 37/63 (58%)
Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ G L  ++T+++L   F  +       +++D  T ++KG+GF++F D +   RA +++
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 150 NEF 152
           N F
Sbjct: 68  NGF 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	170
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-37
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-36
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-35
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-19
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-34
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-16
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-33
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-31
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-30
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-30
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-29
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-16
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-11
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	5e-27
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	9e-27
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-26
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-26
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-26
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-15
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-25
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-25
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-25
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-10
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-23
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-23
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-20
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-19
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	5e-16
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	8e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-15
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-15
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	5e-15
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-14
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-14
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-13
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-14
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-12
2div_A	99	TRNA selenocysteine associated protein; structural	2e-13
2div_A	99	TRNA selenocysteine associated protein; structural	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	3e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-13
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	7e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-13
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	8e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	5e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-12
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	8e-13
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-11
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-13
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-12
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-12
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	8e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-11
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-11
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	6e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-12
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-11
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-10
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-10
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-10
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	7e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-10
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	8e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	8e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-10
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-10
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-10
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-08
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-10
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-08
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-09
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	9e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-09
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-09
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	8e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-09
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-09
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-09
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	5e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-09
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	9e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-09
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-08
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-08
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-08
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-08
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-08
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-08
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-08
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-07
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	5e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	9e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-05
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	9e-06
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	9e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-05
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	2e-05
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-05
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-05
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-05
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-04
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-05
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-05
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	4e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	8e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	8e-04

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  126 bits (319), Expect = 2e-37
 Identities = 49/167 (29%), Positives = 75/167 (44%), Gaps = 26/167 (15%)

Query: 7   GPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 66
           GP+ S +  +        L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+
Sbjct: 1   GPLGS-MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59

Query: 67  GFVSFKDPQDFIRANKEMN-----------------------DDFRLFCGDLGNDVTDEL 103
            +V+F+ P D  RA   MN                           +F  +L   + ++ 
Sbjct: 60  AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKA 119

Query: 104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           L  TFS + + L  KVV D   N +KG+GFV F+  +   RA ++MN
Sbjct: 120 LYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164

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

 Score =  122 bits (308), Expect = 4e-36
 Identities = 38/151 (25%), Positives = 62/151 (41%), Gaps = 21/151 (13%)

Query: 21  NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
           ++  L    L  D+TD  L   F         +++RD +T  + G+ FV F    D  RA
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 81  NKEMN---------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKV 119
            K +N                      D  L+  +L   +TD+ L   F KY S ++  +
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121

Query: 120 VRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           +RDK T + +G  FV +   ++   A   +N
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

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

 Score = 75.7 bits (187), Expect = 5e-18
 Identities = 21/75 (28%), Positives = 37/75 (49%)

Query: 11  SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
           S+ +   E   D  L+  +L   +TD+ L   F KY S ++  ++RDK T + +G  FV 
Sbjct: 78  SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137

Query: 71  FKDPQDFIRANKEMN 85
           +   ++   A   +N
Sbjct: 138 YNKREEAQEAISALN 152

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

 Score =  119 bits (301), Expect = 3e-35
 Identities = 42/149 (28%), Positives = 64/149 (42%), Gaps = 24/149 (16%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L+ G+L   +T+++L + F         K++ D + NK   + FV +    D   A + +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 85  N-----------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR 121
           N                       D F LF GDL  +V DE L   F  +PS+L   V+ 
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121

Query: 122 DKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           D +T  ++G+GFVSF    D   A   M 
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150

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

 Score = 79.9 bits (198), Expect = 1e-19
 Identities = 26/72 (36%), Positives = 37/72 (51%)

Query: 14  KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
            +    ++ F LF GDL  +V DE L   F  +PS+L   V+ D +T  ++G+GFVSF  
Sbjct: 79  SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138

Query: 74  PQDFIRANKEMN 85
             D   A   M 
Sbjct: 139 QDDAQNAMDSMQ 150

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

 Score = 59.1 bits (144), Expect = 1e-11
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 24/94 (25%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ G+L   +T+++L + F         K++ D + NK   + FV +    D   A + +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 150 NEFP-----------------------HLFVGDL 160
           N                          +LFVGDL
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDL 95

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  118 bits (297), Expect = 2e-34
 Identities = 37/147 (25%), Positives = 64/147 (43%), Gaps = 21/147 (14%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L    L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 85  N---------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK 123
           N                      D  L+   L   +T + L + FS+Y   + ++++ D+
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124

Query: 124 RTNKTKGFGFVSFKDPQDFIRANKEMN 150
            T  ++G GF+ F    +   A K +N
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLN 151

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 71.8 bits (177), Expect = 1e-16
 Identities = 18/75 (24%), Positives = 37/75 (49%)

Query: 11  SWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVS 70
           S+ + +     D  L+   L   +T + L + FS+Y   + ++++ D+ T  ++G GF+ 
Sbjct: 77  SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136

Query: 71  FKDPQDFIRANKEMN 85
           F    +   A K +N
Sbjct: 137 FDKRIEAEEAIKGLN 151

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 65.7 bits (161), Expect = 2e-14
 Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 21/92 (22%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L    L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 150 NEFP---------------------HLFVGDL 160
           N                        +L+V  L
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGL 96

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

 Score =  115 bits (290), Expect = 6e-33
 Identities = 33/171 (19%), Positives = 65/171 (38%), Gaps = 32/171 (18%)

Query: 14  KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
           ++        R++ G +  ++ ++ + + F+ +       +  D  T K KGF FV ++ 
Sbjct: 20  QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEV 79

Query: 74  PQDFIRANKEMN--------------------------------DDFRLFCGDLGNDVTD 101
           P+    A ++MN                                   R++   +  D++D
Sbjct: 80  PEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSD 139

Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
           + +   F  +     A + RD  T K KG+GF+ ++  Q    A   MN F
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  112 bits (282), Expect = 3e-31
 Identities = 42/173 (24%), Positives = 67/173 (38%), Gaps = 23/173 (13%)

Query: 5   RPGPISSWIKKTCEDENDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT 63
               I S++K   +      RLF G+L  D+T+E   R F +Y    +  + RD+     
Sbjct: 4   FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR----- 58

Query: 64  KGFGFVSFKDPQDFIRANKEMND---------------DFRLFCGDLGNDVTDELLIRTF 108
            GFGF+  +       A  E++                   L   +L   V++ELL + F
Sbjct: 59  -GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAF 117

Query: 109 SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK 161
           S++    KA VV D    +  G GFV F       +A +   +   L     +
Sbjct: 118 SQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPR 169

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

 Score =  110 bits (276), Expect = 3e-30
 Identities = 25/156 (16%), Positives = 50/156 (32%), Gaps = 26/156 (16%)

Query: 20  ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
             D  L   +L   +T +        + S  +  +V  +RT ++KG+GF  +       R
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 80  ANKEMND------------------------DFRLFCGDLGNDVTD-ELLIRTFSKYPSF 114
           A  ++                             L    L     D + L R  S   S 
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 115 LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
              ++   +   + KGF  + ++  +    A ++ +
Sbjct: 213 TFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQAD 247

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

 Score =  109 bits (275), Expect = 5e-30
 Identities = 32/166 (19%), Positives = 59/166 (35%), Gaps = 23/166 (13%)

Query: 4   LRPGPISSWIKKTCEDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK 62
           L P  I   ++ T     + R +    L  DVT++ +    S Y        ++    +K
Sbjct: 3   LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDK 55

Query: 63  TKGFGFVSFKDPQDFIRANKEMN---------------DDFRLFCGDLGNDVTDELLIRT 107
            KG  FV+  + +    A    +                D  L   +L   +T +     
Sbjct: 56  YKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEEL 115

Query: 108 FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
              + S  +  +V  +RT ++KG+GF  +       RA  ++   P
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP 161

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

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 15/97 (15%), Positives = 31/97 (31%), Gaps = 22/97 (22%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
              ++  +  ++    L  DVT++ +    S Y        ++    +K KG  FV+  +
Sbjct: 14  HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLN 66

Query: 139 PQDFIRANKEMN---------------EFPHLFVGDL 160
            +    A    +                   L V +L
Sbjct: 67  GEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANL 103

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 2/69 (2%)

Query: 18  EDENDFRLFCGDLGNDVTD-ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
              +   L    L     D + L R  S   S    ++   +   + KGF  + ++  + 
Sbjct: 180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEM 238

Query: 77  FIRANKEMN 85
              A ++ +
Sbjct: 239 AEEAQQQAD 247

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

 Score =  105 bits (263), Expect = 2e-29
 Identities = 27/152 (17%), Positives = 58/152 (38%), Gaps = 25/152 (16%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKY-----PSFLKAKVVRDKRTNKTKGFGFVSFKDPQD-- 76
           RL+ G++   +T+E ++  F+        +      V   + N+ K F F+ F+   +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 77  -------------FIRANK-----EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAK 118
                         ++  +      +    +LF G L N + D+ +    + +       
Sbjct: 66  QAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 125

Query: 119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           +V+D  T  +KG+ F  + D     +A   +N
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157

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

 Score = 70.7 bits (174), Expect = 4e-16
 Identities = 15/68 (22%), Positives = 28/68 (41%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                 +LF G L N + D+ +    + +       +V+D  T  +KG+ F  + D    
Sbjct: 90  PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149

Query: 78  IRANKEMN 85
            +A   +N
Sbjct: 150 DQAIAGLN 157

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =   99 bits (250), Expect = 2e-27
 Identities = 32/157 (20%), Positives = 58/157 (36%), Gaps = 28/157 (17%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E    F LF G+L  + +   L    S+  +     VV D RT   + FG+V F+  +D 
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDL 67

Query: 78  IRA----------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFL 115
            +A                      +K++     L   +L  ++T++ L   F       
Sbjct: 68  EKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDA---- 123

Query: 116 KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
             ++    +  K+KG  ++ FK   D  +  +E    
Sbjct: 124 -LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 61.5 bits (150), Expect = 1e-12
 Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 14  KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
           + + +      L   +L  ++T++ L   F         ++    +  K+KG  ++ FK 
Sbjct: 91  RDSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKS 145

Query: 74  PQDFIRANKEMN 85
             D  +  +E  
Sbjct: 146 EADAEKNLEEKQ 157

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 56.5 bits (137), Expect = 8e-11
 Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 23/101 (22%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
            E    F LF G+L  + +   L    S+  +     VV D RT   + FG+V F+  +D
Sbjct: 8   SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAED 66

Query: 142 FIRA----------------------NKEMNEFPHLFVGDL 160
             +A                      +K++     L   +L
Sbjct: 67  LEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNL 107

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 97.0 bits (242), Expect = 5e-27
 Identities = 29/69 (42%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
              ++ LF GDL  DV D +L   F K YPS    KVV D+ T  +KG+GFV F D  +
Sbjct: 5  SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELE 63

Query: 77 FIRANKEMN 85
            RA  E  
Sbjct: 64 QKRALTECQ 72

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 96.2 bits (240), Expect = 9e-27
 Identities = 29/72 (40%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           ++     ++ LF GDL  DV D +L   F K YPS    KVV D+ T  +KG+GFV F D
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60

Query: 139 PQDFIRANKEMN 150
             +  RA  E  
Sbjct: 61  ELEQKRALTECQ 72

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 95.7 bits (239), Expect = 1e-26
 Identities = 23/67 (34%), Positives = 37/67 (55%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
            + F +F GDL  ++T   +   F+ +     A+VV+D  T K+KG+GFVSF +  D  
Sbjct: 3  LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 79 RANKEMN 85
           A ++M 
Sbjct: 63 NAIQQMG 69

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 95.3 bits (238), Expect = 1e-26
 Identities = 23/67 (34%), Positives = 37/67 (55%)

Query: 84  MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
           +   F +F GDL  ++T   +   F+ +     A+VV+D  T K+KG+GFVSF +  D  
Sbjct: 3   LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62

Query: 144 RANKEMN 150
            A ++M 
Sbjct: 63  NAIQQMG 69

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 98.1 bits (245), Expect = 1e-26
 Identities = 30/153 (19%), Positives = 61/153 (39%), Gaps = 28/153 (18%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANK 82
           +F G +    +++ L   F +Y +  +  V+RD+  N  ++KG  FV+F   +  + A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 83  EMN-------------------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA 117
            ++                         +D +LF G +    T+  +   FS +    + 
Sbjct: 66  ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125

Query: 118 KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           +++R      ++G  FV+F        A K M+
Sbjct: 126 RILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMH 157

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 60.3 bits (147), Expect = 3e-12
 Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDF 142
           +D  ++F G +    +++ L   F +Y +  +  V+RD+  N  ++KG  FV+F   +  
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 143 IRANKEMNEFPHLFVGDLK 161
           + A   ++    +  G   
Sbjct: 61  LEAQNALHNM-KVLPGMHH 78

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
               D +LF G +    T+  +   FS +    + +++R      ++G  FV+F      
Sbjct: 91  NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMA 149

Query: 78  IRANKEMN 85
             A K M+
Sbjct: 150 QTAIKAMH 157

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

 Score = 98.1 bits (245), Expect = 1e-25
 Identities = 14/139 (10%), Positives = 37/139 (26%), Gaps = 15/139 (10%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           +   +L        + + F      +   V       K   F  + F      + A  + 
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101

Query: 85  N-------------DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 131
           +              +  L+  +     T   +            +  +   R N ++ F
Sbjct: 102 HKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF 161

Query: 132 GFVSFKDPQDFIRANKEMN 150
            ++     +D     +++N
Sbjct: 162 AYIDVTSKEDARYCVEKLN 180

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

 Score = 93.9 bits (234), Expect = 5e-24
 Identities = 21/167 (12%), Positives = 51/167 (30%), Gaps = 31/167 (18%)

Query: 14  KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
           +       +  L+  +     T   +            +  +   R N ++ F ++    
Sbjct: 109 EIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTS 168

Query: 74  PQDFIRANKEMND----------------------------DFRLFCGDLGNDVTDELLI 105
            +D     +++N                                +   +L  ++ DE L+
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLL 228

Query: 106 R-TFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEMN 150
           R +F  + S  K  +   ++  +      F+ F++     RA  +MN
Sbjct: 229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA-LQMN 274

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

 Score = 95.1 bits (237), Expect = 3e-25
 Identities = 28/172 (16%), Positives = 57/172 (33%), Gaps = 45/172 (26%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKY-----PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           RL+ G++   +T+E ++  F+        +      V   + N+ K F F+ F+   +  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 79  RA----------------------------------------NKEMNDDFRLFCGDLGND 98
           +A                                            +   +LF G L N 
Sbjct: 66  QAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 99  VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           + D+ +    + +       +V+D  T  +KG+ F  + D     +A   +N
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177

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

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 17/81 (20%), Positives = 33/81 (40%)

Query: 5   RPGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 64
            P      +  T   ++  +LF G L N + D+ +    + +       +V+D  T  +K
Sbjct: 97  NPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156

Query: 65  GFGFVSFKDPQDFIRANKEMN 85
           G+ F  + D     +A   +N
Sbjct: 157 GYAFCEYVDINVTDQAIAGLN 177

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 92.4 bits (230), Expect = 4e-25
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +  N F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D 
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70

Query: 78 IRANKEMN 85
            A ++M 
Sbjct: 71 ENAIQQMG 78

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 91.6 bits (228), Expect = 9e-25
 Identities = 25/69 (36%), Positives = 41/69 (59%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           K+ ++ F +F GDL  ++T E +   F+ +     A+VV+D  T K+KG+GFVSF +  D
Sbjct: 10  KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69

Query: 142 FIRANKEMN 150
              A ++M 
Sbjct: 70  AENAIQQMG 78

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 93.0 bits (232), Expect = 9e-25
 Identities = 36/140 (25%), Positives = 67/140 (47%), Gaps = 19/140 (13%)

Query: 20  ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           +   ++F G L  D T++ L   F KY +    K+++D  T +++GFGF+SF+ P     
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 80  A-------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVV 120
                                 E +   ++F G +G DV  +     FS++ + + A+++
Sbjct: 61  VVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120

Query: 121 RDKRTNKTKGFGFVSFKDPQ 140
            DK T +++GFGFV++    
Sbjct: 121 LDKDTGQSRGFGFVTYDSAD 140

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E +   ++F G +G DV  +     FS++ + + A+++ DK T +++GFGFV++      
Sbjct: 83  EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA- 141

Query: 78  IRANKEMNDDFRLFCG 93
              ++   + F  F  
Sbjct: 142 --VDRVCQNKFIDFKD 155

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 55.2 bits (134), Expect = 2e-10
 Identities = 20/66 (30%), Positives = 35/66 (53%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           +  ++F G L  D T++ L   F KY +    K+++D  T +++GFGF+SF+ P      
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 146 NKEMNE 151
            K  + 
Sbjct: 62  VKTQHI 67

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 85.6 bits (213), Expect = 8e-23
 Identities = 26/63 (41%), Positives = 34/63 (53%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          F LF GDL  +V DE L   F  +PS+L   V+ D +T  ++G+GFVSF    D   A  
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 83 EMN 85
           M 
Sbjct: 62 SMQ 64

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 85.6 bits (213), Expect = 8e-23
 Identities = 26/63 (41%), Positives = 34/63 (53%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           F LF GDL  +V DE L   F  +PS+L   V+ D +T  ++G+GFVSF    D   A  
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 148 EMN 150
            M 
Sbjct: 62  SMQ 64

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 86.6 bits (215), Expect = 7e-22
 Identities = 35/149 (23%), Positives = 60/149 (40%), Gaps = 26/149 (17%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68

Query: 78  IRA--------------------------NKEMNDDFRLFCGDLGNDVTDELLIRTFSKY 111
             A                                  ++F G +  D  +  L   F +Y
Sbjct: 69  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128

Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
                 +++ D+ + K +GF FV+F D  
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           KE     +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++
Sbjct: 8   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67

Query: 142 FIRANKEMNEFPH 154
               +  MN  PH
Sbjct: 68  ---VDAAMNARPH 77

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 80.4 bits (199), Expect = 1e-20
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E    F LF G+L  + +   L    S+  +      V D RT   + FG+V F+  +D 
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDL 71

Query: 78 IRANKEMN 85
           +A  E+ 
Sbjct: 72 EKA-LELT 78

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 77.7 bits (192), Expect = 2e-19
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
             F LF G+L  + +   L    S+  +      V D RT   + FG+V F+  +D  +A
Sbjct: 16  TPFNLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEKA 74

Query: 146 NKEMN 150
             E+ 
Sbjct: 75  -LELT 78

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 78.6 bits (194), Expect = 1e-19
 Identities = 28/71 (39%), Positives = 37/71 (52%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
            E  +   LF   L  + TD  L  TF  + + + AKV  DK+T+ +K FGFVSF +P  
Sbjct: 35  IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94

Query: 142 FIRANKEMNEF 152
              A K MN F
Sbjct: 95  AQVAIKAMNGF 105

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 77.8 bits (192), Expect = 2e-19
 Identities = 27/68 (39%), Positives = 35/68 (51%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E      LF   L  + TD  L  TF  + + + AKV  DK+T+ +K FGFVSF +P   
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95

Query: 78  IRANKEMN 85
             A K MN
Sbjct: 96  QVAIKAMN 103

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 70.8 bits (174), Expect = 1e-16
 Identities = 24/63 (38%), Positives = 36/63 (57%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P     A + M
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 150 NEF 152
           N F
Sbjct: 88  NGF 90

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 69.7 bits (171), Expect = 3e-16
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P     A + M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 85 N 85
          N
Sbjct: 88 N 88

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 68.9 bits (169), Expect = 5e-16
 Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
           E +   +LF G L  +  +++L   F K+    +  +++D RT+K++GF F++F++P D 
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61

Query: 143 IRANKEMN 150
             A K+MN
Sbjct: 62  KNAAKDMN 69

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 68.5 bits (168), Expect = 8e-16
 Identities = 22/68 (32%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E ++  +LF G L  +  +++L   F K+    +  +++D RT+K++GF F++F++P D 
Sbjct: 3  EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61

Query: 78 IRANKEMN 85
            A K+MN
Sbjct: 62 KNAAKDMN 69

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 68.4 bits (168), Expect = 7e-16
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 70  SFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 129
           S     D I   + +N    L+  +L + + DE L + FS + +   AKV+ +    ++K
Sbjct: 2   SSGSSGDRITRYQVVN----LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSK 55

Query: 130 GFGFVSFKDPQDFIRANKEMN 150
           GFGFV F  P++  +A  EMN
Sbjct: 56  GFGFVCFSSPEEATKAVTEMN 76

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 67.2 bits (165), Expect = 2e-15
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
               L+  +L + + DE L + FS + +   AKV+ +    ++KGFGFV F  P++  +
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATK 70

Query: 80 ANKEMN 85
          A  EMN
Sbjct: 71 AVTEMN 76

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

 Score = 68.7 bits (168), Expect = 1e-15
 Identities = 20/74 (27%), Positives = 31/74 (41%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
            +         L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+ 
Sbjct: 55  GSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 114

Query: 139 PQDFIRANKEMNEF 152
            +D   A   MNE 
Sbjct: 115 AEDAAAAIDNMNES 128

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

 Score = 67.5 bits (165), Expect = 4e-15
 Identities = 19/68 (27%), Positives = 29/68 (42%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                  L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D 
Sbjct: 59  SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118

Query: 78  IRANKEMN 85
             A   MN
Sbjct: 119 AAAIDNMN 126

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 67.2 bits (165), Expect = 1e-15
 Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFI 143
           +    +F G+L  ++ ++LL  TFS +   L+  K++RD  T  +KG+ F++F       
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 144 RANKEMN 150
            A + MN
Sbjct: 63  AAIEAMN 69

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 67.2 bits (165), Expect = 1e-15
 Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
              +F G+L  ++ ++LL  TFS +   L+  K++RD  T  +KG+ F++F        
Sbjct: 4  GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 80 ANKEMN 85
          A + MN
Sbjct: 64 AIEAMN 69

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

 Score = 66.8 bits (164), Expect = 2e-15
 Identities = 20/64 (31%), Positives = 29/64 (45%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+   L    TD+ L++    Y   +  K + DK TNK KG+GFV F  P    +A   
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 149 MNEF 152
           +   
Sbjct: 67  LKAS 70

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

 Score = 65.6 bits (161), Expect = 4e-15
 Identities = 20/62 (32%), Positives = 29/62 (46%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+   L    TD+ L++    Y   +  K + DK TNK KG+GFV F  P    +A   
Sbjct: 7  GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 84 MN 85
          + 
Sbjct: 67 LK 68

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

 Score = 67.3 bits (165), Expect = 3e-15
 Identities = 12/65 (18%), Positives = 29/65 (44%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+  +L   VT+  L+  F+++       +     T + +G  F++F + +   +A   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 149 MNEFP 153
           +N + 
Sbjct: 87  VNGYK 91

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

 Score = 65.0 bits (159), Expect = 2e-14
 Identities = 12/62 (19%), Positives = 28/62 (45%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+  +L   VT+  L+  F+++       +     T + +G  F++F + +   +A   
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 84 MN 85
          +N
Sbjct: 87 VN 88

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 67.6 bits (165), Expect = 5e-15
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 19  DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
              D +++ G+LGN+     L R F  Y       V R+       GF FV F+DP+D  
Sbjct: 70  CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAA 124

Query: 79  RANKEMN 85
            A +E++
Sbjct: 125 DAVRELD 131

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 67.2 bits (164), Expect = 5e-15
 Identities = 26/109 (23%), Positives = 40/109 (36%), Gaps = 7/109 (6%)

Query: 44  SKYPSFLKAKVVRDKRTNK--TKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTD 101
             +  +     V  + T    TK F                    D +++ G+LGN+   
Sbjct: 28  KVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK 87

Query: 102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
             L R F  Y       V R+       GF FV F+DP+D   A +E++
Sbjct: 88  TELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRELD 131

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

 Score = 67.1 bits (164), Expect = 5e-15
 Identities = 19/74 (25%), Positives = 34/74 (45%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           + N E +    L    +   V +  L + F +Y      K+V D+ T +++G+GFV F+ 
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93

Query: 139 PQDFIRANKEMNEF 152
                +A   +N F
Sbjct: 94  GSSAQQAIAGLNGF 107

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

 Score = 64.8 bits (158), Expect = 3e-14
 Identities = 17/68 (25%), Positives = 31/68 (45%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E +    L    +   V +  L + F +Y      K+V D+ T +++G+GFV F+     
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 78  IRANKEMN 85
            +A   +N
Sbjct: 98  QQAIAGLN 105

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

 Score = 65.3 bits (160), Expect = 8e-15
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
               +   D  +F G+L   V +E+L   F +     K  + +D R  K K FGFV FK 
Sbjct: 8   MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKH 66

Query: 139 PQDFIRANKEMN 150
           P+    A   +N
Sbjct: 67  PESVSYAIALLN 78

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

 Score = 65.3 bits (160), Expect = 8e-15
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          ++E D  +F G+L   V +E+L   F +     K  + +D R  K K FGFV FK P+  
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESV 70

Query: 78 IRANKEMN 85
            A   +N
Sbjct: 71 SYAIALLN 78

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

 Score = 65.4 bits (160), Expect = 1e-14
 Identities = 20/68 (29%), Positives = 34/68 (50%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
           E N D  ++ G L   V++ LL   F +    +   + +D+ T + +G+GFV F   +D 
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 143 IRANKEMN 150
             A K M+
Sbjct: 71  DYAIKIMD 78

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

 Score = 65.0 bits (159), Expect = 1e-14
 Identities = 19/68 (27%), Positives = 33/68 (48%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E   D  ++ G L   V++ LL   F +    +   + +D+ T + +G+GFV F   +D 
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70

Query: 78 IRANKEMN 85
            A K M+
Sbjct: 71 DYAIKIMD 78

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 65.3 bits (160), Expect = 1e-14
 Identities = 25/68 (36%), Positives = 40/68 (58%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
             +D+ +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++  D 
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67

Query: 143 IRANKEMN 150
             A   MN
Sbjct: 68  KDAMMAMN 75

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 63.8 bits (156), Expect = 4e-14
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
             ++ +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++  D 
Sbjct: 8  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67

Query: 78 IRANKEMN 85
            A   MN
Sbjct: 68 KDAMMAMN 75

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

 Score = 63.7 bits (156), Expect = 2e-14
 Identities = 20/68 (29%), Positives = 30/68 (44%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
                L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D   
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 145 ANKEMNEF 152
           A   MNE 
Sbjct: 65  AIDNMNES 72

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

 Score = 62.2 bits (152), Expect = 1e-13
 Identities = 19/67 (28%), Positives = 30/67 (44%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
               L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D   
Sbjct: 5  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 80 ANKEMND 86
          A   MN+
Sbjct: 65 AIDNMNE 71

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

 Score = 63.0 bits (154), Expect = 6e-14
 Identities = 19/72 (26%), Positives = 35/72 (48%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
             N+  +D+  +   +L  D  +  L   F  + S  +  + +DK T ++KGF F+SF  
Sbjct: 7   GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66

Query: 139 PQDFIRANKEMN 150
            +D  RA   ++
Sbjct: 67  REDAARAIAGVS 78

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

 Score = 59.9 bits (146), Expect = 1e-12
 Identities = 17/68 (25%), Positives = 33/68 (48%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
            +++  +   +L  D  +  L   F  + S  +  + +DK T ++KGF F+SF   +D 
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70

Query: 78 IRANKEMN 85
           RA   ++
Sbjct: 71 ARAIAGVS 78

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

 Score = 65.1 bits (158), Expect = 2e-13
 Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 2/64 (3%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
            L+ G+L    TDE L            L+ K   ++   ++KGF  V         +  
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 82  KEMN 85
             + 
Sbjct: 130 DLLP 133

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

 Score = 65.1 bits (158), Expect = 2e-13
 Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 2/64 (3%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
            L+ G+L    TDE L            L+ K   ++   ++KGF  V         +  
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 147 KEMN 150
             + 
Sbjct: 130 DLLP 133

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

 Score = 62.3 bits (152), Expect = 2e-13
 Identities = 13/68 (19%), Positives = 36/68 (52%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +D +  +LF G +  ++ ++ L   F ++    +  V++D+ T   KG  F+++ + +  
Sbjct: 9  KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68

Query: 78 IRANKEMN 85
          ++A   ++
Sbjct: 69 LKAQSALH 76

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

 Score = 60.8 bits (148), Expect = 5e-13
 Identities = 14/66 (21%), Positives = 35/66 (53%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           D  +LF G +  ++ ++ L   F ++    +  V++D+ T   KG  F+++ + +  ++A
Sbjct: 12  DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Query: 146 NKEMNE 151
              ++E
Sbjct: 72  QSALHE 77

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

 Score = 62.8 bits (153), Expect = 2e-13
 Identities = 23/107 (21%), Positives = 41/107 (38%)

Query: 44  SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDEL 103
           S +     + +V       +   G    +    + R   ++     L   +L    + + 
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDT 63

Query: 104 LIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
           L R F KY       + RD+ T +++GF FV F D +D   A   M+
Sbjct: 64  LRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 110

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

 Score = 59.8 bits (145), Expect = 3e-12
 Identities = 20/68 (29%), Positives = 31/68 (45%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           + E    L   +L    + + L R F KY       + RD+ T +++GF FV F D +D 
Sbjct: 43  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102

Query: 78  IRANKEMN 85
             A   M+
Sbjct: 103 EDAMDAMD 110

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 63.3 bits (154), Expect = 2e-13
 Identities = 19/72 (26%), Positives = 32/72 (44%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
             + ++     L   +L    + + L R F KY       + RD+ T +++GF FV F D
Sbjct: 62  HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121

Query: 139 PQDFIRANKEMN 150
            +D   A   M+
Sbjct: 122 KRDAEDAMDAMD 133

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 61.4 bits (149), Expect = 1e-12
 Identities = 20/68 (29%), Positives = 31/68 (45%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           + E    L   +L    + + L R F KY       + RD+ T +++GF FV F D +D 
Sbjct: 66  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125

Query: 78  IRANKEMN 85
             A   M+
Sbjct: 126 EDAMDAMD 133

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 62.0 bits (151), Expect = 2e-13
 Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
                 L+ GDL   + +  + R F+    + +  K++R++ T    G+ FV F D   
Sbjct: 5  SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64

Query: 77 FIRANKEMN 85
            +   ++N
Sbjct: 65 AEKCLHKIN 73

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 61.6 bits (150), Expect = 2e-13
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           L+ GDL   + +  + R F+    + +  K++R++ T    G+ FV F D     +   +
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 149 MN 150
           +N
Sbjct: 72  IN 73

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

 Score = 61.4 bits (150), Expect = 2e-13
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
          + +  L    L    T+  L   FSKY       +V D+++ +++GF FV F++  D   
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72

Query: 80 ANKEMN 85
          A +  N
Sbjct: 73 AKERAN 78

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

 Score = 61.4 bits (150), Expect = 3e-13
 Identities = 18/66 (27%), Positives = 31/66 (46%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           + +  L    L    T+  L   FSKY       +V D+++ +++GF FV F++  D   
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72

Query: 145 ANKEMN 150
           A +  N
Sbjct: 73  AKERAN 78

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

 Score = 61.1 bits (149), Expect = 3e-13
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +D     L+ G+L  DVT+ L+++ FS+       K++ +  +N    + FV F + +D 
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDA 68

Query: 78 IRANKEMN 85
            A   MN
Sbjct: 69 AAALAAMN 76

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

 Score = 60.7 bits (148), Expect = 6e-13
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
            ++      L+ G+L  DVT+ L+++ FS+       K++ +  +N    + FV F + +
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHR 66

Query: 141 DFIRANKEMN 150
           D   A   MN
Sbjct: 67  DAAAALAAMN 76

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

 Score = 61.1 bits (149), Expect = 3e-13
 Identities = 20/69 (28%), Positives = 30/69 (43%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
                  L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D 
Sbjct: 8   MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 143 IRANKEMNE 151
             A   MNE
Sbjct: 68  AAAIDNMNE 76

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

 Score = 60.3 bits (147), Expect = 7e-13
 Identities = 19/69 (27%), Positives = 30/69 (43%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                 L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D 
Sbjct: 8  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 78 IRANKEMND 86
            A   MN+
Sbjct: 68 AAAIDNMNE 76

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 61.5 bits (150), Expect = 4e-13
 Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +F  +L   + ++ L  TFS + + L  KVV D   N +KG+GFV F+  +   RA ++M
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 85 N 85
          N
Sbjct: 66 N 66

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 61.5 bits (150), Expect = 4e-13
 Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +F  +L   + ++ L  TFS + + L  KVV D   N +KG+GFV F+  +   RA ++M
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 150 N 150
           N
Sbjct: 66  N 66

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

 Score = 60.7 bits (148), Expect = 4e-13
 Identities = 19/67 (28%), Positives = 32/67 (47%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
               ++  +L   +T+  L R FSKY   +K  +++DK T K+KG  F+ F D       
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

Query: 146 NKEMNEF 152
            + +N  
Sbjct: 75  TRAINNK 81

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

 Score = 60.7 bits (148), Expect = 5e-13
 Identities = 19/68 (27%), Positives = 33/68 (48%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
             +   ++  +L   +T+  L R FSKY   +K  +++DK T K+KG  F+ F D    
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71

Query: 78 IRANKEMN 85
              + +N
Sbjct: 72 QNCTRAIN 79

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 61.2 bits (149), Expect = 4e-13
 Identities = 14/83 (16%), Positives = 27/83 (32%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
            ++ +   +F  +L  D  +E L     ++      +VV    T  +KG  F  F   + 
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69

Query: 142 FIRANKEMNEFPHLFVGDLKTRS 164
             +     +         L  R 
Sbjct: 70  AQKCLAAASLEAEGGGLKLDGRQ 92

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 59.7 bits (145), Expect = 2e-12
 Identities = 13/80 (16%), Positives = 25/80 (31%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +      +F  +L  D  +E L     ++      +VV    T  +KG  F  F   +  
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 78 IRANKEMNDDFRLFCGDLGN 97
           +     + +       L  
Sbjct: 71 QKCLAAASLEAEGGGLKLDG 90

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

 Score = 61.3 bits (149), Expect = 4e-13
 Identities = 12/62 (19%), Positives = 23/62 (37%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           +    L ++V +  L     KY    + +++   RT K  G   V F   +      K 
Sbjct: 8  EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 84 MN 85
          ++
Sbjct: 68 LH 69

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

 Score = 61.3 bits (149), Expect = 4e-13
 Identities = 12/62 (19%), Positives = 23/62 (37%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +    L ++V +  L     KY    + +++   RT K  G   V F   +      K 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 149 MN 150
           ++
Sbjct: 68  LH 69

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

 Score = 61.1 bits (149), Expect = 4e-13
 Identities = 18/72 (25%), Positives = 30/72 (41%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
            +  +++    L   +L    + + L R F KY       + R+  T   +GF FV F D
Sbjct: 5   SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64

Query: 139 PQDFIRANKEMN 150
            +D   A   M+
Sbjct: 65  RRDAQDAEAAMD 76

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

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 18/68 (26%), Positives = 28/68 (41%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          + +    L   +L    + + L R F KY       + R+  T   +GF FV F D +D 
Sbjct: 9  DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 78 IRANKEMN 85
            A   M+
Sbjct: 69 QDAEAAMD 76

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

 Score = 61.7 bits (150), Expect = 4e-13
 Identities = 18/72 (25%), Positives = 31/72 (43%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
                 + +  L    L    T+  L   FSKY       +V D+++ +++GF FV F++
Sbjct: 38  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97

Query: 139 PQDFIRANKEMN 150
             D   A +  N
Sbjct: 98  VDDAKEAKERAN 109

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

 Score = 60.9 bits (148), Expect = 8e-13
 Identities = 18/62 (29%), Positives = 29/62 (46%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
            L    L    T+  L   FSKY       +V D+++ +++GF FV F++  D   A + 
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 84  MN 85
            N
Sbjct: 108 AN 109

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 60.3 bits (147), Expect = 5e-13
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 78  IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
           I A+K   D  ++F G L  D + + L   F+K+   +   +  D  T +++GFGF+ FK
Sbjct: 2   INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61

Query: 138 DPQDFIRANKEMNEFPH 154
           D        K +++  H
Sbjct: 62  DAAS---VEKVLDQKEH 75

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 58.0 bits (141), Expect = 4e-12
 Identities = 18/73 (24%), Positives = 35/73 (47%)

Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
          I  +  +E+  ++F G L  D + + L   F+K+   +   +  D  T +++GFGF+ FK
Sbjct: 2  INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61

Query: 73 DPQDFIRANKEMN 85
          D     +   +  
Sbjct: 62 DAASVEKVLDQKE 74

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 60.3 bits (147), Expect = 8e-13
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
             N   ++  +LF G L    T E L   FS+Y   +   +++DK TN+++GFGFV FKD
Sbjct: 8   MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

Query: 139 PQDFIRANKEMNEFPH 154
           P         +   PH
Sbjct: 68  PNC---VGTVLASRPH 80

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 57.2 bits (139), Expect = 1e-11
 Identities = 23/59 (38%), Positives = 33/59 (55%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
            +   +LF G L    T E L   FS+Y   +   +++DK TN+++GFGFV FKDP  
Sbjct: 12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70

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

 Score = 60.0 bits (146), Expect = 9e-13
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDFIRA 145
            LF  +L    T+E L   FSK  +     + + K         GFGFV +K P+   +A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 146 NKEMNEF 152
            K++   
Sbjct: 67  LKQLQGH 73

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

 Score = 60.0 bits (146), Expect = 9e-13
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDFIRA 80
           LF  +L    T+E L   FSK  +     + + K         GFGFV +K P+   +A
Sbjct: 7  GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 81 NKEMN 85
           K++ 
Sbjct: 67 LKQLQ 71

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

 Score = 60.0 bits (146), Expect = 1e-12
 Identities = 19/74 (25%), Positives = 39/74 (52%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
              K      RL+ G L  ++T+++L   F  +      +++ D  T ++KG+GF++F D
Sbjct: 18  NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77

Query: 139 PQDFIRANKEMNEF 152
            +   +A +++N F
Sbjct: 78  SECAKKALEQLNGF 91

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

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 17/69 (24%), Positives = 37/69 (53%)

Query: 17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
                 RL+ G L  ++T+++L   F  +      +++ D  T ++KG+GF++F D + 
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80

Query: 77 FIRANKEMN 85
            +A +++N
Sbjct: 81 AKKALEQLN 89

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

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 15/64 (23%), Positives = 34/64 (53%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            ++ G +  D T+E ++   S     +  K++ D +T ++KG+ F+ F+D +    A + 
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 149 MNEF 152
           +N +
Sbjct: 64  LNGY 67

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

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 15/62 (24%), Positives = 33/62 (53%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           ++ G +  D T+E ++   S     +  K++ D +T ++KG+ F+ F+D +    A + 
Sbjct: 4  VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 84 MN 85
          +N
Sbjct: 64 LN 65

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 59.6 bits (145), Expect = 2e-12
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           R  +E     +LF G L  + T+E L   + ++       V+RD  + +++GFGFV+F  
Sbjct: 19  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78

Query: 139 PQDFIRANKEMNEFPH 154
             +    +  M   PH
Sbjct: 79  MAE---VDAAMAARPH 91

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 55.4 bits (134), Expect = 8e-11
 Identities = 18/59 (30%), Positives = 31/59 (52%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          E E   +LF G L  + T+E L   + ++       V+RD  + +++GFGFV+F    +
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 60.3 bits (146), Expect = 2e-12
 Identities = 11/81 (13%), Positives = 26/81 (32%), Gaps = 2/81 (2%)

Query: 74  PQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGF 131
           P      +   N    ++ G      TD+ LI+          ++ K   ++   ++KG+
Sbjct: 42  PAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGY 101

Query: 132 GFVSFKDPQDFIRANKEMNEF 152
             V         +  + +   
Sbjct: 102 AEVVVASENSVHKLLELLPGK 122

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 58.0 bits (140), Expect = 2e-11
 Identities = 9/65 (13%), Positives = 23/65 (35%), Gaps = 2/65 (3%)

Query: 23  FRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
             ++ G      TD+ LI+          ++ K   ++   ++KG+  V         + 
Sbjct: 56  AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115

Query: 81  NKEMN 85
            + + 
Sbjct: 116 LELLP 120

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 58.8 bits (143), Expect = 3e-12
 Identities = 17/72 (23%), Positives = 32/72 (44%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
             + +     L    L    T++ L   FS +   L  +V +D +T  +KGFGFV F + 
Sbjct: 8   VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67

Query: 140 QDFIRANKEMNE 151
           +  ++   + + 
Sbjct: 68  ETQVKVMSQRHM 79

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.9 bits (138), Expect = 2e-11
 Identities = 17/68 (25%), Positives = 31/68 (45%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
            +    L    L    T++ L   FS +   L  +V +D +T  +KGFGFV F + +  
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70

Query: 78 IRANKEMN 85
          ++   + +
Sbjct: 71 VKVMSQRH 78

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

 Score = 58.5 bits (142), Expect = 3e-12
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 25 LFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          +   ++      + ++   S Y   +    ++++DK+T + +GF FV      D  +  +
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 83 EMNDDFRLFCGD 94
           +         D
Sbjct: 72 ILQSLHPPLKID 83

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

 Score = 57.7 bits (140), Expect = 6e-12
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 90  LFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           +   ++      + ++   S Y   +    ++++DK+T + +GF FV      D  +  +
Sbjct: 12  IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 148 EMNEFPHLFVGD 159
            +         D
Sbjct: 72  ILQSLHPPLKID 83

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.8 bits (143), Expect = 4e-12
 Identities = 22/68 (32%), Positives = 36/68 (52%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +D    ++F G L    TD  L + F  +    +A V+ D++T K++G+GFV+  D    
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72

Query: 78 IRANKEMN 85
           RA K+ N
Sbjct: 73 ERACKDPN 80

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 57.3 bits (139), Expect = 2e-11
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
            +++     ++F G L    TD  L + F  +    +A V+ D++T K++G+GFV+  D 
Sbjct: 10  GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 69

Query: 140 QDFIRANKEMN 150
               RA K+ N
Sbjct: 70  AAAERACKDPN 80

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

 Score = 58.3 bits (142), Expect = 4e-12
 Identities = 18/64 (28%), Positives = 37/64 (57%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+ G L  ++T+++L   F  +       +++D  T ++KG+GF++F D +   RA ++
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 149 MNEF 152
           +N F
Sbjct: 67  LNGF 70

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

 Score = 57.6 bits (140), Expect = 6e-12
 Identities = 17/62 (27%), Positives = 36/62 (58%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+ G L  ++T+++L   F  +       +++D  T ++KG+GF++F D +   RA ++
Sbjct: 7  GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 84 MN 85
          +N
Sbjct: 67 LN 68

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

 Score = 58.0 bits (141), Expect = 5e-12
 Identities = 21/62 (33%), Positives = 32/62 (51%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF  +L    ++E L + FS Y    +     D  T K KGF FV+F  P+  ++A  E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 84 MN 85
          ++
Sbjct: 70 VD 71

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

 Score = 58.0 bits (141), Expect = 5e-12
 Identities = 21/62 (33%), Positives = 32/62 (51%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           RLF  +L    ++E L + FS Y    +     D  T K KGF FV+F  P+  ++A  E
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 149 MN 150
           ++
Sbjct: 70  VD 71

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

 Score = 58.5 bits (142), Expect = 6e-12
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
            A +       +F  +L   V  + L   FS     ++A ++ D +  K++G G V+F+ 
Sbjct: 7   GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQ 65

Query: 139 PQDFIRANKEMN 150
             + ++A    N
Sbjct: 66  SIEAVQAISMFN 77

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

 Score = 58.1 bits (141), Expect = 7e-12
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
               +F  +L   V  + L   FS     ++A ++ D +  K++G G V+F+   + ++
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQ 71

Query: 80 ANKEMN 85
          A    N
Sbjct: 72 AISMFN 77

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 57.3 bits (139), Expect = 1e-11
 Identities = 21/83 (25%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 73  DPQDFIRANKEMNDDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 131
                +     M      +F G L    T E L   F ++    +  V+RD  T +++GF
Sbjct: 10  HSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGF 69

Query: 132 GFVSFKDPQDFIRANKEMNEFPH 154
           GFV+F D       +K + +  H
Sbjct: 70  GFVTFMDQAG---VDKVLAQSRH 89

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 53.4 bits (129), Expect = 4e-10
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
             +  ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D    
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG- 79

Query: 78 IRANKEMNDDF 88
             +K +    
Sbjct: 80 --VDKVLAQSR 88

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 56.8 bits (138), Expect = 2e-11
 Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           +    +   ++F G + ++  +  L   F K+    +  ++ D    + +GFGF++F+D 
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 140 QDFIRANKEMNEFPHLFVG 158
           Q     ++ +N   H  +G
Sbjct: 63  QS---VDQAVNMHFHDIMG 78

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 56.0 bits (136), Expect = 3e-11
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                ++F G + ++  +  L   F K+    +  ++ D    + +GFGF++F+D Q  
Sbjct: 6  SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS- 64

Query: 78 IRANKEMNDDFRLFCG 93
             ++ +N  F    G
Sbjct: 65 --VDQAVNMHFHDIMG 78

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

 Score = 56.9 bits (138), Expect = 2e-11
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
            +    LF   L  D T+E L  +F      ++A++V D+ T  +KGFGFV F   +D 
Sbjct: 11 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDA 67

Query: 78 IRANKEMND 86
            A + M D
Sbjct: 68 KAAKEAMED 76

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

 Score = 56.5 bits (137), Expect = 2e-11
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           N        LF   L  D T+E L  +F      ++A++V D+ T  +KGFGFV F   +
Sbjct: 9   NARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEE 65

Query: 141 DFIRANKEMN 150
           D   A + M 
Sbjct: 66  DAKAAKEAME 75

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.9 bits (138), Expect = 2e-11
 Identities = 9/68 (13%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          ++++   L+  +L   + ++ L      +   +  +++RD  +  ++G GF   +  +  
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKC 79

Query: 78 IRANKEMN 85
                 N
Sbjct: 80 EAVIGHFN 87

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.5 bits (137), Expect = 3e-11
 Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+  +L   + ++ L      +   +  +++RD  +  ++G GF   +  +         
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86

Query: 150 N 150
           N
Sbjct: 87  N 87

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

 Score = 56.1 bits (136), Expect = 3e-11
 Identities = 19/68 (27%), Positives = 37/68 (54%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
          D +   +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  ++D +  +
Sbjct: 5  DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 79 RANKEMND 86
           A + +N 
Sbjct: 65 SAMRNLNG 72

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

 Score = 55.7 bits (135), Expect = 5e-11
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  ++D +  + A + 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 149 MNEF 152
           +N  
Sbjct: 70  LNGR 73

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 56.1 bits (136), Expect = 3e-11
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 89

Query: 149 MNEFP 153
            N  P
Sbjct: 90  YNGVP 94

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 56.1 bits (136), Expect = 3e-11
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 89

Query: 84 MN 85
           N
Sbjct: 90 YN 91

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 55.2 bits (134), Expect = 4e-11
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D       +K 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG---VDKV 58

Query: 149 MNEFPH 154
           + +  H
Sbjct: 59  LAQSRH 64

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 52.5 bits (127), Expect = 4e-10
 Identities = 18/53 (33%), Positives = 28/53 (52%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D   
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 54

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 55.7 bits (135), Expect = 4e-11
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F G +   + +  +   F++Y S  + K++ D RT  +KG+GFVSF +  D  +  + 
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69

Query: 149 MNEF 152
              F
Sbjct: 70  QINF 73

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 53.8 bits (130), Expect = 3e-10
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           +F G +   + +  +   F++Y S  + K++ D RT  +KG+GFVSF +  D  +  + 
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69

Query: 84 MND 86
            +
Sbjct: 70 QIN 72

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

 Score = 55.4 bits (134), Expect = 6e-11
 Identities = 17/72 (23%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           ++  +   RL   ++     D  L + F ++   L  +++ ++R +  KGFGFV+F++  
Sbjct: 9   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSA 66

Query: 141 DFIRANKEMNEF 152
           D  RA ++++  
Sbjct: 67  DADRAREKLHGT 78

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

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RL   ++     D  L + F ++   L  +++ ++R +  KGFGFV+F++  D  RA ++
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREK 74

Query: 84 MN 85
          ++
Sbjct: 75 LH 76

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

 Score = 54.9 bits (133), Expect = 7e-11
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +L+ G+L   VT + L + F         K+    +     G+ FV + D    IRA + 
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 84 MNDDFRLF 91
          ++    L 
Sbjct: 64 LSGKVELH 71

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

 Score = 53.4 bits (129), Expect = 2e-10
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +L+ G+L   VT + L + F         K+    +     G+ FV + D    IRA + 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 149 MNEFPHLF 156
           ++    L 
Sbjct: 64  LSGKVELH 71

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 55.8 bits (135), Expect = 7e-11
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95

Query: 149 MNEFP 153
               P
Sbjct: 96  YKGVP 100

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 55.5 bits (134), Expect = 1e-10
 Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95

Query: 84 MN 85
            
Sbjct: 96 YK 97

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

 Score = 56.4 bits (136), Expect = 8e-11
 Identities = 19/70 (27%), Positives = 28/70 (40%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
            K +     L+ G+L    T+E +   FSK     K  +  DK      GF FV +    
Sbjct: 33  EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 92

Query: 141 DFIRANKEMN 150
           D   A + +N
Sbjct: 93  DAENAMRYIN 102

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

 Score = 55.6 bits (134), Expect = 1e-10
 Identities = 18/62 (29%), Positives = 26/62 (41%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
            L+ G+L    T+E +   FSK     K  +  DK      GF FV +    D   A + 
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 84  MN 85
           +N
Sbjct: 101 IN 102

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

 Score = 55.0 bits (133), Expect = 8e-11
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
              K      RLF G+L  D+T+E + + F KY    +  + +D      KGFGF+  + 
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLET 60

Query: 139 PQDFIRANKEMNEFP 153
                 A  E++  P
Sbjct: 61  RTLAEIAKVELDNMP 75

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

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 6/69 (8%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                RLF G+L  D+T+E + + F KY    +  + +D      KGFGF+  +     
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64

Query: 78 IRANKEMND 86
            A  E+++
Sbjct: 65 EIAKVELDN 73

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

 Score = 54.5 bits (132), Expect = 9e-11
 Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 2/66 (3%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
            L+ G+L    TDE L            L+ K   ++   ++KGF  V         + 
Sbjct: 2  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 81 NKEMND 86
             +  
Sbjct: 62 MDLLPK 67

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

 Score = 54.5 bits (132), Expect = 1e-10
 Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 2/66 (3%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
             L+ G+L    TDE L            L+ K   ++   ++KGF  V         + 
Sbjct: 2   IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61

Query: 146 NKEMNE 151
              + +
Sbjct: 62  MDLLPK 67

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

 Score = 55.0 bits (133), Expect = 1e-10
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 6/65 (9%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            ++CG + + +TD+L+ +TFS +   ++ +V  +      KG+ FV F   +    A   
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80

Query: 149 MNEFP 153
           +N   
Sbjct: 81  VNGTT 85

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

 Score = 53.9 bits (130), Expect = 3e-10
 Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 6/68 (8%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
              +  ++CG + + +TD+L+ +TFS +   ++ +V  +      KG+ FV F   +  
Sbjct: 21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESA 74

Query: 78 IRANKEMN 85
            A   +N
Sbjct: 75 AHAIVSVN 82

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.8 bits (132), Expect = 1e-10
 Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKR-TNKTKGFGFVSFKD 73
          +     + RLF G +      E ++   +K     L   V        K +GF FV ++ 
Sbjct: 2  SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61

Query: 74 PQDFIRANKEMNDDFRLFCG 93
           +    A +++        G
Sbjct: 62 HRAAAMARRKLMPGRIQLWG 81

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 2/72 (2%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRAN 146
           RLF G +      E ++   +K     L   V        K +GF FV ++  +    A 
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 147 KEMNEFPHLFVG 158
           +++        G
Sbjct: 70  RKLMPGRIQLWG 81

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

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 14/62 (22%), Positives = 29/62 (46%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           LF   +  + T+E +   F++Y       +  D+RT   KG+  V ++  ++   A + 
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 84 MN 85
          +N
Sbjct: 84 LN 85

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

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 14/62 (22%), Positives = 29/62 (46%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            LF   +  + T+E +   F++Y       +  D+RT   KG+  V ++  ++   A + 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 149 MN 150
           +N
Sbjct: 84  LN 85

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

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 14/65 (21%), Positives = 31/65 (47%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           + + LF   +  + T+E +   F++Y       +  D+RT   KG+  V ++  ++   A
Sbjct: 22  EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81

Query: 146 NKEMN 150
            + +N
Sbjct: 82  MEGLN 86

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

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 14/63 (22%), Positives = 30/63 (47%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          + LF   +  + T+E +   F++Y       +  D+RT   KG+  V ++  ++   A +
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83

Query: 83 EMN 85
           +N
Sbjct: 84 GLN 86

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

 Score = 53.7 bits (130), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
            +   +   ++F  +L  D T ++L   F++    L A +  +    K+KG G V F+ P
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58

Query: 140 QDFIRANKEMNEF 152
           +   RA + MN  
Sbjct: 59  EVAERACRMMNGM 71

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

 Score = 52.6 bits (127), Expect = 5e-10
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F  +L  D T ++L   F++    L A +  +    K+KG G V F+ P+   RA + 
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67

Query: 84 MN 85
          MN
Sbjct: 68 MN 69

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 54.2 bits (131), Expect = 2e-10
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 79  RANKEMNDDF-RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
             N E      RL   ++     D  L + F ++   L  +++ ++R   +KGFGFV+F+
Sbjct: 20  HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFE 77

Query: 138 DPQDFIRANKEMNEF 152
           +  D  RA ++++  
Sbjct: 78  NSADADRAREKLHGT 92

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 53.9 bits (130), Expect = 3e-10
 Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 2/62 (3%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RL   ++     D  L + F ++   L  +++ ++R   +KGFGFV+F++  D  RA ++
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88

Query: 84 MN 85
          ++
Sbjct: 89 LH 90

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

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 12/62 (19%), Positives = 27/62 (43%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
            LF   +  +  ++ +   F  Y       +  D+RT  +KG+  V ++  +  + A + 
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 84  MN 85
           +N
Sbjct: 134 LN 135

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

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 12/62 (19%), Positives = 27/62 (43%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            LF   +  +  ++ +   F  Y       +  D+RT  +KG+  V ++  +  + A + 
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 149 MN 150
           +N
Sbjct: 134 LN 135

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.9 bits (128), Expect = 2e-10
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L  + T E +   F ++     A ++ DK TN+ +GFGFV+F+         K 
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI---VEKV 57

Query: 149 MNEFPH 154
                H
Sbjct: 58  CEIHFH 63

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 52.1 bits (126), Expect = 5e-10
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
          ++F G L  + T E +   F ++     A ++ DK TN+ +GFGFV+F+   
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52

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

 Score = 56.4 bits (135), Expect = 3e-10
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 11/89 (12%)

Query: 89  RLFCGDLGNDVTDE----LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
            ++  +L   +  +     L   FS++   L   V    R+ K +G  FV FK+      
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 67

Query: 145 ANKEMNEFP----HLFVGDLKTRSSITLK 169
           A + M  FP     + +   KT S I  K
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96

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

 Score = 54.9 bits (131), Expect = 1e-09
 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 9/74 (12%)

Query: 24 RLFCGDLGNDVTDE----LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           ++  +L   +  +     L   FS++   L   V    R+ K +G  FV FK+      
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFKEVSSATN 67

Query: 80 ANKEMNDDFRLFCG 93
          A + M      F  
Sbjct: 68 ALRSMQG--FPFYD 79

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

 Score = 50.6 bits (120), Expect = 3e-08
 Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 5/83 (6%)

Query: 71  FKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 130
                   +   E   +  LF  +L  +  + +L   F+++P F + ++V  +       
Sbjct: 191 MPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HD 245

Query: 131 FGFVSFKDPQDFIRANKEMNEFP 153
             FV F +      A   +  F 
Sbjct: 246 IAFVEFDNEVQAGAARDALQGFK 268

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

 Score = 49.5 bits (117), Expect = 9e-08
 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 5/60 (8%)

Query: 26  FCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
           F  +L  +  + +L   F+++P F + ++V  +         FV F +      A   + 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 54.3 bits (131), Expect = 3e-10
 Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 3/100 (3%)

Query: 52  AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKY 111
           A  ++   +  T G    +   PQ      K+  D   ++ G++    T + L   FS  
Sbjct: 3   APCMQTTHSKMTAGAY--TEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE 151
            S  +  ++ DK +   KG+ ++ F +      A   M+E
Sbjct: 61  GSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-VAMDE 99

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          ++ +   ++ G++    T + L   FS   S  +  ++ DK +   KG+ ++ F +    
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91

Query: 78 IRANKEMND 86
            A   M++
Sbjct: 92 DAA-VAMDE 99

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

 Score = 52.7 bits (127), Expect = 5e-10
 Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
             +K++     L   +L  ++T++ L   F         ++    +  K+KG  ++ FK 
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKS 62

Query: 139 PQDFIRANKEMNEF 152
             D  +  +E    
Sbjct: 63  EADAEKNLEEKQGA 76

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

 Score = 52.3 bits (126), Expect = 8e-10
 Identities = 12/72 (16%), Positives = 27/72 (37%), Gaps = 5/72 (6%)

Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
            + +      L   +L  ++T++ L   F         ++    +  K+KG  ++ FK 
Sbjct: 8  CTSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKS 62

Query: 74 PQDFIRANKEMN 85
            D  +  +E  
Sbjct: 63 EADAEKNLEEKQ 74

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

 Score = 52.7 bits (127), Expect = 7e-10
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 10 SSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFV 69
          SS + +        +LF   L    T E L      + +    ++V + R  K KG  +V
Sbjct: 5  SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYV 63

Query: 70 SFKDPQDFIRANKEMN 85
           +++     +A  +M+
Sbjct: 64 EYENESQASQAVMKMD 79

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

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF   L    T E L      + +    ++V + R  K KG  +V +++     +A  +
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMK 77

Query: 149 MN 150
           M+
Sbjct: 78  MD 79

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 51.3 bits (124), Expect = 9e-10
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L  D  +E +   F  +      ++  D +TNK +GF F++FK+ +      K 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP---VKKI 57

Query: 149 MNEFPHLFVG 158
           M +  H    
Sbjct: 58  MEKKYHNVGL 67

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 51.0 bits (123), Expect = 1e-09
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L  D  +E +   F  +      ++  D +TNK +GF F++FK+ +      K 
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP---VKKI 57

Query: 84 MNDDFRLFCG 93
          M   +     
Sbjct: 58 MEKKYHNVGL 67

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

 Score = 51.8 bits (125), Expect = 1e-09
 Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 147
           ++  G L  +VT + ++  FS Y       +  ++   + +KG+ +V F++P +  +A K
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 148 EMNEF 152
            M+  
Sbjct: 66  HMDGG 70

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

 Score = 51.0 bits (123), Expect = 2e-09
 Identities = 15/63 (23%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 82
          ++  G L  +VT + ++  FS Y       +  ++   + +KG+ +V F++P +  +A K
Sbjct: 6  KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 83 EMN 85
           M+
Sbjct: 66 HMD 68

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

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 12/62 (19%), Positives = 27/62 (43%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           LF   +  +  ++ +   F  Y       +  D+RT  +KG+  V ++  +  + A + 
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 84 MN 85
          +N
Sbjct: 88 LN 89

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

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 12/62 (19%), Positives = 27/62 (43%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            LF   +  +  ++ +   F  Y       +  D+RT  +KG+  V ++  +  + A + 
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 149 MN 150
           +N
Sbjct: 88  LN 89

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 51.9 bits (125), Expect = 1e-09
 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 18 EDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
           +E D R +FC  L   +    L   FS        +++ D+ + ++KG  +V F + Q 
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79

Query: 77 FIRA 80
             A
Sbjct: 80 VPLA 83

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 50.8 bits (122), Expect = 5e-09
 Identities = 15/66 (22%), Positives = 27/66 (40%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
            + E  D   +FC  L   +    L   FS        +++ D+ + ++KG  +V F + 
Sbjct: 18  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 77

Query: 140 QDFIRA 145
           Q    A
Sbjct: 78  QSVPLA 83

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

 Score = 51.6 bits (124), Expect = 2e-09
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 78  IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
           IR   E+N    L+  +L   +T E +   F KY    +   +R   T +T+G  +V ++
Sbjct: 1   IRLPPEVNR--ILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYE 55

Query: 138 DPQDFIRANKEMNEFP 153
           D  D   A   ++ F 
Sbjct: 56  DIFDAKNAVDHLSGFN 71

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

 Score = 47.4 bits (113), Expect = 8e-08
 Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 3/62 (4%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+  +L   +T E +   F KY    +   +R   T +T+G  +V ++D  D   A   +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 85 ND 86
          + 
Sbjct: 68 SG 69

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 51.0 bits (123), Expect = 2e-09
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
          + +   ++ G++    T E L   F    S  +  ++ DK +   KGF ++ F D +   
Sbjct: 3  EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 79 RANKEMND-DFR 89
           +   +++  FR
Sbjct: 63 TS-LALDESLFR 73

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 51.0 bits (123), Expect = 2e-09
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           D   ++ G++    T E L   F    S  +  ++ DK +   KGF ++ F D +    +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 146 NKEMNE 151
              ++E
Sbjct: 65  -LALDE 69

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 19/75 (25%), Positives = 27/75 (36%), Gaps = 9/75 (12%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
           +F   LG +VT E +   F +                +  D+ T K KG   VSF DP 
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 76 DFIRANKEMND-DFR 89
              A    +  +F 
Sbjct: 75 SAKAAIDWFDGKEFS 89

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 50.4 bits (121), Expect = 5e-09
 Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 8/80 (10%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGF 131
            +   +D+  +F   LG +VT E +   F +                +  D+ T K KG 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 132 GFVSFKDPQDFIRANKEMNE 151
             VSF DP     A    + 
Sbjct: 66  ATVSFDDPPSAKAAIDWFDG 85

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

 Score = 51.1 bits (123), Expect = 2e-09
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
              D +LF G L    ++E ++R F  +    +  V+R      +KG  FV F    + 
Sbjct: 11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEA 69

Query: 78 IRANKEMN 85
            A   ++
Sbjct: 70 QAAIHALH 77

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

 Score = 50.7 bits (122), Expect = 3e-09
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 1/71 (1%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           +      D +LF G L    ++E ++R F  +    +  V+R      +KG  FV F   
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSH 66

Query: 140 QDFIRANKEMN 150
            +   A   ++
Sbjct: 67  TEAQAAIHALH 77

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 51.1 bits (123), Expect = 3e-09
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 8/70 (11%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           +  M     LF  +L N VT+E+L + FS++    + K ++D        + F+ F +  
Sbjct: 5   SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERD 56

Query: 141 DFIRANKEMN 150
             ++A +EMN
Sbjct: 57  GAVKAMEEMN 66

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 50.0 bits (120), Expect = 7e-09
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 8/63 (12%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           LF  +L N VT+E+L + FS++    + K ++D        + F+ F +    ++A +E
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64

Query: 84 MND 86
          MN 
Sbjct: 65 MNG 67

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 51.2 bits (123), Expect = 3e-09
 Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGF 133
           ++ +D+  +F   LG +VT E +   F +                +  D+ T K KG   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 134 VSFKDPQDFIRANKEMNEF 152
           VSF DP     A    +  
Sbjct: 62  VSFDDPPSAKAAIDWFDGK 80

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 51.2 bits (123), Expect = 3e-09
 Identities = 19/75 (25%), Positives = 27/75 (36%), Gaps = 9/75 (12%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
           +F   LG +VT E +   F +                +  D+ T K KG   VSF DP 
Sbjct: 9  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 76 DFIRANKEMND-DFR 89
              A    +  +F 
Sbjct: 69 SAKAAIDWFDGKEFS 83

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 50.4 bits (121), Expect = 5e-09
 Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
            ND R++ G+L  D+  + +   F KY +     +   +       F FV F+DP+D  
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAE 75

Query: 79 RANKEMN 85
           A    +
Sbjct: 76 DAVYGRD 82

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 50.4 bits (121), Expect = 5e-09
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           N+D R++ G+L  D+  + +   F KY +     +   +       F FV F+DP+D   
Sbjct: 20  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAED 76

Query: 145 ANKEMN 150
           A    +
Sbjct: 77  AVYGRD 82

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 52.4 bits (125), Expect = 5e-09
 Identities = 19/152 (12%), Positives = 44/152 (28%), Gaps = 9/152 (5%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
              N+  +F   +   V+ +  I     Y     +   +D   ++   F         + 
Sbjct: 60  THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFS------TPEQ 113

Query: 78  IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
              N+  +    L   +   +VT+E       +        V      ++    G + + 
Sbjct: 114 AAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD 173

Query: 138 DPQDFIRANKEMNEFPHLFVGDLKTRSSITLK 169
              D +     +N +    + +       TLK
Sbjct: 174 SKSDALETLGFLNHYQ---MKNPNGPYPYTLK 202

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 19/126 (15%), Positives = 37/126 (29%), Gaps = 7/126 (5%)

Query: 25  LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L    L    +  + +   F  Y +  K K ++ K      G   V   D     RA   
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAITH 61

Query: 84  MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
           +N +  +F   +   V+ +  I     Y     +   +D   ++   F            
Sbjct: 62  LN-NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

Query: 144 RANKEM 149
             +  +
Sbjct: 121 HPSNVL 126

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 6/65 (9%)

Query: 90  LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           L    L    +  + +   F  Y +  K K ++ K      G   V   D     RA   
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDRAITH 61

Query: 149 MNEFP 153
           +N   
Sbjct: 62  LNNNF 66

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 52.3 bits (125), Expect = 6e-09
 Identities = 24/181 (13%), Positives = 49/181 (27%), Gaps = 56/181 (30%)

Query: 25  LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRT-------------------NKTK 64
           L   +L  + VT + L   F  Y    + K++ +K+                    N  K
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 96

Query: 65  GFG-----FVSFKDPQDFIRANKEMNDDFR---------------------------LFC 92
             G      +S        R  +E     +                           L  
Sbjct: 97  LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHL 156

Query: 93  GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
            ++   V++E L   FS     +K          K +    +     ++ ++A  +++  
Sbjct: 157 SNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDLHNH 212

Query: 153 P 153
            
Sbjct: 213 D 213

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 14/89 (15%), Positives = 33/89 (37%), Gaps = 15/89 (16%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           L   ++   V++E L   FS     +K          K +    +     ++ ++A  ++
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALIQMGSVEEAVQALIDL 209

Query: 85  NDDFRLFCGDLGNDVTDELLIR-TFSKYP 112
           +           +D+ +   +R +FSK  
Sbjct: 210 H----------NHDLGENHHLRVSFSKST 228

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 51.0 bits (122), Expect = 6e-09
 Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 143
           R++  +L   V ++ L   F +Y  F          +R  +  + KG  F+   + +   
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 144 RANKEMNEFP 153
           +A KE N + 
Sbjct: 107 KALKEANGYV 116

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 48.3 bits (115), Expect = 5e-08
 Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 78
           R++  +L   V ++ L   F +Y  F          +R  +  + KG  F+   + +   
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 79  RANKEMN 85
           +A KE N
Sbjct: 107 KALKEAN 113

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

 Score = 49.6 bits (119), Expect = 7e-09
 Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 8/63 (12%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+    G D+T  LL   FS +        + D   +  +   FV+++  +   +A  E+
Sbjct: 18  LYVY--GEDMTPTLLRGAFSPF------GNIIDLSMDPPRNCAFVTYEKMESADQAVAEL 69

Query: 150 NEF 152
           N  
Sbjct: 70  NGT 72

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

 Score = 49.6 bits (119), Expect = 9e-09
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 8/68 (11%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                 L+    G D+T  LL   FS +        + D   +  +   FV+++  +  
Sbjct: 11 APRKGNTLYVY--GEDMTPTLLRGAFSPF------GNIIDLSMDPPRNCAFVTYEKMESA 62

Query: 78 IRANKEMN 85
           +A  E+N
Sbjct: 63 DQAVAELN 70

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

 Score = 49.6 bits (119), Expect = 7e-09
 Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L   +L    T+E L   F K         V   +  K+KG+ F+ F   +D   A   
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA----TFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 84 MN 85
           N
Sbjct: 73 CN 74

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

 Score = 49.6 bits (119), Expect = 7e-09
 Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L   +L    T+E L   F K         V   +  K+KG+ F+ F   +D   A   
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKA----TFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 149 MN 150
            N
Sbjct: 73  CN 74

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

 Score = 49.6 bits (119), Expect = 9e-09
 Identities = 10/67 (14%), Positives = 21/67 (31%), Gaps = 6/67 (8%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
                 + G++ +  T+  LI  F  +   L  K   +      KG  F+ +   +   
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAA 77

Query: 79 RANKEMN 85
               + 
Sbjct: 78 VCIVALA 84

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

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 6/65 (9%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
             + G++ +  T+  LI  F  +   L  K   +      KG  F+ +   +        
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82

Query: 149 MNEFP 153
           +  FP
Sbjct: 83  LANFP 87

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFV 69
          ED ++  ++   L + VT + L   F +                +  DK T K KG   V
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 70 SFKDPQDFIRANKEMND-DFR 89
          S++DP     A +  +  DF+
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQ 91

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 48.6 bits (116), Expect = 3e-08
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFG 132
             E +D+  ++   L + VT + L   F +                +  DK T K KG  
Sbjct: 9   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68

Query: 133 FVSFKDPQDFIRANKEMNE 151
            VS++DP     A +  + 
Sbjct: 69  TVSYEDPPTAKAAVEWFDG 87

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 48.7 bits (117), Expect = 1e-08
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           ++ G+L    T E +   FS++      K++ D+ T K KGFGFV  ++ +    A  +
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61

Query: 84 MND 86
          +++
Sbjct: 62 LDN 64

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 48.7 bits (117), Expect = 2e-08
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
            ++ G+L    T E +   FS++      K++ D+ T K KGFGFV  ++
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+  +L    ++E++ + F+        K    +R  K + + FV F + +D + A K +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71

Query: 85 ND 86
          N 
Sbjct: 72 NG 73

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+  +L    ++E++ + F+        K    +R  K + + FV F + +D + A K +
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNI------KPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71

Query: 150 N 150
           N
Sbjct: 72  N 72

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +++ G+LG       L R FS Y       + R+       GF FV F+DP+D   A + 
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56

Query: 84 MN 85
          ++
Sbjct: 57 LD 58

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +++ G+LG       L R FS Y       + R+       GF FV F+DP+D   A + 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRG 56

Query: 149 MN 150
           ++
Sbjct: 57  LD 58

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 10/84 (11%)

Query: 67  GFVSFKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN 126
           G V         +  +  N   RLF      DV +  L   F  +    + K++      
Sbjct: 13  GLVPRGSHMHHRQEGELSNT--RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------ 64

Query: 127 KTKGFGFVSFKDPQDFIRANKEMN 150
              GF FV F++ +   +A +E++
Sbjct: 65  --NGFAFVEFEEAESAAKAIEEVH 86

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 47.3 bits (113), Expect = 7e-08
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 8/63 (12%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF      DV +  L   F  +    + K++         GF FV F++ +   +A +E
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 84

Query: 84 MND 86
          ++ 
Sbjct: 85 VHG 87

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 48.4 bits (116), Expect = 2e-08
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 8/66 (12%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           N +++F G++    T + L   F +    ++  VV        K + FV  +   D   
Sbjct: 7  GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKA 58

Query: 80 ANKEMN 85
          A  ++N
Sbjct: 59 AIAQLN 64

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 47.6 bits (114), Expect = 4e-08
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 8/63 (12%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           +++F G++    T + L   F +    ++  VV        K + FV  +   D   A  
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61

Query: 148 EMN 150
           ++N
Sbjct: 62  QLN 64

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

 Score = 48.4 bits (116), Expect = 2e-08
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 11/89 (12%)

Query: 89  RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
            ++  +L   +  + L ++    FS++   L    +   R+ K +G  FV FK+      
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 145 ANKEMNEFP----HLFVGDLKTRSSITLK 169
           A + M  FP     + +   KT S I  K
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 9/74 (12%)

Query: 24 RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           ++  +L   +  + L ++    FS++   L    +   R+ K +G  FV FK+      
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 80 ANKEMNDDFRLFCG 93
          A + M      F  
Sbjct: 67 ALRSMQG--FPFYD 78

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 48.4 bits (116), Expect = 2e-08
 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           E  +  + G+L  +     +   F    S    ++VRDK T+K KGF +V F +     
Sbjct: 12 TEPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLK 70

Query: 79 RA 80
           A
Sbjct: 71 EA 72

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 48.4 bits (116), Expect = 3e-08
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           +  + G+L  +     +   F    S    ++VRDK T+K KGF +V F +      A
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA 72

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 148

Query: 84  MN 85
             
Sbjct: 149 YK 150

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 148

Query: 149 MN 150
             
Sbjct: 149 YK 150

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 48.0 bits (115), Expect = 3e-08
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 6/65 (9%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           RL+ G LG + +   L R F ++ S      V+         F ++ ++       A  +
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 149 MNEFP 153
           M  FP
Sbjct: 73  MRGFP 77

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 47.6 bits (114), Expect = 5e-08
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 6/62 (9%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RL+ G LG + +   L R F ++ S      V+         F ++ ++       A  +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 84 MN 85
          M 
Sbjct: 73 MR 74

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 47.6 bits (114), Expect = 4e-08
 Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 10/75 (13%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
           +   +L  G++    T++ L   F +Y   ++  +V+         + FV  +  +D +
Sbjct: 7  GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAV 58

Query: 79 RANKEMNDDFRLFCG 93
           A + +++    F G
Sbjct: 59 EAIRGLDN--TEFQG 71

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 46.8 bits (112), Expect = 8e-08
 Identities = 11/62 (17%), Positives = 28/62 (45%), Gaps = 8/62 (12%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +L  G++    T++ L   F +Y   ++  +V+         + FV  +  +D + A + 
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRG 63

Query: 149 MN 150
           ++
Sbjct: 64  LD 65

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 49.8 bits (118), Expect = 7e-08
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 25  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
           LF   +  D T+  L R F  Y    +  +V  KR+ K +G+ F+ ++  +D   A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 85  N 85
           +
Sbjct: 165 D 165

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 49.8 bits (118), Expect = 7e-08
 Identities = 17/61 (27%), Positives = 29/61 (47%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           LF   +  D T+  L R F  Y    +  +V  KR+ K +G+ F+ ++  +D   A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 150 N 150
           +
Sbjct: 165 D 165

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 46.4 bits (111), Expect = 1e-07
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 8/62 (12%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G+L  + T++ +   F +Y   L+  ++        K +GFV  +D      A + 
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61

Query: 84 MN 85
          ++
Sbjct: 62 LH 63

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 46.4 bits (111), Expect = 1e-07
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 8/62 (12%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G+L  + T++ +   F +Y   L+  ++        K +GFV  +D      A + 
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61

Query: 149 MN 150
           ++
Sbjct: 62  LH 63

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

 Score = 46.6 bits (111), Expect = 1e-07
 Identities = 16/61 (26%), Positives = 22/61 (36%)

Query: 93  GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
                 V  + L   FSK    +  +   D+ T KTKGF FV      D  +  K  +  
Sbjct: 18  PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77

Query: 153 P 153
            
Sbjct: 78  R 78

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

 Score = 46.3 bits (110), Expect = 2e-07
 Identities = 16/58 (27%), Positives = 22/58 (37%)

Query: 28 GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
                V  + L   FSK    +  +   D+ T KTKGF FV      D  +  K  +
Sbjct: 18 PSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 22/181 (12%), Positives = 49/181 (27%), Gaps = 56/181 (30%)

Query: 25  LFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDK------------------------- 58
           L   +L  + VT + L   F  Y    + K++ +K                         
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65

Query: 59  ------RTNKTKGFGFVSFKDPQDFIRANKEMNDDF--------------------RLFC 92
                 R   +K       ++ Q+     K+  +                       L  
Sbjct: 66  LHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHL 125

Query: 93  GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF 152
            ++   V++E L   FS     +K      K     +    +     ++ ++A  +++  
Sbjct: 126 SNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDLHNH 181

Query: 153 P 153
            
Sbjct: 182 D 182

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 46.8 bits (111), Expect = 5e-07
 Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 15/90 (16%)

Query: 24  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
            L   ++   V++E L   FS     +K      K     +    +     ++ ++A  +
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALID 177

Query: 84  MNDDFRLFCGDLGNDVTDELLIR-TFSKYP 112
           ++           +D+ +   +R +FSK  
Sbjct: 178 LH----------NHDLGENHHLRVSFSKST 197

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 6/73 (8%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          ED+    L+ G LG+ +T+  L   F ++       VV+       +   F+ F   Q  
Sbjct: 8  EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAA 61

Query: 78 IRANKEMNDDFRL 90
            A ++  +   +
Sbjct: 62 EVAAEKSFNKLIV 74

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ G LG+ +T+  L   F ++       VV+       +   F+ F   Q    A ++ 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFK 72
           +  + +   ++   ++        +   FS +      ++ +    T   +GFGFV F 
Sbjct: 7  GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66

Query: 73 DPQDFIRANKEMNDDFRL 90
            QD  +A   +     L
Sbjct: 67 TKQDAKKAFNALCHSTHL 84

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

 Score = 44.6 bits (106), Expect = 8e-07
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 147
           ++   ++        +   FS +      ++ +    T   +GFGFV F   QD  +A  
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 148 EMNEFPHL 155
            +    HL
Sbjct: 77  ALCHSTHL 84

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 45.2 bits (107), Expect = 5e-07
 Identities = 11/70 (15%), Positives = 27/70 (38%), Gaps = 6/70 (8%)

Query: 90  LFCGDLGNDVTDELLIRT---FSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDPQDFI 143
           +F   L   + D  +++    F K+    K  +        ++      +V++   +D +
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 144 RANKEMNEFP 153
           RA + +N   
Sbjct: 78  RAIQCVNNVV 87

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 44.5 bits (105), Expect = 9e-07
 Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 25 LFCGDLGNDVTDELLIRT---FSKYPSFLKAKVVRDKRTNKTK---GFGFVSFKDPQDFI 78
          +F   L   + D  +++    F K+    K  +        ++      +V++   +D +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 79 RANKEMN 85
          RA + +N
Sbjct: 78 RAIQCVN 84

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 44.9 bits (107), Expect = 5e-07
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRA 80
          +  F G+L  DVT+E +   F    +    ++ R+     + KGFG+  F+D    + A
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 44.9 bits (107), Expect = 5e-07
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRA 145
           +  F G+L  DVT+E +   F    +    ++ R+     + KGFG+  F+D    + A
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 44.5 bits (106), Expect = 6e-07
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 5/73 (6%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           ++   +   ++F G    D+T E L + F +Y   +   + +  R      F FV+F D 
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADD 58

Query: 140 QDFIRANKEMNEF 152
           +       E    
Sbjct: 59  KVAQSLCGEDLII 71

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 44.5 bits (106), Expect = 6e-07
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 5/58 (8%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
             +  ++F G    D+T E L + F +Y   +   + +  R      F FV+F D +
Sbjct: 7  HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADDK 59

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 44.6 bits (106), Expect = 8e-07
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRA 80
          +  F G+L  DVT+E +   F    +    ++ R+     + KGFG+  F+D    + A
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 44.6 bits (106), Expect = 8e-07
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRA 145
           +  F G+L  DVT+E +   F    +    ++ R+     + KGFG+  F+D    + A
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

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

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 11/89 (12%), Positives = 26/89 (29%), Gaps = 11/89 (12%)

Query: 89  RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
            +   ++  +V  E L        S     L    +    ++   G  ++ F   +    
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQA 87

Query: 145 ANKEMNEFP----HLFVGDLKTRSSITLK 169
             +    +P     L +   +T  S   +
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQSQVAE 116

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

 Score = 42.2 bits (99), Expect = 8e-06
 Identities = 7/67 (10%), Positives = 18/67 (26%), Gaps = 7/67 (10%)

Query: 24 RLFCGDLGNDVTDELLIRT----FSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
           +   ++  +V  E L        S     L    +    ++   G  ++ F   +    
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQA 87

Query: 80 ANKEMND 86
            +    
Sbjct: 88 FVEAFQG 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 9/70 (12%), Positives = 22/70 (31%), Gaps = 3/70 (4%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
           +     +L   ++   +  E+L     +Y      + V             V++      
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQA 67

Query: 143 IRANKEMNEF 152
            +A  ++N F
Sbjct: 68  RQALDKLNGF 77

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 8/68 (11%), Positives = 22/68 (32%), Gaps = 3/68 (4%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          + +   +L   ++   +  E+L     +Y      + V             V++      
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQA 67

Query: 78 IRANKEMN 85
           +A  ++N
Sbjct: 68 RQALDKLN 75

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 2/77 (2%)

Query: 14 KKTCEDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
          +   +++   R ++      D T + +          L  ++ R       KG  FV F 
Sbjct: 2  RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFD 60

Query: 73 DPQDFIRANKEMNDDFR 89
            +   +  +     ++
Sbjct: 61 SIESAKKFVETPGQKYK 77

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 39.3 bits (92), Expect = 7e-05
 Identities = 10/69 (14%), Positives = 20/69 (28%), Gaps = 1/69 (1%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           K    +  ++      D T + +          L  ++ R       KG  FV F   + 
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIES 64

Query: 142 FIRANKEMN 150
             +  +   
Sbjct: 65  AKKFVETPG 73

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 42.6 bits (101), Expect = 3e-06
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F G    D+T++ L   FS+Y   +   + +  R      F FV+F D Q       E
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCGE 61

Query: 149 MNEF 152
               
Sbjct: 62  DLII 65

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 42.2 bits (100), Expect = 4e-06
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
           +F G    D+T++ L   FS+Y   +   + +  R      F FV+F D Q
Sbjct: 7  GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQ 53

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 41.3 bits (97), Expect = 9e-06
 Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 8/75 (10%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 78
          RL+ G++   +T+E ++  F+               V   + N+ K F F+ F+   +  
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE-- 65

Query: 79 RANKEMNDDFRLFCG 93
             + M  D  +F G
Sbjct: 66 -TTQAMAFDGIIFQG 79

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 6/67 (8%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 143
           RL+ G++   +T+E ++  F+               V   + N+ K F F+ F+   +  
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 144 RANKEMN 150
           +A    +
Sbjct: 68  QA-MAFD 73

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

 Score = 41.4 bits (97), Expect = 9e-06
 Identities = 9/69 (13%), Positives = 18/69 (26%), Gaps = 5/69 (7%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                 ++ G+L  D     L R   +        V         +   F+ + D    
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALREL-----GSVPLRLTWQGPRRRAFLHYPDSAAA 69

Query: 78 IRANKEMND 86
           +A   +  
Sbjct: 70 QQAVSCLQG 78

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

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 9/64 (14%), Positives = 18/64 (28%), Gaps = 5/64 (7%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
              ++ G+L  D     L R   +        V         +   F+ + D     +A 
Sbjct: 19  AADVYVGNLPRDARVSDLKRALREL-----GSVPLRLTWQGPRRRAFLHYPDSAAAQQAV 73

Query: 147 KEMN 150
             + 
Sbjct: 74  SCLQ 77

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.8 bits (98), Expect = 9e-06
 Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 6/73 (8%)

Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
          I+          +  G LGN V+   L+    K        +  +K       + F  ++
Sbjct: 18 IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYR 71

Query: 73 DPQDFIRANKEMN 85
            ++  RA   +N
Sbjct: 72 TTEESKRAYVTLN 84

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 6/61 (9%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +  G LGN V+   L+    K        +  +K       + F  ++  ++  RA   +
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83

Query: 150 N 150
           N
Sbjct: 84  N 84

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

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 18/71 (25%), Positives = 26/71 (36%), Gaps = 11/71 (15%)

Query: 24 RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          R+F G+L    V    +   FSKY       V         KG+ FV + + +    A  
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80

Query: 83 EMNDDFRLFCG 93
            N   R+  G
Sbjct: 81 GENG--RVLAG 89

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

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 9/63 (14%)

Query: 89  RLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           R+F G+L    V    +   FSKY       V         KG+ FV + + +    A  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80

Query: 148 EMN 150
             N
Sbjct: 81  GEN 83

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 9/67 (13%), Positives = 24/67 (35%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
               +   ++   V+ + ++  F  Y     +  ++        G   V+F+   +   
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 80 ANKEMND 86
          A  ++ND
Sbjct: 73 AVIDLND 79

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

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 9/68 (13%), Positives = 25/68 (36%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
               +   ++   V+ + ++  F  Y     +  ++        G   V+F+   +   A
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 146 NKEMNEFP 153
             ++N+ P
Sbjct: 74  VIDLNDRP 81

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

 Score = 40.0 bits (94), Expect = 3e-05
 Identities = 9/68 (13%), Positives = 24/68 (35%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
                +   ++   V+ + ++  F  Y     +  ++        G   V+F+   +  
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 79 RANKEMND 86
           A  ++ND
Sbjct: 72 AAVIDLND 79

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

 Score = 39.6 bits (93), Expect = 5e-05
 Identities = 9/68 (13%), Positives = 25/68 (36%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
               +   ++   V+ + ++  F  Y     +  ++        G   V+F+   +   A
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 146 NKEMNEFP 153
             ++N+ P
Sbjct: 74  VIDLNDRP 81

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 7/77 (9%)

Query: 74  PQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGF 133
                        + R+    L    + + L     +      A V RD       G G 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54

Query: 134 VSFKDPQDFIRANKEMN 150
           V F   +D   A ++++
Sbjct: 55  VEFVRKEDMTYAVRKLD 71

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 39.8 bits (93), Expect = 4e-05
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 7/65 (10%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          + R+    L    + + L     +      A V RD       G G V F   +D   A 
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAV 67

Query: 82 KEMND 86
          +++++
Sbjct: 68 RKLDN 72

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 10/69 (14%), Positives = 19/69 (27%), Gaps = 6/69 (8%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           +    L + V +  L+    ++       V+        K    V F+D      A    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77

Query: 150 NEFPHLFVG 158
            +      G
Sbjct: 78  ADNQIYIAG 86

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 11/69 (15%), Positives = 20/69 (28%), Gaps = 6/69 (8%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          +    L + V +  L+    ++       V+        K    V F+D      A    
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77

Query: 85 NDDFRLFCG 93
           D+     G
Sbjct: 78 ADNQIYIAG 86

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 11/71 (15%)

Query: 24 RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          RLF G+L   +V+ E L R FS Y   ++  +           FGF+ F +PQ    A +
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75

Query: 83 EMNDDFRLFCG 93
            +    +  G
Sbjct: 76 XESQ--EMNFG 84

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)

Query: 89  RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           RLF G+L   +V+ E L R FS Y   ++  +           FGF+ F +PQ    A +
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75

Query: 148 EMN 150
             +
Sbjct: 76  XES 78

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 38.9 bits (91), Expect = 6e-05
 Identities = 7/66 (10%), Positives = 20/66 (30%), Gaps = 7/66 (10%)

Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
              +   +L  D   + +      Y        ++    ++ K   FV+  + +    A
Sbjct: 4  GSSGILVKNLPQDSNCQEVHDLLKDY-------DLKYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 81 NKEMND 86
           +  + 
Sbjct: 57 IQMFHQ 62

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 7/62 (11%), Positives = 20/62 (32%), Gaps = 7/62 (11%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +   +L  D   + +      Y        ++    ++ K   FV+  + +    A + 
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDY-------DLKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 149 MN 150
            +
Sbjct: 60  FH 61

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 13/63 (20%), Positives = 21/63 (33%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           +  ND  +    L    T E +++ FS          +      K  G  FV F   +  
Sbjct: 38  DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97

Query: 78  IRA 80
            +A
Sbjct: 98  EKA 100

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 12/65 (18%), Positives = 22/65 (33%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           + +  +D  +    L    T E +++ FS          +      K  G  FV F   +
Sbjct: 36  SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQE 95

Query: 141 DFIRA 145
              +A
Sbjct: 96  LAEKA 100

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           +   R+   +L   VT ++L + FSK+ + LK          +      + + DP     
Sbjct: 44  SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQH 99

Query: 145 ANKEMNEFP 153
           A   ++   
Sbjct: 100 AKLSLDGQN 108

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 4/63 (6%)

Query: 23  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
            R+   +L   VT ++L + FSK+ + LK          +      + + DP     A  
Sbjct: 47  LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 102

Query: 83  EMN 85
            ++
Sbjct: 103 SLD 105

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

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 11/71 (15%)

Query: 24 RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          RLF G+L   +V+ E L R FS Y   ++  +           FGF+ F +PQ    A +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIE 63

Query: 83 EMNDDFRLFCG 93
            +    +  G
Sbjct: 64 CESQ--EMNFG 72

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

 Score = 36.0 bits (84), Expect = 9e-04
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)

Query: 89  RLFCGDL-GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
           RLF G+L   +V+ E L R FS Y   ++  +           FGF+ F +PQ    A +
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIE 63

Query: 148 EMN 150
             +
Sbjct: 64  CES 66

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 11/63 (17%), Positives = 22/63 (34%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +  ND  +    L    + E +++ FS          +      ++ G  FV F   +  
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 78 IRA 80
           +A
Sbjct: 71 EKA 73

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 36.3 bits (84), Expect = 7e-04
 Identities = 10/63 (15%), Positives = 22/63 (34%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 142
           +  +D  +    L    + E +++ FS          +      ++ G  FV F   +  
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 143 IRA 145
            +A
Sbjct: 71  EKA 73

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 8/59 (13%)

Query: 98  DVTDELLIRTFSKYPSFLKAKVVR---DKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP 153
           +    ++ + FSK+      K+      +   KTKG+ F+ +  P   + A K  + + 
Sbjct: 18  EKLKNVIHKIFSKF-----GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYK 71

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 35.8 bits (83), Expect = 7e-04
 Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 8/56 (14%)

Query: 33 DVTDELLIRTFSKYPSFLKAKVVR---DKRTNKTKGFGFVSFKDPQDFIRANKEMN 85
          +    ++ + FSK+      K+      +   KTKG+ F+ +  P   + A K  +
Sbjct: 18 EKLKNVIHKIFSKF-----GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNAD 68

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 36.3 bits (84), Expect = 8e-04
 Identities = 9/66 (13%), Positives = 20/66 (30%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
                +        ++   +T   +++     P    A  V      +  G   V FK+ 
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 140 QDFIRA 145
            D  ++
Sbjct: 68  DDARKS 73

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 36.3 bits (84), Expect = 8e-04
 Identities = 9/63 (14%), Positives = 20/63 (31%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           +         ++   +T   +++     P    A  V      +  G   V FK+  D 
Sbjct: 11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 78 IRA 80
           ++
Sbjct: 71 RKS 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	170
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.98
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.91
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.88
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.83
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.83
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.82
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.82
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.81
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.81
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.8
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.8
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.79
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.79
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.79
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.79
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.78
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.78
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.78
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.77
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.77
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.77
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.77
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.77
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.76
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.76
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.75
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.75
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.75
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.75
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.74
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.74
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.74
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.74
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.74
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.74
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.73
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.73
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.72
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.72
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.72
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.71
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.71
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.71
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.71
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.71
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.71
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.71
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.71
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.71
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.71
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.7
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.7
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.7
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.7
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.7
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.7
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.7
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.7
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.7
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.7
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.7
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.7
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.7
2div_A	99	TRNA selenocysteine associated protein; structural	99.7
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.7
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.7
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.7
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.69
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.69
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.69
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.69
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.69
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.69
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.69
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.69
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.69
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.69
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.68
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.68
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.68
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.68
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.68
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.51
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.68
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.68
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.68
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.67
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.67
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.67
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.67
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.67
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.66
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.66
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.66
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.66
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.66
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.66
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.66
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.66
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.66
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.66
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.65
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.65
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.65
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.65
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.65
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.65
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.65
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.65
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.64
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.64
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.64
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.64
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.64
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.64
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.64
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.64
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.64
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.64
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.64
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.63
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.63
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.63
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.63
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.63
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.63
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.63
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.63
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.63
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.62
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.62
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.62
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.62
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.62
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.62
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.62
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.61
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.61
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.6
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.6
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.6
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.6
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.6
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.59
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.59
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.59
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.59
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.59
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.59
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.58
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.58
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.58
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.58
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.57
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.57
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.57
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.57
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.57
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.57
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.57
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.56
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.56
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.56
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.56
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.56
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.55
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.55
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.55
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.54
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.54
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.54
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.54
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.3
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.54
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.53
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.53
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.53
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.52
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.52
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.52
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.51
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.51
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.51
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.51
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.51
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.51
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.5
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.5
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.5
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.5
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.49
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.48
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.48
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.48
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.47
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.47
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.47
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.47
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.47
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.46
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.46
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.46
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.45
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.45
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.44
1x5p_A	97	Negative elongation factor E; structure genomics,	99.43
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.4
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.38
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.38
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.37
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.36
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.31
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.26
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.23
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.18
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.14
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.14
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.13
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.11
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.1
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.04
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.97
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.94
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.82
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.52
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.35
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.31
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.24
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	98.03
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.96
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.93
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.93
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.87
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.66
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.58
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.54
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.52
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.52
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.4
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.22
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.8
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.04
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.67
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.5
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	95.41
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	94.96
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.45
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.52
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	88.73

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=2.2e-36  Score=221.52  Aligned_cols=150  Identities=33%  Similarity=0.493  Sum_probs=135.6

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------   87 (170)
                      +.....+.++|||+|||+++|+++|+++|+.||.|.+|++++++.++.++|||||+|.+.++|.+|+..+++.       
T Consensus         8 p~~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i   87 (213)
T 4f02_A            8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV   87 (213)
T ss_dssp             -------CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccc
Confidence            3444456789999999999999999999999999999999999989999999999999999999999988763       


Q ss_pred             ----------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          88 ----------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        88 ----------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                                      .+|||+|||+.+++++|+++|+.||.|..+.+++|.  +.++|||||+|.+.++|.+|++.|||
T Consensus        88 ~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng  165 (213)
T 4f02_A           88 RIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG  165 (213)
T ss_dssp             EEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             ccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCC
Confidence                            489999999999999999999999999999999885  45799999999999999999999999


Q ss_pred             CCccccCCeeEEEEeecc
Q psy7847         152 FPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       152 ~~~~~~~~~~i~v~~~~~  169 (170)
                         ..++|++|+|.++.+
T Consensus       166 ---~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          166 ---MLLNDRKVFVGRFKS  180 (213)
T ss_dssp             ---CEETTEECEEEECCC
T ss_pred             ---CEECCEEEEEEEcCC
Confidence               999999999999864

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

Probab=100.00  E-value=4.5e-35  Score=205.54  Aligned_cols=143  Identities=31%  Similarity=0.512  Sum_probs=135.0

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------------
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------------   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------------   87 (170)
                      ++|||+|||+++++++|+++|+.||.|.++.+++++ ++.++|+|||+|.+.++|.+|+..+++.               
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            589999999999999999999999999999999986 6789999999999999999999887763               


Q ss_pred             --------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          88 --------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        88 --------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                              .+|+|+|||+.+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|+..|||   ..++|
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g  156 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG---QDLNG  156 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTT---CEETT
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCC---CccCC
Confidence                    4899999999999999999999999999999999988899999999999999999999999999   99999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      ++|+|+||.+
T Consensus       157 ~~i~v~~a~~  166 (166)
T 3md3_A          157 RPLRINWAAK  166 (166)
T ss_dssp             EECEEEESCC
T ss_pred             cEEEEEecCC
Confidence            9999999874

>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=100.00  E-value=2.6e-35  Score=207.39  Aligned_cols=145  Identities=27%  Similarity=0.499  Sum_probs=136.6

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH---cCC-----------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE---MND-----------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~---~~~-----------   86 (170)
                      ++++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..   +++           
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccch
Confidence            468999999999999999999999999999999999988899999999999999999999986   333           


Q ss_pred             -----CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          87 -----DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        87 -----~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                           ..+|||+|||+.+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|++ +|+   ..++|++
T Consensus        82 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~---~~~~g~~  157 (167)
T 2cjk_A           82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKF---IDFKDRK  157 (167)
T ss_dssp             HHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSE---ECSSSSC
T ss_pred             hhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCC---EEeCCeE
Confidence                 3599999999999999999999999999999999998889999999999999999999998 888   9999999


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      |+|.++.+
T Consensus       158 i~V~~a~p  165 (167)
T 2cjk_A          158 IEIKRAEP  165 (167)
T ss_dssp             EEEEECCC
T ss_pred             EEEeecCC
Confidence            99999976

>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=100.00  E-value=1.4e-34  Score=203.69  Aligned_cols=144  Identities=26%  Similarity=0.410  Sum_probs=136.4

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------------   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------------   87 (170)
                      ++++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+++.             
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            4689999999999999999999999999999999999889999999999999999999999987752             


Q ss_pred             --------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          88 --------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        88 --------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                              .+|+|+|||..+++++|+++|++||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.|||   ..+.|
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g  158 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN---VIPEG  158 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CCCTT
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcC---CEecC
Confidence                    5999999999999999999999999999999999988899999999999999999999999999   88866


Q ss_pred             --eeEEEEee
Q psy7847         160 --LKTRSSIT  167 (170)
Q Consensus       160 --~~i~v~~~  167 (170)
                        ++|+|+||
T Consensus       159 ~~~~l~V~~A  168 (168)
T 1b7f_A          159 GSQPLSVRLA  168 (168)
T ss_dssp             CSSCCEEEEC
T ss_pred             CCeEEEEEeC
Confidence              99999986

>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=100.00  E-value=1.7e-34  Score=204.28  Aligned_cols=147  Identities=20%  Similarity=0.342  Sum_probs=133.2

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCC--CcCCEEEEEeCCHHHHHHHHHHcCCC-----------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANKEMNDD-----------   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~--~~~~~afv~f~~~~~a~~~~~~~~~~-----------   87 (170)
                      ++++|||+|||+++++++|+++|+.||.|.++++++++.++  .++|||||+|.+.++|.+|++.+++.           
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            46899999999999999999999999999999999998776  89999999999999999999987752           


Q ss_pred             --------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCC
Q psy7847          88 --------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP  153 (170)
Q Consensus        88 --------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~  153 (170)
                                    .+|||+|||+.+++++|+++|++||.|..+.+.+++ ++.++|+|||+|.+.++|.+|++.|||..
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQ  160 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSC
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCc
Confidence                          489999999999999999999999999999999986 58899999999999999999999999932


Q ss_pred             ccccCCeeEEEEeec
Q psy7847         154 HLFVGDLKTRSSITL  168 (170)
Q Consensus       154 ~~~~~~~~i~v~~~~  168 (170)
                      ....++++|+|+||+
T Consensus       161 ~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          161 TMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CCTTCSSCCEEEECC
T ss_pred             ccCCCCCCeEEEecC
Confidence            222225999999985

>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=100.00  E-value=1.4e-34  Score=208.54  Aligned_cols=151  Identities=25%  Similarity=0.410  Sum_probs=137.7

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC--------
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND--------   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~--------   86 (170)
                      +..++.+.++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+...+.        
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~   85 (196)
T 1l3k_A            6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   85 (196)
T ss_dssp             --CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEee
Confidence            444566788999999999999999999999999999999999988899999999999999999999976221        


Q ss_pred             ------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHH
Q psy7847          87 ------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE  148 (170)
Q Consensus        87 ------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  148 (170)
                                        ..+|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|+..
T Consensus        86 v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  165 (196)
T 1l3k_A           86 PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ  165 (196)
T ss_dssp             EEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC
T ss_pred             eecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh
Confidence                              25899999999999999999999999999999999988899999999999999999999986


Q ss_pred             hcCCCccccCCeeEEEEeecc
Q psy7847         149 MNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       149 l~~~~~~~~~~~~i~v~~~~~  169 (170)
                       ++   ..++|+.|+|+++.+
T Consensus       166 -~~---~~~~G~~i~v~~a~~  182 (196)
T 1l3k_A          166 -KY---HTVNGHNCEVRKALS  182 (196)
T ss_dssp             -SC---CEETTEECEEEECC-
T ss_pred             -CC---cEECCEEEEEEecCC
Confidence             78   999999999999875

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

Probab=100.00  E-value=3.7e-35  Score=214.46  Aligned_cols=148  Identities=23%  Similarity=0.385  Sum_probs=137.8

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-----------
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-----------   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-----------   87 (170)
                      ....++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|++.+++.           
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            345689999999999999999999999999999999999888999999999999999999999977752           


Q ss_pred             ---------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q psy7847          88 ---------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN  146 (170)
Q Consensus        88 ---------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~  146 (170)
                                           .+|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|+|||+|.+.++|.+|+
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~  184 (216)
T 2qfj_A          105 PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV  184 (216)
T ss_dssp             CSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH
T ss_pred             CCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHH
Confidence                                 49999999999999999999999999999999999888999999999999999999999


Q ss_pred             HHhcCCCccccCCeeEEEEeecc
Q psy7847         147 KEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       147 ~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      +.|||   ..++|+.|+|+++..
T Consensus       185 ~~l~g---~~~~g~~i~V~~a~~  204 (216)
T 2qfj_A          185 SSMNL---FDLGGQYLRVGKAVT  204 (216)
T ss_dssp             HHHTT---CBCSSSBCEEEECSS
T ss_pred             HHccC---CEeCCcEEEEEEecC
Confidence            99999   999999999999864

>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=100.00  E-value=3.1e-34  Score=201.44  Aligned_cols=143  Identities=25%  Similarity=0.392  Sum_probs=134.9

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--------------
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--------------   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--------------   87 (170)
                      +++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|+|||+|.+.++|.+|++.+++.              
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            578999999999999999999999999999999999889999999999999999999999987762              


Q ss_pred             -------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          88 -------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        88 -------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                             .+|+|+|||+.+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|.+|++.|||   ..++|+
T Consensus        82 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~  158 (167)
T 1fxl_A           82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG---QKPSGA  158 (167)
T ss_dssp             CCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CCCTTC
T ss_pred             CcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcC---CccCCC
Confidence                   4899999999999999999999999999999999988899999999999999999999999999   889885


Q ss_pred             --eEEEEee
Q psy7847         161 --KTRSSIT  167 (170)
Q Consensus       161 --~i~v~~~  167 (170)
                        +|+|+||
T Consensus       159 ~~~i~v~~A  167 (167)
T 1fxl_A          159 TEPITVKFA  167 (167)
T ss_dssp             SSCCEEEEC
T ss_pred             ccceEEEeC
Confidence              4888886

>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=99.98  E-value=1.3e-31  Score=189.17  Aligned_cols=138  Identities=22%  Similarity=0.379  Sum_probs=126.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcC----C-------CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC--
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKY----P-------SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD--   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~----g-------~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~--   87 (170)
                      ++++|||+|||+++++++|+++|+.|    |       .+.++.+.      .++|||||+|.+.++|.+|+ .+++.  
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            56899999999999999999999999    6       66666654      34799999999999999999 77652  


Q ss_pred             -------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHH
Q psy7847          88 -------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE  148 (170)
Q Consensus        88 -------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~  148 (170)
                                         .+|+|+|||+.+++++|+++|++||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  155 (172)
T ss_dssp             TTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH
T ss_pred             cCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence                               5899999999999999999999999999999999988899999999999999999999999


Q ss_pred             hcCCCccccCCeeEEEEeec
Q psy7847         149 MNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       149 l~~~~~~~~~~~~i~v~~~~  168 (170)
                      |||   ..++|++|+|+||.
T Consensus       156 l~g---~~~~g~~l~V~~As  172 (172)
T 2g4b_A          156 LNG---MQLGDKKLLVQRAS  172 (172)
T ss_dssp             HTT---CEETTEECEEEECC
T ss_pred             cCC---CEECCeEEEEEeCC
Confidence            999   99999999999974

>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=99.98  E-value=6.3e-31  Score=199.76  Aligned_cols=145  Identities=19%  Similarity=0.273  Sum_probs=137.0

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------------   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------------   87 (170)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|+|||+|.+.++|.+|+..+++.             
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            4678999999999999999999999999999999999889999999999999999999999888762             


Q ss_pred             -----------ceEEecCCCCCC-CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcc
Q psy7847          88 -----------FRLFCGDLGNDV-TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL  155 (170)
Q Consensus        88 -----------~~l~v~nlp~~~-~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  155 (170)
                                 .+|||+|||+.+ ++++|+++|+.||.|..+.+.+++ ++.++|+|||+|.+.++|.+|+..|||   .
T Consensus       174 ~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g---~  249 (284)
T 3smz_A          174 AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADG---L  249 (284)
T ss_dssp             GGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTT---C
T ss_pred             CCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCC---C
Confidence                       489999999995 999999999999999999999887 788999999999999999999999999   9


Q ss_pred             ccCCeeEEEEeecc
Q psy7847         156 FVGDLKTRSSITLK  169 (170)
Q Consensus       156 ~~~~~~i~v~~~~~  169 (170)
                      .++|++|+|+|+.+
T Consensus       250 ~~~g~~l~v~~a~~  263 (284)
T 3smz_A          250 SLGGSHLRVSFCAP  263 (284)
T ss_dssp             EETTEECEEEECCS
T ss_pred             ccCCeEEEEEEecC
Confidence            99999999999875

>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=99.97  E-value=6.2e-32  Score=191.59  Aligned_cols=144  Identities=22%  Similarity=0.301  Sum_probs=127.2

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC---------
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---------   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~---------   86 (170)
                      ..++.+.++|||+|||.++++++|+++|..||.+..+ ++.+..+|.++|||||+|.+.++|.+|++ +++         
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~   84 (175)
T 1fje_B            7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK   84 (175)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-CCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-EEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEE
Confidence            4456678999999999999999999999999977663 33444578899999999999999999994 664         


Q ss_pred             --------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCC
Q psy7847          87 --------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus        87 --------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  152 (170)
                                    ..+|||+|||+.+++++|+++|++||.|..+     ..++.++|+|||+|.+.++|.+|+..||| 
T Consensus        85 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g-  158 (175)
T 1fje_B           85 LEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQG-  158 (175)
T ss_dssp             EECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTE-
T ss_pred             EecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCC-
Confidence                          2599999999999999999999999988766     34688899999999999999999999999 


Q ss_pred             CccccCCeeEEEEeecc
Q psy7847         153 PHLFVGDLKTRSSITLK  169 (170)
Q Consensus       153 ~~~~~~~~~i~v~~~~~  169 (170)
                        ..++|++|+|+|+.+
T Consensus       159 --~~~~g~~i~v~~a~~  173 (175)
T 1fje_B          159 --AEIDGRSVSLYYTGE  173 (175)
T ss_dssp             --EEETTEEEEEEECSS
T ss_pred             --CEECCeEEEEEecCC
Confidence              999999999999875

>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=99.97  E-value=3.4e-30  Score=195.73  Aligned_cols=140  Identities=21%  Similarity=0.282  Sum_probs=130.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-------------
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-------------   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-------------   86 (170)
                      .++++|||+|||+++++++|+++|+.|| +.++.+      +.++|||||+|.+.++|.+|+..+++             
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~   92 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ   92 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEec
Confidence            4578999999999999999999999999 888887      45678999999999999999998876             


Q ss_pred             --CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          87 --DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        87 --~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                        ..+|||+|||+.+++++|+++|+.||.|..+.++.++.++.++|+|||+|.+.++|.+|+..|||   ..++|++|+|
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~---~~~~g~~i~v  169 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG---KPLGPRTLYV  169 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCC---CEeCCcEEEE
Confidence              35899999999999999999999999999999999988899999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus       170 ~~a~~  174 (284)
T 3smz_A          170 HWTDA  174 (284)
T ss_dssp             EECCG
T ss_pred             EECCC
Confidence            99864

>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=99.97  E-value=1e-29  Score=191.40  Aligned_cols=144  Identities=27%  Similarity=0.355  Sum_probs=128.7

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC---------
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD---------   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~---------   87 (170)
                      ....+.++|||+|||+++|+++|+++|+.||.|.++.+.++      +|||||+|.+.++|.+|+..+++.         
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            33456689999999999999999999999999999999654      589999999999999999988763         


Q ss_pred             ------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC---
Q psy7847          88 ------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG---  158 (170)
Q Consensus        88 ------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~---  158 (170)
                            .+|||+|||+.+++++|+++|+.||.|..+.+..+. ++.++|+|||+|.+.++|.+|+..||+.  ..+.   
T Consensus        91 ~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~--~~~~~~~  167 (261)
T 3sde_A           91 RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDG--AFLLTTT  167 (261)
T ss_dssp             EECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHS--CEESSSS
T ss_pred             eecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCC--eEEecCC
Confidence                  599999999999999999999999999999999995 8899999999999999999999999441  4444   


Q ss_pred             CeeEEEEeecc
Q psy7847         159 DLKTRSSITLK  169 (170)
Q Consensus       159 ~~~i~v~~~~~  169 (170)
                      +++|.|.++..
T Consensus       168 ~r~i~v~~~~~  178 (261)
T 3sde_A          168 PRPVIVEPMEQ  178 (261)
T ss_dssp             CCBCEEEECCC
T ss_pred             CceEEEeeccc
Confidence            89999998753

>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=99.97  E-value=1.2e-29  Score=192.46  Aligned_cols=141  Identities=21%  Similarity=0.373  Sum_probs=128.1

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHH----HHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~----~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------   87 (170)
                      +..++++|||+|||.++++++|+    ++|+.||.|.+|++++   +|.++|||||+|.+.++|.+|++.+++.      
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            45568899999999999999977    8999999999999875   6789999999999999999999876641      


Q ss_pred             --------------------------------------------------------------------------------
Q psy7847          88 --------------------------------------------------------------------------------   87 (170)
Q Consensus        88 --------------------------------------------------------------------------------   87 (170)
                                                                                                      
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence                                                                                            


Q ss_pred             ----------------------------------------------ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEee
Q psy7847          88 ----------------------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVR  121 (170)
Q Consensus        88 ----------------------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~  121 (170)
                                                                    .+|||+|||..+++++|+++|+.||.|..+.+..
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                                          3499999999999999999999999999999986


Q ss_pred             cCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC-CeeEEEEeecc
Q psy7847         122 DKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG-DLKTRSSITLK  169 (170)
Q Consensus       122 ~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-~~~i~v~~~~~  169 (170)
                      ++     +|+|||+|.+.++|.+|++.|||   ..++ |++|+|+|+.+
T Consensus       242 ~~-----~g~afV~f~~~~~A~~A~~~l~g---~~~~~g~~l~v~~akk  282 (282)
T 3pgw_A          242 GR-----HDIAFVEFDNEVQAGAARDALQG---FKITQNNAMKISFAKK  282 (282)
T ss_pred             CC-----CcEEEEEeCCHHHHHHHHHHcCC---cEeCCCCEEEEEEecC
Confidence            64     68999999999999999999999   8888 99999999864

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

Probab=99.97  E-value=6.2e-30  Score=184.39  Aligned_cols=139  Identities=22%  Similarity=0.387  Sum_probs=125.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcC----C-------CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC---
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKY----P-------SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~----g-------~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~---   86 (170)
                      .+++|||+|||+++++++|+++|+.|    |       .+.++.+      +.++|||||+|.+.++|.+|+ .+++   
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            46899999999999999999999999    4       4555544      455799999999999999999 6654   


Q ss_pred             --------------------------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCc
Q psy7847          87 --------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT  128 (170)
Q Consensus        87 --------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~  128 (170)
                                                            ..+|||+|||+.+++++|+++|++||.|..+.+.+++.++.+
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence                                                  259999999999999999999999999999999999888999


Q ss_pred             ccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         129 KGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       129 ~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      +|+|||+|.+.++|.+|++.|||   ..++|+.|+|+++.+
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~~a~~  193 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNG---MQLGDKKLLVQRASV  193 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTT---CEETTEECEEEESCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCC---CEECCEEEEEEECCC
Confidence            99999999999999999999999   999999999999875

>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=99.97  E-value=5.3e-30  Score=195.36  Aligned_cols=147  Identities=10%  Similarity=0.150  Sum_probs=124.8

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC---------
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---------   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~---------   86 (170)
                      ...+...++|||+|||+++++++|+++|+.||.|.++++++++ .+ ++|||||+|.+.++|.+|++ +++         
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~~-~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~  111 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KK-NFRFARIEFARYDGALAAIT-KTHKVVGQNEII  111 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECT-TS-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CC-CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEE
Confidence            3345567899999999999999999999999999999999986 33 57999999999999999995 664         


Q ss_pred             -----CceEEecCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          87 -----DFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        87 -----~~~l~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                           ..+|||+|||+.+++++|+++|+.|| .|..+.+++++. +.++|||||+|.+.++|.+|+..|||   ..++|+
T Consensus       112 v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~  187 (292)
T 2ghp_A          112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNG---LKIEGY  187 (292)
T ss_dssp             EEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTT---CEETTE
T ss_pred             EEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCC---CEeCCc
Confidence                 36999999999999999999999999 999999988874 77899999999999999999999999   999999


Q ss_pred             eEEEEeecc
Q psy7847         161 KTRSSITLK  169 (170)
Q Consensus       161 ~i~v~~~~~  169 (170)
                      +|+|.++.+
T Consensus       188 ~l~v~~a~~  196 (292)
T 2ghp_A          188 TLVTKVSNP  196 (292)
T ss_dssp             ECEEEECCC
T ss_pred             EEEEEECCC
Confidence            999999864

>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=99.97  E-value=1.6e-29  Score=186.95  Aligned_cols=141  Identities=18%  Similarity=0.220  Sum_probs=127.2

Q ss_pred             CCCCCCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC---------
Q psy7847          17 CEDENDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND---------   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~---------   86 (170)
                      ....++++|||+|||+ ++++++|+++|+.||.|.++++++++     +|||||+|.+.++|.+|++.+++         
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3345678999999999 99999999999999999999998875     68999999999999999986654         


Q ss_pred             -----------------------------------------------CceEEecCCCCCCCHHHHHHHhccCC-CeeEEE
Q psy7847          87 -----------------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAK  118 (170)
Q Consensus        87 -----------------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g-~i~~~~  118 (170)
                                                                     ..+|||+|||+.+++++|+++|+.|| .|..+.
T Consensus       104 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~  183 (229)
T 2adc_A          104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK  183 (229)
T ss_dssp             EECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEE
T ss_pred             EEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEE
Confidence                                                           14699999999999999999999999 999998


Q ss_pred             EeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC-CeeEEEEeeccC
Q psy7847         119 VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG-DLKTRSSITLKG  170 (170)
Q Consensus       119 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-~~~i~v~~~~~~  170 (170)
                      +..+     .+|+|||+|.+.++|.+|++.|||   ..++ |++|+|+|+.+.
T Consensus       184 i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g---~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          184 FFQK-----DRKMALIQMGSVEEAVQALIDLHN---HDLGENHHLRVSFSKST  228 (229)
T ss_dssp             ECSS-----STTCEEEEESSHHHHHHHHHHHTT---CBSSSSCBCEEEECSSC
T ss_pred             EEEC-----CCcEEEEEECCHHHHHHHHHHHCC---CccCCCCeEEEEEecCC
Confidence            8653     278999999999999999999999   8888 999999998763

>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=99.97  E-value=7.2e-30  Score=194.64  Aligned_cols=144  Identities=15%  Similarity=0.262  Sum_probs=128.0

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ..++|||+|||+++++++|+++|+.|| .|.++.++.++ .|.++|||||+|.+.++|.+|+..+++.            
T Consensus       116 ~~~~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          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            578999999999999999999999999 99999999886 4889999999999999999999977752            


Q ss_pred             ----------------ceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCC-CCCcccEEEEEecCHHHHHHHHHHh
Q psy7847          88 ----------------FRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEM  149 (170)
Q Consensus        88 ----------------~~l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l  149 (170)
                                      .+|||+|||+. +++++|+++|+.||.|..+.+.++.. ++.++|+|||+|.+.++|.+|+ .|
T Consensus       195 ~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l  273 (292)
T 2ghp_A          195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QM  273 (292)
T ss_dssp             CCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GG
T ss_pred             CCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hh
Confidence                            58999999999 99999999999999999999998874 4889999999999999999999 99


Q ss_pred             cCCCccccCCeeEEEEeecc
Q psy7847         150 NEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       150 ~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ||   ..++|++|+|+|+.+
T Consensus       274 ~g---~~~~g~~i~V~~a~~  290 (292)
T 2ghp_A          274 NR---SLLGNREISVSLADK  290 (292)
T ss_dssp             TT---EEETTEEEEEEECCC
T ss_pred             cC---CEECCcEEEEEEecC
Confidence            99   999999999999976

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=1.9e-29  Score=182.19  Aligned_cols=137  Identities=18%  Similarity=0.231  Sum_probs=124.6

Q ss_pred             CCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-------------
Q psy7847          21 NDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-------------   86 (170)
Q Consensus        21 ~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-------------   86 (170)
                      .+++|||+|||+ ++++++|+++|+.||.|.++++++++     +|||||+|.+.++|.+|+..+++             
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            357999999999 99999999999999999999998764     68999999999999999986654             


Q ss_pred             -------------------------------------------CceEEecCCCCCCCHHHHHHHhccCC-CeeEEEEeec
Q psy7847          87 -------------------------------------------DFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRD  122 (170)
Q Consensus        87 -------------------------------------------~~~l~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~  122 (170)
                                                                 ..+|+|+|||..+++++|+++|+.|| .|..+.+..+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence                                                       23599999999999999999999999 9999998664


Q ss_pred             CCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC-CeeEEEEeeccC
Q psy7847         123 KRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG-DLKTRSSITLKG  170 (170)
Q Consensus       123 ~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~-~~~i~v~~~~~~  170 (170)
                      .     +|+|||+|.+.++|.+|+..|||   ..++ |++|+|+|+.+.
T Consensus       157 ~-----~g~afV~f~~~~~A~~A~~~l~g---~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 D-----RKMALIQMGSVEEAVQALIDLHN---HDLGENHHLRVSFSKST  197 (198)
T ss_dssp             T-----SSCEEEECSSHHHHHHHHHHHTS---SCCSSCCSCCEEEECCC
T ss_pred             C-----CcEEEEEeCCHHHHHHHHHHhcC---CccCCCCeEEEEeeccc
Confidence            3     78999999999999999999999   8888 999999999763

>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=99.96  E-value=1.1e-28  Score=179.71  Aligned_cols=137  Identities=16%  Similarity=0.182  Sum_probs=120.1

Q ss_pred             CCcEEEEcCCC-CCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------------
Q psy7847          21 NDFRLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------------   87 (170)
Q Consensus        21 ~~~~v~v~nLp-~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------------   87 (170)
                      ++.+|||+||| .++++++|+++|+.||.|.+++++++     ++|||||+|.+.++|..|++.+++.            
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46799999999 79999999999999999999999865     3699999999999999999877541            


Q ss_pred             ----------------------------------------------ceEEecCCCCCCCHHHHHHHhccCCCe--eEEEE
Q psy7847          88 ----------------------------------------------FRLFCGDLGNDVTDELLIRTFSKYPSF--LKAKV  119 (170)
Q Consensus        88 ----------------------------------------------~~l~v~nlp~~~~~~~l~~~f~~~g~i--~~~~~  119 (170)
                                                                    .+|||+|||+.+++++|+++|++||.|  ..+.+
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence                                                          159999999999999999999999998  88888


Q ss_pred             eecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe----eEEEEee
Q psy7847         120 VRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL----KTRSSIT  167 (170)
Q Consensus       120 ~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~----~i~v~~~  167 (170)
                      ..+.  +.++|+|||+|.+.++|.+|+..|||   ..++++    ++.|.++
T Consensus       158 ~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng---~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK--SERSSSGLLEWDSKSDALETLGFLNH---YQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC--SSSSEEEEEECSSHHHHHHHHHHHTT---CEECCSSSSSCEECEEE
T ss_pred             EcCC--CCCceEEEEEeCCHHHHHHHHHHhCC---CCccCCCCCcceEEEec
Confidence            7764  45579999999999999999999999   777775    5555543

>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=99.91  E-value=4.8e-24  Score=148.98  Aligned_cols=114  Identities=22%  Similarity=0.275  Sum_probs=103.4

Q ss_pred             EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----------------------------------CceEEecCCC
Q psy7847          51 KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----------------------------------DFRLFCGDLG   96 (170)
Q Consensus        51 ~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----------------------------------~~~l~v~nlp   96 (170)
                      .+.++.+.  ..++|||||+|.+.++|++++..+++                                  ..+|||+|||
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            45666664  36899999999999999999976541                                  3699999999


Q ss_pred             CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847          97 NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus        97 ~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      +++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.++.+
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~~a~~  149 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG---AVLDGRELRVQMARY  149 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTT---EESSSSEEEEEEECC
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC---CEECCeEEEEEECCC
Confidence            9999999999999999999999999988899999999999999999999999999   999999999999875

>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=3.1e-22  Score=129.54  Aligned_cols=82  Identities=26%  Similarity=0.346  Sum_probs=78.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|++||.|..+.+.+|+.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng---~~~~gr~l~V~   94 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG---LRLQSKTIKVS   94 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            356899999999999999999999999999999999998999999999999999999999999999   99999999999


Q ss_pred             eeccC
Q psy7847         166 ITLKG  170 (170)
Q Consensus       166 ~~~~~  170 (170)
                      ||.++
T Consensus        95 ~AkPS   99 (99)
T 4fxv_A           95 YARPS   99 (99)
T ss_dssp             ECCBC
T ss_pred             EeeCC
Confidence            99874

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

Probab=99.84  E-value=1.7e-20  Score=123.52  Aligned_cols=81  Identities=17%  Similarity=0.188  Sum_probs=77.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+++|+.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng---~~~~gr~i~V~   81 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHL---TSVMGNIIHAQ   81 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCC---CEECCeEEEEE
Confidence            357999999999999999999999999999999999998899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        82 ~a~~   85 (110)
T 3s8s_A           82 LDIK   85 (110)
T ss_dssp             ECST
T ss_pred             ECCC
Confidence            9865

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

Probab=99.84  E-value=4.4e-21  Score=123.10  Aligned_cols=82  Identities=15%  Similarity=0.286  Sum_probs=74.9

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCC--eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCC-ccccCCeeEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPS--FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP-HLFVGDLKTRS  164 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~--i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~-~~~~~~~~i~v  164 (170)
                      .+|||+|||+.+|+++|+++|++||.  +..+++++|+.++.++|||||+|.+.++|.+|++.|||.+ ...++|++|+|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V   89 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV   89 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEE
Confidence            48999999999999999999999995  6689999999899999999999999999999999999942 23689999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +||..
T Consensus        90 ~~Aks   94 (95)
T 2lkz_A           90 DFAKS   94 (95)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99975

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.83  E-value=3.3e-21  Score=122.79  Aligned_cols=80  Identities=18%  Similarity=0.196  Sum_probs=74.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .+|||+|||+++++++|+++|++|| .|..+.+++|+.++.++|||||+|.+.++|.+|++.+++  ...++|++|+|+|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~--~~~~~gr~i~V~~   79 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQH--SLNILGQKVSMHY   79 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTT--EEEETTEEEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCC--CeEECCEEEEEEE
Confidence            5899999999999999999999999 799999999998999999999999999999999998744  1789999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        80 a~~   82 (91)
T 2lxi_A           80 SDP   82 (91)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            875

>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=99.83  E-value=7e-20  Score=114.34  Aligned_cols=79  Identities=35%  Similarity=0.578  Sum_probs=76.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.|||   ..++|++|+|+++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g---~~~~g~~l~v~~a   78 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQG---QDLNGRPLRINWA   78 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTT---CEETTEECEEEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcC---CeeCCcEEEEEec
Confidence            5899999999999999999999999999999999988899999999999999999999999999   9999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus        79 ~~   80 (83)
T 3md1_A           79 AK   80 (83)
T ss_dssp             CC
T ss_pred             Cc
Confidence            75

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.82  E-value=7.5e-20  Score=115.19  Aligned_cols=81  Identities=31%  Similarity=0.561  Sum_probs=76.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   81 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG---QWLGGRQIRTN   81 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC---CEECCeEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        82 ~a~~   85 (87)
T 3bs9_A           82 WATR   85 (87)
T ss_dssp             EEC-
T ss_pred             ecCC
Confidence            9975

>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=99.82  E-value=4.1e-20  Score=128.00  Aligned_cols=100  Identities=27%  Similarity=0.400  Sum_probs=92.0

Q ss_pred             CcCCEEEEEeCCHHHHHHHHHHc-C------------------------------------CCceEEecCCCCCCCHHHH
Q psy7847          62 KTKGFGFVSFKDPQDFIRANKEM-N------------------------------------DDFRLFCGDLGNDVTDELL  104 (170)
Q Consensus        62 ~~~~~afv~f~~~~~a~~~~~~~-~------------------------------------~~~~l~v~nlp~~~~~~~l  104 (170)
                      .-+|+++++|.+.++|+++++.+ +                                    ..++|||+|||+.+++++|
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l   90 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTEL   90 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCCEEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHHH
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCCceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHH
Confidence            56899999999999999999777 1                                    2369999999999999999


Q ss_pred             HHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         105 IRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       105 ~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      +++|++||.|..+.+.++     ++|||||+|.+.++|.+|+..|||   ..++|++|+|+++.+
T Consensus        91 ~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~~a~~  147 (150)
T 2i2y_A           91 ERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG---RTLCGCRVRVELSNG  147 (150)
T ss_dssp             HHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSS---SCSSSSCCEEEECCC
T ss_pred             HHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCC---CEECCeEEEEEEcCC
Confidence            999999999999999876     489999999999999999999999   999999999999875

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

Probab=99.82  E-value=1.2e-19  Score=116.12  Aligned_cols=82  Identities=26%  Similarity=0.334  Sum_probs=77.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|+|||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   90 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG---MELDGRRIRVS   90 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT---EEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            357999999999999999999999999999999999988889999999999999999999999999   99999999999


Q ss_pred             eeccC
Q psy7847         166 ITLKG  170 (170)
Q Consensus       166 ~~~~~  170 (170)
                      ++..+
T Consensus        91 ~a~~g   95 (95)
T 2cqc_A           91 GPSSG   95 (95)
T ss_dssp             CCSCC
T ss_pred             ecCCC
Confidence            99764

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.82  E-value=8.8e-20  Score=114.39  Aligned_cols=81  Identities=26%  Similarity=0.379  Sum_probs=76.5

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v   81 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE---SELFGRTIRV   81 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCC---CEECCcEEEE
Confidence            3467999999999999999999999999999999999988899999999999999999999999999   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      +++.
T Consensus        82 ~~ak   85 (85)
T 3mdf_A           82 NLAK   85 (85)
T ss_dssp             EECC
T ss_pred             EEcC
Confidence            9973

>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=99.81  E-value=2.5e-20  Score=118.34  Aligned_cols=79  Identities=18%  Similarity=0.203  Sum_probs=72.2

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      .+|||+|||+++++++|+++|++||  .|..+.+..++.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g---~~~~gr~i~V~   78 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK---RELHGQNPVVT   78 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGG---SCSSSCCCEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCC---CeeCCEEEEEE
Confidence            4799999999999999999999999  999999999988999999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        79 ~~~~   82 (90)
T 3p5t_L           79 PSNK   82 (90)
T ss_dssp             CC--
T ss_pred             ECCC
Confidence            9864

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

Probab=99.81  E-value=2.7e-19  Score=114.45  Aligned_cols=81  Identities=22%  Similarity=0.423  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~   80 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG---FELAGRPMRVG   80 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTT---CCSSSSCCEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCC---CeeCCcEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        81 ~a~~   84 (95)
T 2dnz_A           81 HVTE   84 (95)
T ss_dssp             ESSC
T ss_pred             Eccc
Confidence            9865

>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=99.81  E-value=6.4e-20  Score=121.67  Aligned_cols=80  Identities=30%  Similarity=0.504  Sum_probs=59.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-------------
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-------------   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-------------   87 (170)
                      .+.+|||+|||+++++++|+++|+.||.|.++++++++  +.++|||||+|.+.++|.+|++.+++.             
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45689999999999999999999999999999999985  458999999999999999999988863             


Q ss_pred             ----------------ceEEecCCCCCCCHH
Q psy7847          88 ----------------FRLFCGDLGNDVTDE  102 (170)
Q Consensus        88 ----------------~~l~v~nlp~~~~~~  102 (170)
                                      .+|||+|||+++|++
T Consensus        82 ~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           82 SRKEREAELGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             CCCC---------------------------
T ss_pred             CccccccccccccCCCCceEeCCCCCCcccc
Confidence                            268888888888776

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

Probab=99.81  E-value=1.9e-19  Score=115.58  Aligned_cols=80  Identities=20%  Similarity=0.369  Sum_probs=76.5

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||..+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V~~   78 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG---YQLGSRFLKCGY   78 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCC---CeECCeEEEEEE
Confidence            46899999999999999999999999999999999988899999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        79 a~~   81 (96)
T 2x1f_A           79 SSN   81 (96)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            875

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

Probab=99.81  E-value=2.4e-20  Score=127.18  Aligned_cols=102  Identities=21%  Similarity=0.212  Sum_probs=76.1

Q ss_pred             CEEEEEeCCHHHHHHHHHHcCC--------------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCC
Q psy7847          65 GFGFVSFKDPQDFIRANKEMND--------------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR  124 (170)
Q Consensus        65 ~~afv~f~~~~~a~~~~~~~~~--------------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~  124 (170)
                      .++|..+.+...+..|+..+++                    .++|||+|||+.+++++|+++|+.||.|..+.+..++.
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~   84 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY   84 (135)
T ss_dssp             ------------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSS
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC
Confidence            3567777777778888877664                    25899999999999999999999999999999999888


Q ss_pred             CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         125 TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       125 ~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.|+.+
T Consensus        85 ~g~~~G~afV~F~~~~~A~~Ai~~l~g---~~i~g~~l~V~~a~~  126 (135)
T 2lea_A           85 TKESRGFAFVRFHDKRDAEDAMDAMDG---AVLDGRELRVQMARY  126 (135)
T ss_dssp             SSSCCSCCEEECSCHHHHHHHHTTTTT---CCSSSSCCEEEECCC
T ss_pred             CCccceEEEEEECCHHHHHHHHHHcCC---CEECCEEEEEEECCC
Confidence            899999999999999999999999999   999999999999875

>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=99.81  E-value=1.6e-19  Score=119.73  Aligned_cols=78  Identities=31%  Similarity=0.474  Sum_probs=72.9

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|++||.|..+.++++.  +.++|||||+|.+.++|.+|++.|||   ..++|++|+|.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~---~~~~g~~i~V~~   79 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG---MLLNDRKVFVGR   79 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCC---CEECCEEEEEEE
Confidence            4689999999999999999999999999999999985  45799999999999999999999999   999999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        80 a~~   82 (115)
T 4f25_A           80 FKS   82 (115)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            754

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

Probab=99.81  E-value=3.1e-19  Score=114.00  Aligned_cols=80  Identities=26%  Similarity=0.423  Sum_probs=76.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++.||+   ..++|++|+|+
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   91 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINN---KQLFGRVIKAS   91 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTT---EEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCC---CeeCCcEEEEE
Confidence            457999999999999999999999999999999999988889999999999999999999999999   99999999999


Q ss_pred             eec
Q psy7847         166 ITL  168 (170)
Q Consensus       166 ~~~  168 (170)
                      |+.
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            973

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

Probab=99.81  E-value=4.6e-20  Score=119.43  Aligned_cols=80  Identities=21%  Similarity=0.131  Sum_probs=76.1

Q ss_pred             CceEEecCCCC------CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC-
Q psy7847          87 DFRLFCGDLGN------DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD-  159 (170)
Q Consensus        87 ~~~l~v~nlp~------~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~-  159 (170)
                      .++|||+|||+      .+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||   ..++| 
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng---~~~~g~   82 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG---KRLDLK   82 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT---CBSSSS
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCC---cccCCC
Confidence            46899999999      999999999999999999999999998899999999999999999999999999   99998 


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      ++|+|+++.+
T Consensus        83 r~l~V~~a~~   92 (100)
T 3ns6_A           83 HRLFLYTMKD   92 (100)
T ss_dssp             CBCEEEESHH
T ss_pred             eEEEEEECch
Confidence            9999999864

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

Probab=99.81  E-value=2.5e-19  Score=116.40  Aligned_cols=81  Identities=23%  Similarity=0.331  Sum_probs=77.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|+..|||   ..++|+.|+|.
T Consensus        14 ~~~~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           14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG---FGYDHLILNVE   90 (103)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCC---CeeCCcEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        91 ~a~~   94 (103)
T 2cq0_A           91 WAKP   94 (103)
T ss_dssp             ESSC
T ss_pred             ECCC
Confidence            9875

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

Probab=99.81  E-value=3.4e-19  Score=114.90  Aligned_cols=81  Identities=26%  Similarity=0.319  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus         7 ~~~~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            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG---QVFQGRMLHVL   83 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT---EESSSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCC---CEECCcEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        84 ~a~~   87 (99)
T 1whw_A           84 PSTI   87 (99)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9865

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.80  E-value=3.7e-19  Score=114.81  Aligned_cols=80  Identities=25%  Similarity=0.266  Sum_probs=76.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeE--------EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLK--------AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV  157 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~  157 (170)
                      ...+|||+|||+.+++++|+++|++||.|..        +.+..++.++.++|||||+|.+.++|.+|++.|||   ..+
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g---~~~   88 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG---KEF   88 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTT---CBS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCC---CEe
Confidence            3579999999999999999999999999999        99999988899999999999999999999999999   999


Q ss_pred             CCeeEEEEeec
Q psy7847         158 GDLKTRSSITL  168 (170)
Q Consensus       158 ~~~~i~v~~~~  168 (170)
                      +|+.|+|.+|.
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999974

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

Probab=99.80  E-value=1e-19  Score=114.19  Aligned_cols=82  Identities=28%  Similarity=0.395  Sum_probs=77.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++.|||   ..++|+.++++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~~~~~   80 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA---SGVQAQMAKQS   80 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH---HTCCEESCCSS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcC---CeEeeEEEeec
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eeccC
Q psy7847         166 ITLKG  170 (170)
Q Consensus       166 ~~~~~  170 (170)
                      ++.++
T Consensus        81 ~~~sg   85 (85)
T 1x4e_A           81 GPSSG   85 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            88754

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5.8e-19  Score=113.85  Aligned_cols=80  Identities=20%  Similarity=0.343  Sum_probs=75.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||..+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++ ||+   ..++|++|+|.
T Consensus         9 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~---~~~~g~~l~V~   84 (99)
T 2dgs_A            9 KSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHF---HDIMGKKVEVK   84 (99)
T ss_dssp             SCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCC---CBSSSCBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCC---CEECCeEEEEE
Confidence            35799999999999999999999999999999999998889999999999999999999999 999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        85 ~a~~   88 (99)
T 2dgs_A           85 RAEP   88 (99)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9865

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

Probab=99.80  E-value=6.3e-19  Score=113.85  Aligned_cols=80  Identities=18%  Similarity=0.293  Sum_probs=76.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..++ ++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        16 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~   91 (100)
T 2do4_A           16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDG---MTIKENIIKVA   91 (100)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT---EESSSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            35799999999999999999999999999999999988 889999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        92 ~a~~   95 (100)
T 2do4_A           92 ISNS   95 (100)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9875

>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=99.80  E-value=3.5e-19  Score=116.85  Aligned_cols=81  Identities=21%  Similarity=0.443  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|+
T Consensus        25 ~~~~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           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG---FELAGRPMKVG  101 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTT---CCSSSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            357999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus       102 ~a~~  105 (108)
T 2jrs_A          102 HVTE  105 (108)
T ss_dssp             CSCS
T ss_pred             Eccc
Confidence            9875

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

Probab=99.80  E-value=3.9e-19  Score=115.99  Aligned_cols=81  Identities=17%  Similarity=0.260  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|+..|||   ..++|+.|+|.
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~   98 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG---QDLMGQPISVD   98 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTT---CBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcC---CEECCcEEEEE
Confidence            357899999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        99 ~a~~  102 (106)
T 1p27_B           99 WCFV  102 (106)
T ss_dssp             ESEE
T ss_pred             eecC
Confidence            9865

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.9e-19  Score=115.40  Aligned_cols=81  Identities=27%  Similarity=0.479  Sum_probs=76.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+ .+++++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v   80 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNG---QYLCNRPITV   80 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTT---CEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCC---CEECCEEEEE
Confidence            45799999999999999999999999999999 9999988899999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        81 ~~a~~   85 (96)
T 1x5t_A           81 SYAFK   85 (96)
T ss_dssp             EESCC
T ss_pred             EEecc
Confidence            99865

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=5.2e-19  Score=117.06  Aligned_cols=81  Identities=32%  Similarity=0.566  Sum_probs=77.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~   90 (115)
T 2dgo_A           14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG---QWLGGRQIRTN   90 (115)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT---CEETTEECEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        91 ~a~~   94 (115)
T 2dgo_A           91 WATR   94 (115)
T ss_dssp             ESSC
T ss_pred             EccC
Confidence            9864

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

Probab=99.80  E-value=2.8e-19  Score=115.89  Aligned_cols=81  Identities=26%  Similarity=0.374  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.||+   ..++|++|+|.
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~V~   87 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE---SELFGRTIRVN   87 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCC---CEECCcEEEEE
Confidence            357999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        88 ~a~~   91 (102)
T 2cqb_A           88 LAKP   91 (102)
T ss_dssp             ECCC
T ss_pred             eCCC
Confidence            9865

>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=99.80  E-value=4e-19  Score=113.65  Aligned_cols=82  Identities=28%  Similarity=0.423  Sum_probs=76.7

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+.+++++|+++|++||.|..+.+.+++. +.++|||||+|.+.++|.+|++.||+   ..++|++|+|
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V   89 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNG---IRLYGRPINV   89 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCC---CEECCCEEEE
Confidence            3457999999999999999999999999999999999884 88999999999999999999999999   9999999999


Q ss_pred             EeeccC
Q psy7847         165 SITLKG  170 (170)
Q Consensus       165 ~~~~~~  170 (170)
                      .++..+
T Consensus        90 ~~a~~G   95 (95)
T 2ywk_A           90 SGPSSG   95 (95)
T ss_dssp             ECCCCC
T ss_pred             EEcCCC
Confidence            998764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.9e-19  Score=115.83  Aligned_cols=81  Identities=35%  Similarity=0.515  Sum_probs=77.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.||+   ..++|++|+|.
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   87 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG---KSVDGRQIRVD   87 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT---CCTTSCCCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCC---CEECCeEEEEE
Confidence            457999999999999999999999999999999999988889999999999999999999999999   89999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        88 ~a~~   91 (102)
T 1x5s_A           88 QAGK   91 (102)
T ss_dssp             EEEC
T ss_pred             ECCC
Confidence            9875

>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=99.80  E-value=3.7e-19  Score=115.89  Aligned_cols=81  Identities=23%  Similarity=0.358  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|++.||+   ..++|++|+|.
T Consensus        14 ~~~~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           14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDM---IKLYGKPIRVN   90 (105)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSS---CBCSSCBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCC---CeECCeEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        91 ~a~~   94 (105)
T 1x5u_A           91 KASA   94 (105)
T ss_dssp             ETTT
T ss_pred             ECCC
Confidence            9865

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

Probab=99.79  E-value=3e-19  Score=115.99  Aligned_cols=82  Identities=23%  Similarity=0.330  Sum_probs=77.5

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ....+|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus        11 ~~~~~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           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG---AELDGRELRV   87 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSS---CCBTTBCCEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCC---CEECCcEEEE
Confidence            3457999999999999999999999999999999999988899999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++..
T Consensus        88 ~~a~~   92 (103)
T 2dnm_A           88 QVARY   92 (103)
T ss_dssp             EECSS
T ss_pred             EECCc
Confidence            99864

>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=99.79  E-value=7.3e-19  Score=115.56  Aligned_cols=81  Identities=16%  Similarity=0.260  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc------CCCccccCC
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN------EFPHLFVGD  159 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~------~~~~~~~~~  159 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+..||      +   ..++|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~---~~~~g   90 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGG---LKLDG   90 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCC---EESSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCC---cEEcC
Confidence            45799999999999999999999999999999999998889999999999999999999999999      9   99999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      ++|+|.++.+
T Consensus        91 ~~l~v~~a~~  100 (111)
T 1x4h_A           91 RQLKVDLAVT  100 (111)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEEECCC
Confidence            9999999865

>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=99.79  E-value=4.4e-19  Score=117.45  Aligned_cols=81  Identities=30%  Similarity=0.449  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.||+   ..++|+.|+|.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~  100 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG---FQIGMKRLKVQ  100 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            347999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus       101 ~a~~  104 (115)
T 2cpz_A          101 LKRS  104 (115)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            9865

>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=99.79  E-value=2e-19  Score=115.05  Aligned_cols=82  Identities=15%  Similarity=0.178  Sum_probs=75.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.||+   ..++|++|+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g---~~~~gr~l~v~   90 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND---RPIGSRKVKLS   90 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCC---CeECCcEEEEE
Confidence            457999999999999999999999999999888888888889999999999999999999999999   99999999999


Q ss_pred             eeccC
Q psy7847         166 ITLKG  170 (170)
Q Consensus       166 ~~~~~  170 (170)
                      ++..+
T Consensus        91 ~a~sg   95 (95)
T 2ek1_A           91 GPSSG   95 (95)
T ss_dssp             CCC--
T ss_pred             eccCC
Confidence            98764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3.4e-19  Score=114.92  Aligned_cols=81  Identities=19%  Similarity=0.288  Sum_probs=76.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCee-EEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee---
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFL-KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK---  161 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~-~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~---  161 (170)
                      ...+|||+|||+.+++++|+++|++||.|. .+.+++++.++.++|||||+|.+.++|.+|++.|||   ..++|+.   
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~~~~   84 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKING---KPLPGATPAK   84 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTT---SEESSCSSCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcC---CccCCCCcce
Confidence            357999999999999999999999999999 999999988899999999999999999999999999   9999999   


Q ss_pred             -EEEEeecc
Q psy7847         162 -TRSSITLK  169 (170)
Q Consensus       162 -i~v~~~~~  169 (170)
                       |+|+|+..
T Consensus        85 ~l~v~~a~~   93 (99)
T 2div_A           85 RFKLNYATY   93 (99)
T ss_dssp             ECCEEETTC
T ss_pred             eEEEeecCC
Confidence             99999875

>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=99.79  E-value=7e-19  Score=115.56  Aligned_cols=81  Identities=15%  Similarity=0.322  Sum_probs=77.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V~  101 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG---AEIMGQTIQVD  101 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCC---CEECCcEEEEE
Confidence            357999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus       102 ~a~~  105 (110)
T 1oo0_B          102 WCFV  105 (110)
T ss_dssp             ESEE
T ss_pred             Eccc
Confidence            9864

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.79  E-value=1.9e-19  Score=110.29  Aligned_cols=75  Identities=23%  Similarity=0.369  Sum_probs=71.6

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++ +|+   ..++|++|+|.+|
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-IHF---HEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSC---CCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCC---CEECCEEEEEEeC
Confidence            58999999999999999999999999999999998889999999999999999999998 899   9999999999886

>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=99.79  E-value=5.1e-19  Score=111.50  Aligned_cols=80  Identities=20%  Similarity=0.385  Sum_probs=74.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC-cccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK-TKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~-~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..+|||+|||+++++++|+++|++||.|..+.+..++.++. ++|+|||+|.+.++|.+|++.|||   ..++|+.|+|+
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~   80 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDG---GQIDGQEITAT   80 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCC---CeECCeEEEEE
Confidence            46899999999999999999999999999999998876555 899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        81 ~a~~   84 (88)
T 4a8x_A           81 AVLA   84 (88)
T ss_dssp             EECC
T ss_pred             ECCC
Confidence            9865

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.79  E-value=1.2e-18  Score=113.78  Aligned_cols=80  Identities=20%  Similarity=0.283  Sum_probs=76.4

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ....+|||+|||+.+++++|+++|+.||.|..+.+..++ ++.++|+|||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V  102 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG---VPLDGRPMNI  102 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCC---CEeCCcEEEE
Confidence            456899999999999999999999999999999999998 899999999999999999999999999   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      .++.
T Consensus       103 ~~a~  106 (107)
T 3ulh_A          103 QLVT  106 (107)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9986

>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=99.79  E-value=6.8e-19  Score=111.21  Aligned_cols=79  Identities=18%  Similarity=0.294  Sum_probs=75.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+.+++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|.+|+ .|||   ..++|++|+|.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g---~~~~g~~l~V~~   81 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDE---SLFRGRQIKVIP   81 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTT---CEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCC---CEECCcEEEEEE
Confidence            368999999999999999999999999999999999888999999999999999999999 8999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        82 a~~   84 (89)
T 3ucg_A           82 KRT   84 (89)
T ss_dssp             TTT
T ss_pred             ccC
Confidence            864

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

Probab=99.79  E-value=8.8e-19  Score=114.45  Aligned_cols=81  Identities=15%  Similarity=0.243  Sum_probs=76.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeec-CCCCCcccEEEEEecCHHHHHHHHHHh-cCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRD-KRTNKTKGFGFVSFKDPQDFIRANKEM-NEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~~~~i~  163 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.++++ +.++.++|||||+|.+.++|.+|+..| |+   ..++|++|+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~---~~~~g~~l~   90 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS---THLYGRRLV   90 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC---CBSSSCBCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccC---CeECCCEEE
Confidence            4579999999999999999999999999999999988 678899999999999999999999999 89   999999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.|+.+
T Consensus        91 v~~a~~   96 (107)
T 2cph_A           91 LEWADS   96 (107)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            999875

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.79  E-value=5.2e-19  Score=123.29  Aligned_cols=81  Identities=12%  Similarity=0.180  Sum_probs=76.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ...+|||+|||+++++++|+++|+.||  .|..+.++.|+.++.++|||||+|.+.++|.+|+..|||   ..++|+.|+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng---~~~~Gr~l~  130 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG---KVLNGEKVD  130 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTT---CEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC---CEECCeEeE
Confidence            457999999999999999999999999  999999999988999999999999999999999999999   999999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.++.+
T Consensus       131 V~~a~~  136 (156)
T 3n9u_C          131 VRPATR  136 (156)
T ss_dssp             EEECCH
T ss_pred             EEEcCC
Confidence            999864

>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=99.78  E-value=4.8e-19  Score=115.15  Aligned_cols=79  Identities=24%  Similarity=0.405  Sum_probs=75.9

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|.++
T Consensus         9 ~~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            9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG---REFSGRALRVDNA   85 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSS---BSCSSSCBEEEET
T ss_pred             cEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCC---CeeCCcEEEEEeC
Confidence            5899999999999999999999999999999999988899999999999999999999999999   9999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus        86 ~~   87 (104)
T 1p1t_A           86 AS   87 (104)
T ss_dssp             TC
T ss_pred             CC
Confidence            65

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

Probab=99.78  E-value=6e-19  Score=113.53  Aligned_cols=81  Identities=27%  Similarity=0.378  Sum_probs=75.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCC---CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR---TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ..++|||+|||+++++++|+++|+.||.|..+.+..++.   ++.++|||||+|.+.++|.+|++.|||   ..++|++|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l   80 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQG---HTVDGHKL   80 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTT---CEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCC---CeeCCeEE
Confidence            457899999999999999999999999999999998875   447899999999999999999999999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        81 ~V~~a~~   87 (98)
T 2cpf_A           81 EVRISER   87 (98)
T ss_dssp             EEECSSC
T ss_pred             EEEEccC
Confidence            9999865

>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=99.78  E-value=9.3e-19  Score=116.24  Aligned_cols=81  Identities=26%  Similarity=0.481  Sum_probs=76.6

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ....+|||+|||+++++++|+++|++||.|..+.+..++ ++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g---~~~~g~~l~V   80 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNG---KSLHGKAIKV   80 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSS---CBCSSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCC---CEECCEEEEE
Confidence            345799999999999999999999999999999999988 889999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        81 ~~a~~   85 (116)
T 2fy1_A           81 EQAKK   85 (116)
T ss_dssp             EECCC
T ss_pred             EECCC
Confidence            99864

>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=99.78  E-value=1.7e-18  Score=112.79  Aligned_cols=80  Identities=20%  Similarity=0.271  Sum_probs=75.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC---eeE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD---LKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~---~~i  162 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+.+++ ++.++|||||+|.+.++|.+|++.|||   ..+.+   ++|
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~gg~~~~l   89 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHG---SQTMPGASSSL   89 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSS---CCCCTTCSSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcC---CccCCCCCccE
Confidence            46799999999999999999999999999999999987 788999999999999999999999999   77777   999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        90 ~V~~a~~   96 (105)
T 2dnh_A           90 VVKFADT   96 (105)
T ss_dssp             EEEESCS
T ss_pred             EEEECcc
Confidence            9999865

>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=99.78  E-value=7.5e-19  Score=118.79  Aligned_cols=81  Identities=23%  Similarity=0.352  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        45 ~~~~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           45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG---MELDGRRIRVD  121 (129)
T ss_dssp             CSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTT---CCSSSSCCEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            357999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus       122 ~a~~  125 (129)
T 2kxn_B          122 FSIT  125 (129)
T ss_dssp             CCSS
T ss_pred             EecC
Confidence            9865

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.2e-19  Score=114.71  Aligned_cols=77  Identities=12%  Similarity=0.031  Sum_probs=72.9

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|++||.|..+.+++++. +.++|||||+|.+.++|.+|+. +|+   ..++|+.|+|.+
T Consensus        11 ~~~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           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPG---QKYKETDLLILF   85 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSC---CCCTTTTCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCC---CEECCEEEEEEE
Confidence            46999999999999999999999999999999999986 9999999999999999999999 899   999999999998


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            64

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.78  E-value=7e-19  Score=116.95  Aligned_cols=79  Identities=35%  Similarity=0.495  Sum_probs=75.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~V~  115 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG---FQVGTKRLKVQ  115 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCC---CEETTEECCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             ee
Q psy7847         166 IT  167 (170)
Q Consensus       166 ~~  167 (170)
                      |+
T Consensus       116 ~a  117 (118)
T 2khc_A          116 LK  117 (118)
T ss_dssp             EC
T ss_pred             ec
Confidence            87

>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=99.78  E-value=2.9e-19  Score=143.07  Aligned_cols=79  Identities=22%  Similarity=0.383  Sum_probs=76.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|||   ..++|+.|+|.|+
T Consensus       103 ~~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          103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG---KKIDGRRVLVDVE  179 (437)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCC---CEECCEEEEEEEe
Confidence            5999999999999999999999999999999999988899999999999999999999999999   9999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      ..
T Consensus       180 ~~  181 (437)
T 3pgw_S          180 RG  181 (437)
T ss_pred             CC
Confidence            64

>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=99.78  E-value=6.9e-19  Score=114.80  Aligned_cols=81  Identities=17%  Similarity=0.340  Sum_probs=76.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc---CCeeE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV---GDLKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~---~~~~i  162 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.||+   ..+   ++++|
T Consensus        12 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g---~~~~~~~g~~l   88 (106)
T 2dgp_A           12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHE---QKTLPGMNRPI   88 (106)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTT---TCCCTTCSSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcC---CcccCCCCceE
Confidence            357999999999999999999999999999999999988899999999999999999999999999   666   89999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        89 ~v~~a~~   95 (106)
T 2dgp_A           89 QVKPADS   95 (106)
T ss_dssp             EEEECCC
T ss_pred             EEEECCc
Confidence            9999865

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.6e-18  Score=112.51  Aligned_cols=79  Identities=29%  Similarity=0.522  Sum_probs=74.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..+  ++.++|||||+|.+.++|.+|++.||+   ..++|++|+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~V~   88 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG---RIVATKPLYVA   88 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTT---CBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCC---CEeCCcEEEEE
Confidence            3579999999999999999999999999999999987  788999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        89 ~a~~   92 (103)
T 2d9p_A           89 LAQR   92 (103)
T ss_dssp             ECSS
T ss_pred             Eecc
Confidence            9865

>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=99.78  E-value=2.1e-18  Score=108.62  Aligned_cols=79  Identities=23%  Similarity=0.389  Sum_probs=73.6

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+.+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++ +++   ..++|++|+|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~---~~~~g~~i~v   84 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKE---HRLDGRVIDP   84 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSC---EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCC---CEECCEEEEE
Confidence            456799999999999999999999999999999999998889999999999999999999997 477   7899999999


Q ss_pred             Eee
Q psy7847         165 SIT  167 (170)
Q Consensus       165 ~~~  167 (170)
                      .+|
T Consensus        85 ~~A   87 (87)
T 3s7r_A           85 KKA   87 (87)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            876

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.9e-18  Score=112.18  Aligned_cols=79  Identities=24%  Similarity=0.398  Sum_probs=74.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.|| |..+.+++++.++.++|||||+|.+.++|.+|+ .||+   ..++|++|+|.
T Consensus        14 ~~~~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           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDG---ALLGDRSLRVD   88 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTT---CEETTEECEEE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCC---CeECCeEEEEE
Confidence            357999999999999999999999996 999999999888999999999999999999999 8999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        89 ~a~~   92 (103)
T 2dng_A           89 IAEG   92 (103)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9865

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.78  E-value=7.1e-19  Score=109.91  Aligned_cols=74  Identities=8%  Similarity=0.111  Sum_probs=69.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..-|+|+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.++++|.+|++.||+   ..++|+.|+|.+
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~---~~l~gr~I~V~~   77 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNN---CVLANTTIFAES   77 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTT---EEETTEEEEEEC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcC---CEECCcEEEEEE
Confidence            45789999999999999999999999999998855      589999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      |.+
T Consensus        78 A~e   80 (89)
T 2wbr_A           78 PSE   80 (89)
T ss_dssp             CCH
T ss_pred             CCH
Confidence            853

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

Probab=99.77  E-value=6.4e-19  Score=113.39  Aligned_cols=81  Identities=12%  Similarity=0.159  Sum_probs=75.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g---~~~~g~~l~V~   90 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND---RPIGSRKVKLV   90 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCC---CeeCCeEEEEE
Confidence            457999999999999999999999999998888888887899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        91 ~a~~   94 (98)
T 2cqp_A           91 LGSG   94 (98)
T ss_dssp             ESSC
T ss_pred             EcCC
Confidence            9863

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.3e-18  Score=114.84  Aligned_cols=81  Identities=25%  Similarity=0.242  Sum_probs=76.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV  157 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~  157 (170)
                      ..++|||+|||+.+++++|+++|++||.|.        .+.+..++.++.++|||||+|.+.++|.+|++.|||   ..+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~   90 (113)
T 2cpe_A           14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG---KDF   90 (113)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT---CEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCC---Ccc
Confidence            457999999999999999999999999998        699999988899999999999999999999999999   999


Q ss_pred             CCeeEEEEeecc
Q psy7847         158 GDLKTRSSITLK  169 (170)
Q Consensus       158 ~~~~i~v~~~~~  169 (170)
                      +|++|+|.++.+
T Consensus        91 ~g~~l~V~~a~~  102 (113)
T 2cpe_A           91 QGSKLKVSLARK  102 (113)
T ss_dssp             TTEECEEECSSC
T ss_pred             CCCEEEEEECCC
Confidence            999999999865

>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=99.77  E-value=1.7e-18  Score=111.19  Aligned_cols=78  Identities=13%  Similarity=0.146  Sum_probs=72.8

Q ss_pred             CCceEEecCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          86 DDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                      ...+|||+|||+.+++++|+    ++|++||.|..+.++.++..   +|||||+|.+.++|.+|++.|||   ..++|++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g---~~~~gr~   81 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHR---YKIGSKK   81 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTT---EEETTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCC---CEECCeE
Confidence            45799999999999999999    99999999999999988643   88999999999999999999999   9999999


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      |+|+++.+
T Consensus        82 l~V~~a~~   89 (96)
T 2dgx_A           82 ILVSLATG   89 (96)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEcCC
Confidence            99999865

>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=99.77  E-value=1.1e-18  Score=114.96  Aligned_cols=81  Identities=16%  Similarity=0.264  Sum_probs=74.3

Q ss_pred             CCceEEecCCCCCCCHHHHH---HHhccCCCeeEEEEeecCCC---CCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          86 DDFRLFCGDLGNDVTDELLI---RTFSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~---~~f~~~g~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      ...+|||+|||+.+++++|.   ++|++||.|..+.+.++...   +.++|||||+|.+.++|.+|++.|||   ..++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng---~~~~g   90 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN---VVVDG   90 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTT---EEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCC---CEECC
Confidence            35699999999999999999   99999999999999888753   35679999999999999999999999   99999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      ++|+|.++.+
T Consensus        91 r~l~V~~a~~  100 (111)
T 2cpi_A           91 RTLKASLGTT  100 (111)
T ss_dssp             EEEEEESCCC
T ss_pred             EEEEEEeccc
Confidence            9999999875

>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=99.77  E-value=2.3e-18  Score=112.01  Aligned_cols=79  Identities=25%  Similarity=0.475  Sum_probs=74.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCC-CCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..++|||+|||+.+++++|+++|+.|| |..+.+++++.+ +.++|||||+|.+.++|.+|+ .||+   ..++|++|+|
T Consensus        14 ~~~~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           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNE---ESLGNKRIRV   88 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGT---CEETTEECEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCC---CEeCCcEEEE
Confidence            357999999999999999999999999 999999998876 889999999999999999999 9999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        89 ~~a~~   93 (104)
T 1wi8_A           89 DVADQ   93 (104)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99865

>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=99.77  E-value=1.8e-18  Score=116.25  Aligned_cols=81  Identities=17%  Similarity=0.260  Sum_probs=76.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|.
T Consensus        21 ~~~~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           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG---QDLMGQPISVD   97 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTT---CBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC---CeeCCeEEEEE
Confidence            357999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        98 ~a~~  101 (126)
T 3ex7_B           98 WCFV  101 (126)
T ss_dssp             ESEE
T ss_pred             EecC
Confidence            9864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.2e-18  Score=113.30  Aligned_cols=80  Identities=40%  Similarity=0.624  Sum_probs=75.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhcc-CCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccc-cCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF-VGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~-~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~-~~~~~i~  163 (170)
                      ...+|||+|||+.+++++|+++|+. ||.|..+.+.+++ ++.++|||||+|.+.++|.+|++.||+   .. ++|++|+
T Consensus         8 ~~~~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            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQG---AVGLGSKPVR   83 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTT---CCSSSSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccC---CcccCCEeEE
Confidence            3579999999999999999999999 9999999999998 899999999999999999999999999   88 9999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.++.+
T Consensus        84 v~~a~~   89 (104)
T 2dhg_A           84 LSVAIP   89 (104)
T ss_dssp             CCBCCC
T ss_pred             EEEccC
Confidence            999864

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=4.2e-18  Score=114.22  Aligned_cols=81  Identities=19%  Similarity=0.272  Sum_probs=76.8

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+.+++++|+++|+.||.|..+.+..++ ++.++|||||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V  108 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG---VPLDGRPMDI  108 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTT---EESSSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCC---CEECCcEEEE
Confidence            345799999999999999999999999999999999998 889999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++..
T Consensus       109 ~~a~~  113 (124)
T 2kt5_A          109 QLVAS  113 (124)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99875

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

Probab=99.77  E-value=2.5e-18  Score=109.25  Aligned_cols=79  Identities=25%  Similarity=0.348  Sum_probs=74.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.++  ++.++|||||+|.+.++|.+|++.||+   ..++|+.|+|.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g---~~~~g~~l~v~   81 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNG---MKLSGREIDVR   81 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTT---CCBTTBCCCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCC---CEECCcEEEEE
Confidence            4579999999999999999999999999999999874  688899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        82 ~a~~   85 (92)
T 2dgv_A           82 IDRN   85 (92)
T ss_dssp             ECSC
T ss_pred             EcCC
Confidence            9865

>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=99.77  E-value=1.5e-18  Score=114.64  Aligned_cols=78  Identities=17%  Similarity=0.239  Sum_probs=74.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|+ .|||   ..++|+.|+|.++
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g---~~~~g~~l~V~~a  101 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTG---QRLLGVPIIVQAS  101 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTT---EEETTEEEEEEEH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCC---CEeCCeEEEEEec
Confidence            69999999999999999999999999999999999888999999999999999999999 9999   9999999999997


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus       102 ~~  103 (114)
T 2cq4_A          102 QA  103 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.77  E-value=6.3e-18  Score=109.68  Aligned_cols=79  Identities=24%  Similarity=0.399  Sum_probs=73.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..++.  .++|||||+|.+.++|.+|+..||+   ..++|++|+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~   88 (103)
T 2cq3_A           14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHG---TVVEGRKIEVN   88 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            357999999999999999999999999999999998863  3899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        89 ~a~~   92 (103)
T 2cq3_A           89 NATA   92 (103)
T ss_dssp             ECCS
T ss_pred             Eccc
Confidence            9865

>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=99.77  E-value=4.2e-18  Score=110.54  Aligned_cols=79  Identities=22%  Similarity=0.338  Sum_probs=73.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+++  +.++|||||+|.+.++|.+|+..||+   ..++|++|+|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~   88 (103)
T 2cqi_A           14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNG---RKILGKEVKVN   88 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTT---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCC---CCcCCCeEEEE
Confidence            45799999999999999999999999999999999885  33689999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        89 ~a~~   92 (103)
T 2cqi_A           89 WATT   92 (103)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9864

>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=99.77  E-value=2.8e-18  Score=110.79  Aligned_cols=69  Identities=28%  Similarity=0.359  Sum_probs=64.6

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+.++|||+|||+++|+++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|++.+|+.
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~   84 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGL   84 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCC
Confidence            345678999999999999999999999999999999999989999999999999999999999999863

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.76  E-value=3.5e-18  Score=110.04  Aligned_cols=78  Identities=12%  Similarity=0.118  Sum_probs=69.7

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..+.+|||+|||+.+++++|+++|++||.|..+.++++      +|+|||+|.+.++|..|++.||+.+ ..++|++|.|
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~-~~i~Gr~i~V   91 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQ-IYIAGHPAFV   91 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSC-EEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCC-ceeCCcEEEE
Confidence            45689999999999999999999999999999988753      7899999999999999999999821 2488999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +|+..
T Consensus        92 ~~S~~   96 (100)
T 3r27_A           92 NYSTS   96 (100)
T ss_dssp             EECSC
T ss_pred             Eeccc
Confidence            99875

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

Probab=99.76  E-value=2e-18  Score=117.89  Aligned_cols=80  Identities=20%  Similarity=0.350  Sum_probs=76.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||..+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|.+
T Consensus        42 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~~  118 (139)
T 1u6f_A           42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG---FNILNKRLKVAL  118 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTT---EECSSCEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC---CEECCeEEEEEE
Confidence            47999999999999999999999999999999999988889999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus       119 a~~  121 (139)
T 1u6f_A          119 AAS  121 (139)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            875

>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=99.76  E-value=9.1e-19  Score=113.24  Aligned_cols=81  Identities=25%  Similarity=0.461  Sum_probs=73.5

Q ss_pred             cCCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecC-CCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          84 MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK-RTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        84 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ....++|||+|||+++++++|+++|+.|| |..+.+.+++ .++.++|||||+|.+.++|.+|+ .|||   ..++|+.|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g---~~~~g~~l   90 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNE---ESLGNRRI   90 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTT---CCBTTBCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCC---CEECCeEE
Confidence            34568999999999999999999999999 9999999987 58899999999999999999999 8999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        91 ~V~~a~~   97 (100)
T 2j76_E           91 RVDVADQ   97 (100)
T ss_dssp             CCEECCC
T ss_pred             EEEeccC
Confidence            9999875

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.76  E-value=2.6e-19  Score=113.49  Aligned_cols=78  Identities=23%  Similarity=0.376  Sum_probs=73.3

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.+ |.+|+..|||   ..++|++|+|++|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g---~~~~g~~l~V~~a   77 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDN---TDFMGRTIRVTEA   77 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCS---SCCSSSSCSEEEC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCC---CEECCeEEEEEEc
Confidence            47999999999999999999999999999999999888999999999999999 9999999999   9999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus        78 ~~   79 (90)
T 2ki2_A           78 NP   79 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            75

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

Probab=99.76  E-value=5.7e-18  Score=111.81  Aligned_cols=80  Identities=21%  Similarity=0.293  Sum_probs=75.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+..++ ++.++|||||+|.+.++|.+|++.||+   ..++|+.|+|.
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~   89 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNG---QLLFDRPMHVK   89 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCC---CEeCCCEEEEE
Confidence            35799999999999999999999999999999999987 588999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        90 ~a~~   93 (114)
T 2do0_A           90 MDER   93 (114)
T ss_dssp             ECSC
T ss_pred             Eccc
Confidence            9863

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=6e-18  Score=107.40  Aligned_cols=78  Identities=15%  Similarity=0.210  Sum_probs=73.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.| .|..+.++++ .++.++|+|||+|.+.++|.+|++ ||+   ..++|+.|+|.
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g---~~~~gr~i~v~   82 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNR---EYMGGRYIEVF   82 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCS---EEETTEEEEEE
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCC---ceeCCcEEEEE
Confidence            35799999999999999999999999 9999999998 588999999999999999999999 999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        83 ~a~~   86 (91)
T 2dgw_A           83 REKS   86 (91)
T ss_dssp             EESS
T ss_pred             ECCc
Confidence            9875

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

Probab=99.76  E-value=5.2e-18  Score=118.07  Aligned_cols=82  Identities=24%  Similarity=0.268  Sum_probs=78.0

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ....+|||+|||+.+++++|+++|+.||.|..|.++.++.++.++|||||+|.+.++|.+|++.||+   ..++|+.|+|
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V  113 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING---TRLDDRIIRT  113 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT---SEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC---CEECCeEEEE
Confidence            4568999999999999999999999999999999999988899999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .|+.+
T Consensus       114 ~~a~~  118 (156)
T 1h2v_Z          114 DWDAG  118 (156)
T ss_dssp             EEESC
T ss_pred             EECCC
Confidence            99864

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

Probab=99.76  E-value=3.2e-18  Score=116.82  Aligned_cols=79  Identities=27%  Similarity=0.395  Sum_probs=75.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~  138 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE---SELFGRTIRVN  138 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTE---EEETTEEEEEE
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             ee
Q psy7847         166 IT  167 (170)
Q Consensus       166 ~~  167 (170)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.1e-18  Score=112.33  Aligned_cols=80  Identities=29%  Similarity=0.416  Sum_probs=75.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|+.. |+   ..++|+.|+|.
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~---~~~~g~~l~V~   90 (105)
T 2dh8_A           15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RP---HTLDGRNIDPK   90 (105)
T ss_dssp             SSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CS---EEETTEEEBCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CC---CeECCEEEEEE
Confidence            457999999999999999999999999999999999988899999999999999999999998 99   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        91 ~a~~   94 (105)
T 2dh8_A           91 PCTP   94 (105)
T ss_dssp             CSCC
T ss_pred             EccC
Confidence            9864

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.76  E-value=4e-18  Score=114.23  Aligned_cols=79  Identities=18%  Similarity=0.262  Sum_probs=75.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||.++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|+ .|||   ..++|+.|+|.+
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g---~~~~g~~l~V~~  111 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDE---TVFRGRTIKVLP  111 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTT---CEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCC---CeECCeEEEEEE
Confidence            469999999999999999999999999999999999888999999999999999999999 7999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus       112 a~~  114 (124)
T 2jwn_A          112 KRT  114 (124)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.6e-18  Score=111.62  Aligned_cols=76  Identities=9%  Similarity=0.029  Sum_probs=68.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|++.|++. ...++|++|+|+|
T Consensus        16 ~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~-~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSV-TPVLRGQPIYIQF   88 (105)
T ss_dssp             CCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTS-CCEETTEECCBCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccC-CceECCEEEEEEE
Confidence            579999999999999999999999999999999875      799999999999999999988641 1678999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        89 A~~   91 (105)
T 1sjq_A           89 SNH   91 (105)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            865

>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=99.75  E-value=9.3e-18  Score=110.82  Aligned_cols=80  Identities=14%  Similarity=0.289  Sum_probs=74.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc--------
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV--------  157 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~--------  157 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.+.+++ ++.++|||||+|.+.++|.+|+..|||   ..+        
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g---~~~~~~~~~~~   99 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNG---KFIKTPPGVSA   99 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBT---CCCCCCTTSCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCC---CEEcCCccccC
Confidence            45799999999999999999999999999999999998 889999999999999999999999999   777        


Q ss_pred             CCeeEEEEeecc
Q psy7847         158 GDLKTRSSITLK  169 (170)
Q Consensus       158 ~~~~i~v~~~~~  169 (170)
                      .+++|+|.|+.+
T Consensus       100 ~~~~l~v~~a~p  111 (114)
T 1x5o_A          100 PTEPLLCKFSGP  111 (114)
T ss_dssp             CSSCBEEEECCC
T ss_pred             CCCceeEEccCC
Confidence            688899999875

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.75  E-value=7.1e-19  Score=119.16  Aligned_cols=80  Identities=14%  Similarity=0.284  Sum_probs=75.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeE--EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcc----ccCC
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLK--AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL----FVGD  159 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~--~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~----~~~~  159 (170)
                      ...+|||+|||+++++++|+++|++||.|..  +.+++|+.++.++|||||+|.+. +|.+|+..|||   .    .++|
T Consensus        22 ~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g---~~~~~~~~g   97 (131)
T 2m2b_A           22 ANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQA---LHPPLTIDG   97 (131)
T ss_dssp             CCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTT---CCCSCCGGG
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcC---CCCCccCCC
Confidence            3569999999999999999999999999976  99999998999999999999999 99999999999   7    9999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      +.|+|.++.+
T Consensus        98 r~l~V~~a~~  107 (131)
T 2m2b_A           98 KTINVEFAKG  107 (131)
T ss_dssp             CCCCCEECCC
T ss_pred             EEEEEEECCC
Confidence            9999999864

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=5.6e-18  Score=112.26  Aligned_cols=78  Identities=22%  Similarity=0.381  Sum_probs=74.7

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|++. |+   ..++|+.|+|.++
T Consensus        28 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~---~~~~g~~l~V~~a  103 (116)
T 1x4b_A           28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RP---HSIDGRVVEPKRA  103 (116)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CS---EEETTEEEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CC---cEECCEEEEEEEC
Confidence            6999999999999999999999999999999999988899999999999999999999998 98   9999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus       104 ~~  105 (116)
T 1x4b_A          104 VA  105 (116)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>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=99.75  E-value=3.2e-18  Score=112.15  Aligned_cols=81  Identities=17%  Similarity=0.269  Sum_probs=75.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCC-eeEEEEe-ecCCCCCcccEEEEEecCHHHHHHHHHHhc--CCCccccCCee
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVV-RDKRTNKTKGFGFVSFKDPQDFIRANKEMN--EFPHLFVGDLK  161 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~-~~~~~~~~~g~afv~f~~~~~a~~a~~~l~--~~~~~~~~~~~  161 (170)
                      ..++|||+|||+.+++++|+++|+.||. |..+.++ .++.++.++|||||+|.+.++|.+|+..||  +   ..++|++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~---~~~~g~~   83 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR---IQLWGHQ   83 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCC---SCBTTBC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCC---ceecCCe
Confidence            4579999999999999999999999998 9999988 777778999999999999999999999997  6   8899999


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      |+|.|+.+
T Consensus        84 l~V~~a~~   91 (109)
T 2dis_A           84 IAVDWAEP   91 (109)
T ss_dssp             CEEEESCS
T ss_pred             EEEEEcCC
Confidence            99999874

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.75  E-value=8e-18  Score=110.48  Aligned_cols=81  Identities=22%  Similarity=0.384  Sum_probs=73.9

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+.+++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|+..+ +   ..++|+.|+|
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~---~~l~g~~l~V   98 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-R---HELDSKTIDP   98 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-C---EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-C---CcCCCEEEEE
Confidence            34579999999999999999999999999999999999888999999999999999999999975 6   8999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        99 ~~a~~  103 (109)
T 2rs2_A           99 KVAFP  103 (109)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99864

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=5.4e-18  Score=111.28  Aligned_cols=79  Identities=23%  Similarity=0.384  Sum_probs=73.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||..+++++|+++|++||.|..+.+.+++  +.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        28 ~~~~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           28 QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHG---TVVEGRKIEVN  102 (109)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            35799999999999999999999999999999999885  34899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus       103 ~a~~  106 (109)
T 2err_A          103 NATA  106 (109)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.7e-18  Score=111.59  Aligned_cols=80  Identities=28%  Similarity=0.444  Sum_probs=74.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.+|+    .++|++|+|.
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~----~~~g~~l~V~   91 (116)
T 2cqd_A           16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP----IIDGRKANVN   91 (116)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC----EETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC----cCCCEEEEEE
Confidence            357999999999999999999999999999999999988899999999999999999999998886    4889999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        92 ~a~~   95 (116)
T 2cqd_A           92 LAYL   95 (116)
T ss_dssp             ESTT
T ss_pred             Eccc
Confidence            9854

>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=99.75  E-value=3.4e-18  Score=113.08  Aligned_cols=79  Identities=11%  Similarity=0.120  Sum_probs=74.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCe-eEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSF-LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i-~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..++|||+|||+.+++++|+++|+.||.| ..+.+++++ ++.++|||||+|.+.++|.+|++. |+   ..++|+.|+|
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~---~~~~gr~i~v   88 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HR---KKLNGREAFV   88 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CS---EEETTEEEEE
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CC---CccCCeEEEE
Confidence            35799999999999999999999999999 889999998 899999999999999999999997 99   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        89 ~~a~~   93 (114)
T 2cpy_A           89 HVVTL   93 (114)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99864

>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=99.75  E-value=9e-18  Score=117.98  Aligned_cols=81  Identities=15%  Similarity=0.322  Sum_probs=76.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+.+|++||.|..+.+..++.++.++|||||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V~  147 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG---AEIMGQTIQVD  147 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            356899999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus       148 ~a~~  151 (165)
T 1rk8_A          148 WCFV  151 (165)
T ss_dssp             ESEE
T ss_pred             EecC
Confidence            9864

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=2.2e-18  Score=105.97  Aligned_cols=75  Identities=24%  Similarity=0.405  Sum_probs=71.0

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|++||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.++    ..++|++|+|.+|
T Consensus         2 ~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~----~~~~g~~l~v~~a   76 (77)
T 1uaw_A            2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR----HELDSKTIDPKVA   76 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT----CCCSSCCCEEEEC
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC----CccCCEEEEEEec
Confidence            79999999999999999999999999999999998889999999999999999999999777    6789999999987

>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=9.4e-19  Score=107.15  Aligned_cols=75  Identities=24%  Similarity=0.426  Sum_probs=70.8

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++. ++   ..++|+.|+|.+|
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-KY---HNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SS---CCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CC---CeECCEEEEEEEC
Confidence            589999999999999999999999999999999988899999999999999999999995 88   8899999999875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.74  E-value=5e-18  Score=113.02  Aligned_cols=79  Identities=13%  Similarity=0.097  Sum_probs=73.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCC---eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPS---FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ..++|||+|||+++++++|+++|+.||.   |..+.+++++. +.++|||||+|.+.++|.+|++ +|+   ..++|+.|
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g---~~~~gr~i   90 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDR---ESMGHRYI   90 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTT---EEETTEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCC---CeECCeEE
Confidence            3578999999999999999999999999   89999999885 8999999999999999999999 999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        91 ~V~~a~~   97 (118)
T 2db1_A           91 EVFKSHR   97 (118)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            9998853

>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=99.74  E-value=8.5e-18  Score=109.41  Aligned_cols=79  Identities=16%  Similarity=0.119  Sum_probs=73.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...+|||+|||+.+++++|+++|++||.|.. +.++.+ .++.++|||||+|.+.++|.+|++. |+   ..++++.|+|
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~---~~~~gr~i~v   88 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HK---ERIGHRYIEI   88 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TT---CCSSSSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-Cc---chhCCcEEEE
Confidence            3579999999999999999999999999987 888888 5899999999999999999999997 99   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        89 ~~~~~   93 (104)
T 1wg5_A           89 FKSSR   93 (104)
T ss_dssp             EEECT
T ss_pred             EECCH
Confidence            98864

>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=99.74  E-value=1.8e-17  Score=107.54  Aligned_cols=79  Identities=22%  Similarity=0.312  Sum_probs=73.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|+.  ++   ..++|+.|+|.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~---~~~~g~~l~v~   88 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QR---HMIDGRWCDCK   88 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SC---EEETTEEEEEE
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cC---CeeCCeEEEEE
Confidence            45789999999999999999999999999999999998889999999999999999999999  46   88999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        89 ~a~~   92 (103)
T 2cqg_A           89 LPNS   92 (103)
T ss_dssp             CCCT
T ss_pred             ecCC
Confidence            9865

>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=99.74  E-value=4.5e-18  Score=110.22  Aligned_cols=77  Identities=10%  Similarity=0.048  Sum_probs=69.1

Q ss_pred             CCceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...+|||+|||+ .+++++|+++|++||.|..+.++++      +|+|||+|.+.++|..|++.||+. ...++|++|+|
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~-~~~~~Gr~l~V   86 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTT-PALVFGKPVRV   86 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHS-CCEETTEECEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCC-CceECCcEEEE
Confidence            457999999999 9999999999999999999999865      579999999999999999999861 14589999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        87 ~~a~~   91 (102)
T 1x4d_A           87 HLSQK   91 (102)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99974

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.74  E-value=1.8e-18  Score=107.54  Aligned_cols=73  Identities=16%  Similarity=0.251  Sum_probs=67.1

Q ss_pred             ceEEecCCCCCC------CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe-
Q psy7847          88 FRLFCGDLGNDV------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL-  160 (170)
Q Consensus        88 ~~l~v~nlp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~-  160 (170)
                      ++|||+|||+.+      ++++|+++|++||.|..+.+.+  .++.++|||||+|.+.++|.+|+..|||   ..++|+ 
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng---~~~~g~~   76 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADG---YKLDKQH   76 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSS---CCCSSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcC---cccCCce
Confidence            589999999999      7799999999999999998873  4788999999999999999999999999   999999 


Q ss_pred             eEEEE
Q psy7847         161 KTRSS  165 (170)
Q Consensus       161 ~i~v~  165 (170)
                      +|+|+
T Consensus        77 ~l~V~   81 (81)
T 2krb_A           77 TFRVN   81 (81)
T ss_dssp             CCCCC
T ss_pred             eEEeC
Confidence            88874

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

Probab=99.74  E-value=1.1e-17  Score=110.05  Aligned_cols=68  Identities=18%  Similarity=0.199  Sum_probs=64.7

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+|+.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~   71 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLT   71 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCC
Confidence            45789999999999999999999999999999999999989999999999999999999999999974

>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=99.74  E-value=1.2e-17  Score=111.04  Aligned_cols=77  Identities=9%  Similarity=0.026  Sum_probs=69.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|++.+++. ...++|++|+|.
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~-~~~l~Gr~l~V~  102 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSV-TPVLRGQPIYIQ  102 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHH-CCCBTTBCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccC-CceECCeEEEEE
Confidence            4579999999999999999999999999999999875      799999999999999999998841 157999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+..
T Consensus       103 ~a~~  106 (119)
T 2ad9_A          103 FSNH  106 (119)
T ss_dssp             ECSS
T ss_pred             EccC
Confidence            9865

>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=99.74  E-value=4.6e-18  Score=115.77  Aligned_cols=78  Identities=14%  Similarity=0.080  Sum_probs=73.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCC---eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPS---FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ..+|||+|||+++++++|+++|++||.   |..+.+++|+. +.++|||||+|.+.++|.+|++ +|+   ..++|+.|+
T Consensus        44 ~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g---~~l~gr~i~  118 (136)
T 2hgl_A           44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDR---ESMGHRYIE  118 (136)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTE---EESSSSEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCC---CEECCEEEE
Confidence            579999999999999999999999999   88999999985 9999999999999999999999 999   999999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.++..
T Consensus       119 V~~a~~  124 (136)
T 2hgl_A          119 VFKSHR  124 (136)
T ss_dssp             EEECCH
T ss_pred             EEECCh
Confidence            998753

>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=99.74  E-value=2.2e-17  Score=106.95  Aligned_cols=77  Identities=10%  Similarity=0.061  Sum_probs=68.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|++.|++. ...++|++|+|.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~-~~~~~Gr~l~V~   86 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAV-TPHLRNQPIYIQ   86 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHS-CCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccC-CceECCcEEEEE
Confidence            4579999999999999999999999999999988764      799999999999999999987531 177999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+..
T Consensus        87 ~a~~   90 (101)
T 2cq1_A           87 YSNH   90 (101)
T ss_dssp             ECSC
T ss_pred             EcCc
Confidence            9865

>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=99.74  E-value=1.9e-17  Score=108.53  Aligned_cols=78  Identities=22%  Similarity=0.342  Sum_probs=71.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|.+|++.||+   ..++|++|+|.
T Consensus        21 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~V~   94 (109)
T 1x4a_A           21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDG---YDYDGYRLRVE   94 (109)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCC---CEECCeEEEEE
Confidence            3579999999999999999999999999999998654   45799999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        95 ~a~~   98 (109)
T 1x4a_A           95 FPRS   98 (109)
T ss_dssp             CCCC
T ss_pred             Eccc
Confidence            9865

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=4.6e-18  Score=110.89  Aligned_cols=78  Identities=17%  Similarity=0.254  Sum_probs=72.0

Q ss_pred             CceEEecCCCCCC------CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          87 DFRLFCGDLGNDV------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        87 ~~~l~v~nlp~~~------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      .++|||+|||+.+      ++++|+++|++||.|..+.+.+  .++.++|||||+|.+.++|.+|+..|||   ..++|+
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g---~~~~g~   89 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADG---YKLDKQ   89 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSS---EECSTT
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCC---cccCCC
Confidence            4689999999999      7899999999999999998873  4788999999999999999999999999   999998


Q ss_pred             -eEEEEeecc
Q psy7847         161 -KTRSSITLK  169 (170)
Q Consensus       161 -~i~v~~~~~  169 (170)
                       +|+|.++..
T Consensus        90 ~~l~V~~a~~   99 (105)
T 2nlw_A           90 HTFRVNLFTD   99 (105)
T ss_dssp             CEEEEECSCC
T ss_pred             ceEEEEEcch
Confidence             999999863

>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=99.73  E-value=1.6e-17  Score=108.12  Aligned_cols=77  Identities=9%  Similarity=0.098  Sum_probs=68.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.++++      +|||||+|.+.++|.+|++.||+. ...++|++|+|.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~-~~~i~Gr~l~V~   86 (104)
T 1wex_A           14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADV-PVYIAGQQAFFN   86 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHS-CCBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccC-CceECCEEEEEE
Confidence            4579999999999999999999999999999988753      789999999999999999998761 145899999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+..
T Consensus        87 ~a~~   90 (104)
T 1wex_A           87 YSTS   90 (104)
T ss_dssp             ECSS
T ss_pred             EccC
Confidence            9864

>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=99.73  E-value=8.3e-18  Score=109.15  Aligned_cols=77  Identities=12%  Similarity=0.097  Sum_probs=71.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|+.||. ..+.+++++ ++.++|||||+|.+.++|.+|++ +|+   ..++++.|+|..
T Consensus        15 ~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~---~~~~gr~i~V~~   88 (102)
T 1wez_A           15 GHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDK---ANMQHRYVELFL   88 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSS---CCSSSSCCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCC---CeECCcEEEEEE
Confidence            469999999999999999999999995 599999998 89999999999999999999995 799   999999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus        89 ~~~   91 (102)
T 1wez_A           89 NST   91 (102)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.73  E-value=2.7e-18  Score=109.18  Aligned_cols=65  Identities=18%  Similarity=0.266  Sum_probs=61.0

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +.+|||+|||+++|+++|+++|+.|| .|.++++++++.+|.++|||||+|.+.++|.+|++.+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~   66 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQH   66 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCC
Confidence            46899999999999999999999999 899999999998999999999999999999999987653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.9e-17  Score=108.62  Aligned_cols=75  Identities=16%  Similarity=0.195  Sum_probs=70.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+|||+|||+.+++++|+++|+.| .|..+.+++|+. +.++|+|||+|.+.++|.+|+ .+|+   ..++|+.|+|..+
T Consensus        17 ~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~---~~~~gr~i~V~~a   90 (109)
T 2dnn_A           17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNR---MLMIQRYVEVSPA   90 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTT---EEETTEEEEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCC---CeECCeEEEEEEC
Confidence            589999999999999999999999 899999999874 899999999999999999999 6999   9999999999877


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus        91 ~   91 (109)
T 2dnn_A           91 T   91 (109)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.73  E-value=2.5e-18  Score=115.35  Aligned_cols=80  Identities=19%  Similarity=0.269  Sum_probs=73.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.+..++.++|||||+|.+.++|.+|+. ||+   ..++|+.|+|.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g---~~~~gr~i~V~   99 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHK---QYMGNRFIQVH   99 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCS---BCSTTSCBEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCC---CeECCcEEEEE
Confidence            45799999999999999999999999999886666666689999999999999999999999 999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus       100 ~a~~  103 (124)
T 1wel_A          100 PITK  103 (124)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            9864

>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=99.73  E-value=2.8e-17  Score=105.52  Aligned_cols=75  Identities=21%  Similarity=0.390  Sum_probs=69.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC--CeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG--DLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~--~~~i~  163 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|++.||+   ..++  |++|+
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g---~~~~~~g~~l~   86 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRG---FPLGGPDRRLR   86 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTT---CBCSSSSCBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCC---CEeCCCCcEEE
Confidence            4579999999999999999999999999999988654      78999999999999999999999   8888  99999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.|+.+
T Consensus        87 V~~a~~   92 (97)
T 1why_A           87 VDFAKS   92 (97)
T ss_dssp             EEECCC
T ss_pred             EEECCC
Confidence            999875

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

Probab=99.73  E-value=2.7e-17  Score=106.28  Aligned_cols=77  Identities=23%  Similarity=0.305  Sum_probs=70.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|   .++.+ .++.++|||||+|.+.++|.+|+..||+   ..++|++|+|.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   86 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNK---REIEGRAIRLE   86 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSS---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCC---CEeCCeEEEEE
Confidence            45799999999999999999999999977   45555 4788999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        87 ~a~~   90 (101)
T 2fc9_A           87 LQGP   90 (101)
T ss_dssp             ECSS
T ss_pred             EcCC
Confidence            9865

>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=99.72  E-value=2.3e-17  Score=106.30  Aligned_cols=76  Identities=26%  Similarity=0.413  Sum_probs=70.5

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+.+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g---~~~~g~~l~v   83 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDN---MPLRGKQLRV   83 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTT---CCBTTBCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCC---CEeCCceEEE
Confidence            34579999999999999999999999999999998754      78999999999999999999999   8999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        84 ~~a~~   88 (99)
T 2cpj_A           84 RFACH   88 (99)
T ss_dssp             EESSC
T ss_pred             EEcCC
Confidence            99865

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.72  E-value=1.4e-17  Score=109.64  Aligned_cols=78  Identities=12%  Similarity=0.071  Sum_probs=70.8

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCC-CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ....+|||+|||+++++++|+++|++|| .|..+.+..+    .++|||||+|.+.++|.+|++.|||   ..++|+.|+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng---~~l~Gr~i~   98 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNN---IEFRGSVIT   98 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTT---EEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCC---CEECCeEEE
Confidence            3457999999999999999999999999 8999888532    3689999999999999999999999   999999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.++..
T Consensus        99 V~~a~~  104 (111)
T 2jvr_A           99 VERDDN  104 (111)
T ss_dssp             EEESCC
T ss_pred             EEECCC
Confidence            999863

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.5e-17  Score=103.14  Aligned_cols=73  Identities=19%  Similarity=0.396  Sum_probs=68.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..||+   ..++|++|+|.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   75 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHH---YKLHGVNINVE   75 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTT---CBCSSCBCEEE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcC---CccCCcEEEEE
Confidence            45799999999999999999999999999999886        57999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        76 ~a~~   79 (90)
T 2dnq_A           76 ASKN   79 (90)
T ss_dssp             CSSC
T ss_pred             ECCC
Confidence            9865

>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=99.72  E-value=8.4e-18  Score=124.08  Aligned_cols=81  Identities=17%  Similarity=0.193  Sum_probs=75.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCC--CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ...+|||+|||+.+++++|+++|+.||  .|..|.+++|+.++.++|||||+|.+.++|.+|++.||+   ..++|+.|+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng---~~~~Gr~l~  143 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK---RELHGQNPV  143 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTT---SCBTTBCCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC---CeECCEEeE
Confidence            456899999999999999999999999  999999999988999999999999999999999999999   999999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |.++.+
T Consensus       144 V~~a~~  149 (229)
T 3q2s_C          144 VTPVNK  149 (229)
T ss_dssp             EEECCH
T ss_pred             EEECCC
Confidence            999853

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=3.5e-17  Score=107.17  Aligned_cols=74  Identities=19%  Similarity=0.179  Sum_probs=69.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC-----e
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD-----L  160 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~-----~  160 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+..+       |||||+|.+.++|.+|++.||+   ..++|     +
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g---~~~~g~~~~~~   83 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN---TKFRSHEGETA   83 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSS---EEEECTTSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCc---CCccCCcCcce
Confidence            3579999999999999999999999999999999775       8999999999999999999999   99999     9


Q ss_pred             eEEEEeecc
Q psy7847         161 KTRSSITLK  169 (170)
Q Consensus       161 ~i~v~~~~~  169 (170)
                      .|+|.++.+
T Consensus        84 ~i~V~~a~~   92 (108)
T 1x4c_A           84 YIRVKVDGP   92 (108)
T ss_dssp             EEEEEESSC
T ss_pred             EEEEEeCCC
Confidence            999999865

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

Probab=99.72  E-value=2e-17  Score=111.33  Aligned_cols=78  Identities=10%  Similarity=0.062  Sum_probs=70.6

Q ss_pred             CCceEEecCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          86 DDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                      ...+|||+|||+.+++++|+    ++|++||.|..|.+.+   ++.++|||||+|.+.++|..|+..|||   ..+.|++
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng---~~l~gr~  101 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQG---YPFQGNP  101 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTT---CCCTTSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCC---CEeCCCE
Confidence            35799999999999999876    6999999999987753   567899999999999999999999999   9999999


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      |+|.|+..
T Consensus       102 l~V~~a~~  109 (127)
T 2a3j_A          102 LVITFSET  109 (127)
T ss_dssp             CEEEECCC
T ss_pred             EEEEEccC
Confidence            99999864

>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=99.72  E-value=3.4e-18  Score=116.81  Aligned_cols=78  Identities=10%  Similarity=0.064  Sum_probs=71.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|++|| +..+.+++|+. +.++|||||+|.+.++|.+|+ .+|+   ..++++.|+|.
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g---~~l~gR~i~V~  118 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDR---ANMQHRYIELF  118 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCS---CSSSSCCCCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCC---CEECCEEEEEE
Confidence            346999999999999999999999999 67999999975 999999999999999999999 7899   99999999998


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      .+.+
T Consensus       119 ~a~~  122 (139)
T 2hgn_A          119 LNST  122 (139)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            8764

>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=99.72  E-value=4.3e-17  Score=107.76  Aligned_cols=78  Identities=19%  Similarity=0.207  Sum_probs=71.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.||.|..+.+.++   +.++|||||+|.+.++|.+|+..|||   ..++|+.|+|.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~v~   80 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSG---FNVSNRYLVVL   80 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTT---CBSSSCBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCC---CEECCeEEEEE
Confidence            3579999999999999999999999999999999865   44589999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        81 ~a~~   84 (115)
T 3lqv_A           81 YYNA   84 (115)
T ss_dssp             ECCH
T ss_pred             EecC
Confidence            9863

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

Probab=99.72  E-value=2.8e-17  Score=108.20  Aligned_cols=74  Identities=12%  Similarity=0.082  Sum_probs=68.8

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+.+++++|+++|++||.|..+.+.+      ++|+|||+|.+.++|.+|+..|||   ..++|++|+|.|
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V~~   80 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAY---SKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTT---CBSSSSBCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCC---CEECCeEEEEEE
Confidence            46899999999999999999999999999998864      478999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus        81 a~~   83 (111)
T 1whx_A           81 API   83 (111)
T ss_dssp             EET
T ss_pred             CCC
Confidence            864

>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=99.72  E-value=3.7e-17  Score=102.35  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=68.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHh-cCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM-NEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~~~~i~v  164 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.+.++      +|+|||+|.+.++|.+|++.| |+   ..++|++|+|
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~---~~~~g~~l~v   81 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNK---LIVNGRRLNV   81 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTT---CEETTEECCE
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCC---eeECCCEEEE
Confidence            3579999999999999999999999999999999864      789999999999999999998 98   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      .|+.
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9973

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=107.68  Aligned_cols=73  Identities=26%  Similarity=0.503  Sum_probs=69.4

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +|||+|||+++++++|+++|++||.|..+.+..+     ++|||||+|.+.++|.+|++.|||   ..++|++|+|.++.
T Consensus         2 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~~a~   73 (101)
T 2hvz_A            2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG---KVICGSRVRVELST   73 (101)
T ss_dssp             EEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHH---SCSSSCCCEEEESS
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCC---CeECCcEEEEEEcc
Confidence            7999999999999999999999999999999876     689999999999999999999999   89999999999986


Q ss_pred             c
Q psy7847         169 K  169 (170)
Q Consensus       169 ~  169 (170)
                      +
T Consensus        74 ~   74 (101)
T 2hvz_A           74 G   74 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.72  E-value=4.8e-18  Score=111.15  Aligned_cols=79  Identities=16%  Similarity=0.171  Sum_probs=73.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCC---eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPS---FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ..++|||+|||+++++++|+++|+.||.   |..+.+++++. +.++|+|||+|.+.++|.+|+. +|+   ..++|+.|
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~---~~~~gr~i   84 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHR---MYMGQRYV   84 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTT---CCSSSSCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCc---ceeCCeEE
Confidence            3578999999999999999999999888   89999999886 9999999999999999999999 999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        85 ~V~~a~~   91 (107)
T 2lmi_A           85 EVYEINN   91 (107)
T ss_dssp             CCEECCH
T ss_pred             EEEECCH
Confidence            9998763

>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=99.71  E-value=5.9e-17  Score=112.95  Aligned_cols=80  Identities=28%  Similarity=0.384  Sum_probs=76.2

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +++|||+|||+.+++++|+++|+.||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.|||   ..++|++|+|.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~---~~~~g~~l~v~~   78 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG---LRLQTKTIKVSY   78 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCC---CccCCceEEEEe
Confidence            46899999999999999999999999999999999988899999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        79 ~~~   81 (167)
T 1fxl_A           79 ARP   81 (167)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.71  E-value=3.3e-17  Score=107.38  Aligned_cols=78  Identities=21%  Similarity=0.424  Sum_probs=72.3

Q ss_pred             HcCCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          83 EMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        83 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      .-...++|||+|||..+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|||   ..++|++|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l   91 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG---TTIEGHVV   91 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTT---CEETTEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCC---CEECCcEE
Confidence            3445689999999999999999999999999999999875      78999999999999999999999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.|+.+
T Consensus        92 ~v~~a~~   98 (109)
T 1x4g_A           92 KCYWGKE   98 (109)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9999865

>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=99.71  E-value=7.6e-17  Score=103.63  Aligned_cols=75  Identities=27%  Similarity=0.399  Sum_probs=69.6

Q ss_pred             cCCCceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          84 MNDDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        84 ~~~~~~l~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      .+...+|||+|||+ .+++++|+++|+.||.|..+.+.        +|||||+|.+.++|.+|++.|||   ..++|++|
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l   87 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQ---EMNFGKKL   87 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTT---SEETTEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCC---CEECCEEE
Confidence            34568999999998 99999999999999999999882        78999999999999999999999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++..
T Consensus        88 ~V~~a~~   94 (97)
T 2xnq_A           88 ILEVSSS   94 (97)
T ss_dssp             EEEECCC
T ss_pred             EEEecCC
Confidence            9999865

>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=99.71  E-value=4.5e-17  Score=113.81  Aligned_cols=81  Identities=26%  Similarity=0.354  Sum_probs=76.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~---~~~~g~~l~v~   78 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG---ITVRNKRLKVS   78 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCC---CEeCCcEEEEE
Confidence            357899999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        79 ~~~~   82 (168)
T 1b7f_A           79 YARP   82 (168)
T ss_dssp             ECCC
T ss_pred             ecCC
Confidence            9864

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

Probab=99.71  E-value=9.9e-17  Score=102.22  Aligned_cols=70  Identities=27%  Similarity=0.460  Sum_probs=65.2

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|++.+++
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   80 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINN   80 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTT
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCC
Confidence            3445678999999999999999999999999999999999988899999999999999999999999886

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

Probab=99.71  E-value=6.2e-17  Score=104.72  Aligned_cols=78  Identities=29%  Similarity=0.452  Sum_probs=71.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|+.|   ..+.++.++.++.++|||||+|.+.++|.+|++.||+   ..++|+.|+|.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~V~   87 (102)
T 2fc8_A           14 PSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED---GEIDGNKVTLD   87 (102)
T ss_dssp             CCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC---CeECCeEEEEE
Confidence            45799999999999999999999977   3677777877889999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        88 ~a~~   91 (102)
T 2fc8_A           88 WAKP   91 (102)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            9875

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

Probab=99.71  E-value=3.3e-17  Score=105.88  Aligned_cols=74  Identities=15%  Similarity=0.175  Sum_probs=69.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||..+++++|+++|+.||.|..+.+.+      ++|||||+|.+.++|.+|+..|||   ..++|+.|+|+|
T Consensus        27 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V~~   97 (101)
T 2la4_A           27 VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALAN---FPFQGRNLRTGW   97 (101)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTT---CEETTEECCCCB
T ss_pred             CCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCC---CeECCeEEEEEe
Confidence            57999999999999999999999999999998873      479999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            875

>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=99.71  E-value=1.9e-17  Score=106.16  Aligned_cols=79  Identities=22%  Similarity=0.320  Sum_probs=72.4

Q ss_pred             CCCceEEecCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          85 NDDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      ....+|||+|||+.+++++|+    ++|++||.|..+.+.+   ++.++|||||+|.+.++|.+|+..|||   ..++|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~   79 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG---FPFYDK   79 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTT---CEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCC---CEECCc
Confidence            456799999999999999999    9999999999998864   356789999999999999999999999   999999


Q ss_pred             eEEEEeecc
Q psy7847         161 KTRSSITLK  169 (170)
Q Consensus       161 ~i~v~~~~~  169 (170)
                      +|+|+++.+
T Consensus        80 ~l~v~~a~~   88 (97)
T 1nu4_A           80 PMRIQYAKT   88 (97)
T ss_dssp             ECEEEECSS
T ss_pred             EEEEEEccC
Confidence            999999875

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.71  E-value=7.6e-17  Score=105.63  Aligned_cols=74  Identities=20%  Similarity=0.326  Sum_probs=69.4

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ....+|||+|||+.+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|+..|||   ..++|+.|+|
T Consensus        29 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V   97 (108)
T 2jvo_A           29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHG---KSFANQPLEV   97 (108)
T ss_dssp             CSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCC---CEECCeEEEE
Confidence            346799999999999999999999999999999886        68999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        98 ~~a~~  102 (108)
T 2jvo_A           98 VYSKL  102 (108)
T ss_dssp             ESCSC
T ss_pred             EEecC
Confidence            99865

>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=99.71  E-value=2.3e-17  Score=108.43  Aligned_cols=78  Identities=12%  Similarity=0.145  Sum_probs=68.9

Q ss_pred             CCCceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          85 NDDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        85 ~~~~~l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ....+|||+|||++ +++++|+++|++||.|..+.+.+.      +|||||+|.+.++|.+|++.||+. ...++|++|+
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~-~~~l~Gr~l~   95 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKK-ALWFQGRCVK   95 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHS-CCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccC-CceECCEEEE
Confidence            34679999999998 999999999999999999998643      799999999999999999988641 1568999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |+|+.+
T Consensus        96 V~~a~~  101 (112)
T 1x4f_A           96 VDLSEK  101 (112)
T ss_dssp             EEEECS
T ss_pred             EEECcc
Confidence            999975

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

Probab=99.71  E-value=7.4e-17  Score=102.97  Aligned_cols=72  Identities=25%  Similarity=0.370  Sum_probs=66.6

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...++.+.++|||+|||+++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|+..+++
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   79 (95)
T 2cqc_A            8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG   79 (95)
T ss_dssp             CCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            344556688999999999999999999999999999999999988899999999999999999999999886

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

Probab=99.71  E-value=4.4e-17  Score=104.64  Aligned_cols=75  Identities=16%  Similarity=0.220  Sum_probs=68.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+.+++++|+++|++||.|. +.+..+    .++|||||+|.+.++|.+|++.|||   ..++|++|+|.+
T Consensus        19 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~~   90 (97)
T 2e5j_A           19 AADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQG---LRLGTDTLRVAL   90 (97)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTT---CCSSSSCCEEEE
T ss_pred             CCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCC---CEECCcEEEEEE
Confidence            57999999999999999999999999997 566554    4689999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        91 a~~   93 (97)
T 2e5j_A           91 ARQ   93 (97)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

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

Probab=99.71  E-value=1.4e-17  Score=106.64  Aligned_cols=67  Identities=16%  Similarity=0.325  Sum_probs=62.1

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCC--eeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPS--FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~--v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .-.+|||+|||+++|+++|+++|++||.  +.+|++++++.+|.++|||||+|.+.++|.+|++.+++.
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~   76 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSL   76 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSS
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCC
Confidence            3468999999999999999999999995  679999999999999999999999999999999998864

>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=99.71  E-value=8.8e-17  Score=104.53  Aligned_cols=72  Identities=26%  Similarity=0.435  Sum_probs=66.5

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..++.+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|.+|+..+++
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   79 (105)
T 1x5u_A            8 PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDM   79 (105)
T ss_dssp             CCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSS
T ss_pred             CcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCC
Confidence            344556688999999999999999999999999999999999988899999999999999999999999886

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.71  E-value=7e-17  Score=117.74  Aligned_cols=80  Identities=31%  Similarity=0.448  Sum_probs=76.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|++||.|..|.+++|+.++.++|||||+|.+.++|.+|++.+|+   ..+.|+.+++.+
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~---~~~~g~~i~~~~   91 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF---DVIKGKPVRIMW   91 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhh---hhcCCccccccc
Confidence            46999999999999999999999999999999999998999999999999999999999999999   999999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus        92 ~~~   94 (213)
T 4f02_A           92 SQR   94 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            753

>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=99.70  E-value=6.4e-17  Score=101.69  Aligned_cols=68  Identities=25%  Similarity=0.499  Sum_probs=62.5

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      ..++.+.++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.
T Consensus         5 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   72 (87)
T 3s7r_A            5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ   72 (87)
T ss_dssp             --CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh
Confidence            44556788999999999999999999999999999999999988899999999999999999999965

>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=99.70  E-value=4.7e-17  Score=107.56  Aligned_cols=92  Identities=22%  Similarity=0.249  Sum_probs=79.2

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----ceEEe--
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----FRLFC--   92 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~~l~v--   92 (170)
                      +..+++|||+|||.++++++|+++|+.||.|.++.++.+   +.++|||||+|.+.++|.+|+..+|+.    ..|.|  
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            445789999999999999999999999999999999864   556899999999999999999998874    34444  


Q ss_pred             -------cCCCCCCCHHHHHHHhccCCC
Q psy7847          93 -------GDLGNDVTDELLIRTFSKYPS  113 (170)
Q Consensus        93 -------~nlp~~~~~~~l~~~f~~~g~  113 (170)
                             .+++...++++|+++|++||.
T Consensus        82 a~~~~~~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           82 YNANRAFQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CCHHHHTTTSCHHHHHHHHHHHHHHHCC
T ss_pred             ecCChhhhhhhHhHhHHHHHHHHHHhCC
Confidence                   356777889999999998875

>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=99.70  E-value=1e-16  Score=104.97  Aligned_cols=73  Identities=23%  Similarity=0.491  Sum_probs=67.1

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +....+.+.++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..+++
T Consensus        18 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g   90 (108)
T 2jrs_A           18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG   90 (108)
T ss_dssp             SSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTT
T ss_pred             ccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCC
Confidence            3445566678999999999999999999999999999999999988899999999999999999999998886

>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=99.70  E-value=6.9e-17  Score=101.03  Aligned_cols=69  Identities=28%  Similarity=0.470  Sum_probs=64.8

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+.++|||+|||+++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|++.+++.
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   72 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNES   72 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCC
Confidence            446789999999999999999999999999999999999889999999999999999999999998873

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.70  E-value=1.1e-16  Score=103.15  Aligned_cols=72  Identities=25%  Similarity=0.312  Sum_probs=66.2

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeE--------EEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLK--------AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~--------i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+...++|||+|||.++++++|+++|+.||.|.+        ++++.++.+|.++|||||+|.+.++|.+|++.+++.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            344556789999999999999999999999999999        999999888999999999999999999999988864

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

Probab=99.70  E-value=5.5e-17  Score=105.20  Aligned_cols=72  Identities=25%  Similarity=0.373  Sum_probs=66.5

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..+..+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|+..+++
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   77 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG   77 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSS
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCC
Confidence            344556688999999999999999999999999999999999988899999999999999999999998886

>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=99.70  E-value=7.5e-17  Score=108.92  Aligned_cols=73  Identities=25%  Similarity=0.360  Sum_probs=67.6

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+..++.+.++|||+|||+++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|+..+++
T Consensus        38 ~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng  110 (129)
T 2kxn_B           38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG  110 (129)
T ss_dssp             CCSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            3455567788999999999999999999999999999999999988899999999999999999999999886

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.70  E-value=5.7e-17  Score=115.19  Aligned_cols=79  Identities=19%  Similarity=0.275  Sum_probs=75.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+.+++++|+++|+.||.|..|.+..++ ++.++|+|||+|.+.++|.+|++.|||   ..++|++|+|.|
T Consensus        88 ~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng---~~l~Gr~l~V~~  163 (177)
T 2f3j_A           88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG---VPLDGRPMDIQL  163 (177)
T ss_dssp             CEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTT---CBCSSSBCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            5799999999999999999999999999999999988 889999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus       164 a~~  166 (177)
T 2f3j_A          164 VAS  166 (177)
T ss_dssp             ESS
T ss_pred             ecC
Confidence            864

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

Probab=99.70  E-value=9.1e-17  Score=104.16  Aligned_cols=73  Identities=23%  Similarity=0.376  Sum_probs=67.1

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +..+..+.++|||+|||.++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|+..+++.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~   80 (103)
T 2cq0_A            8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGF   80 (103)
T ss_dssp             SCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCC
Confidence            3445566889999999999999999999999999999999999889999999999999999999999998863

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=3.3e-18  Score=110.67  Aligned_cols=79  Identities=24%  Similarity=0.293  Sum_probs=71.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|+.||.|.. .++.+..++.++|||||+|.+.++|.+|++ |||   ..++|+.|+|.
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g---~~~~g~~l~V~   90 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTG---LKVFGNEIKLE   90 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGG---CCBTTBCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCC---cEECCcEEEEE
Confidence            4579999999999999999999999998877 556666678899999999999999999999 999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        91 ~a~~   94 (101)
T 1fj7_A           91 KPKG   94 (101)
T ss_dssp             CCSC
T ss_pred             EcCC
Confidence            9864

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.70  E-value=9e-17  Score=106.68  Aligned_cols=71  Identities=38%  Similarity=0.472  Sum_probs=65.7

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+..+.++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|++.+++.
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  105 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGF  105 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCC
Confidence            34556789999999999999999999999999999999999888999999999999999999999999873

>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=99.70  E-value=1.3e-16  Score=105.50  Aligned_cols=71  Identities=34%  Similarity=0.472  Sum_probs=65.6

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....+.++|||+|||.++++++|+++|+.||.|.++++++++.++.+++||||+|.+.++|.+|++.+++
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   89 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG   89 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCC
Confidence            34445678999999999999999999999999999999999988899999999999999999999999886

>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=99.70  E-value=8e-18  Score=111.27  Aligned_cols=81  Identities=15%  Similarity=0.149  Sum_probs=69.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g---~~~~g~~l~v~  100 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG---YKLYGKILVIE  100 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTT---CBCSSCBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCC---CEeCCcEEEEE
Confidence            357999999999999999999999999984332222222677899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus       101 ~a~~  104 (115)
T 2cpx_A          101 FGKN  104 (115)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9865

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

Probab=99.70  E-value=5.7e-17  Score=101.50  Aligned_cols=67  Identities=30%  Similarity=0.496  Sum_probs=63.4

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   69 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA   69 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcC
Confidence            4578999999999999999999999999999999999988899999999999999999999998875

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

Probab=99.70  E-value=3.5e-17  Score=105.74  Aligned_cols=67  Identities=25%  Similarity=0.250  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCC------CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGN------DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~------~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+++|||+|||.      ++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+++
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng   76 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG   76 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            3467999999999      999999999999999999999999998899999999999999999999998886

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.6e-16  Score=100.99  Aligned_cols=73  Identities=15%  Similarity=0.368  Sum_probs=68.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+        +||||+|.+.++|.+|+..||+   ..++|+.|+|+
T Consensus         9 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~V~   77 (92)
T 2dgt_A            9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDN---TEFQGKRMHVQ   77 (92)
T ss_dssp             SSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTT---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCC---CeeCCcEEEEE
Confidence            457999999999999999999999999999998863        4999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        78 ~a~~   81 (92)
T 2dgt_A           78 LSTS   81 (92)
T ss_dssp             ESSC
T ss_pred             EccC
Confidence            9865

>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=99.70  E-value=1.2e-16  Score=102.90  Aligned_cols=69  Identities=30%  Similarity=0.447  Sum_probs=64.8

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|+..+++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   72 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG   72 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCC
Confidence            345678999999999999999999999999999999999988899999999999999999999999886

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

Probab=99.70  E-value=1e-16  Score=102.76  Aligned_cols=76  Identities=26%  Similarity=0.400  Sum_probs=68.7

Q ss_pred             HcCCCceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          83 EMNDDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        83 ~~~~~~~l~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                      ......+|||+|||+ .+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|++.|||   ..++|++
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~   74 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQ---EMNFGKK   74 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTC---SSCBTTT
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCC---CeeCCcE
Confidence            345678999999998 99999999999999999999883        78999999999999999999999   9999999


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      |+|.++.+
T Consensus        75 l~V~~a~~   82 (96)
T 2kvi_A           75 LILEVSSS   82 (96)
T ss_dssp             BCEEEEEC
T ss_pred             EEEEEcCc
Confidence            99999864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=9.5e-17  Score=103.30  Aligned_cols=69  Identities=22%  Similarity=0.398  Sum_probs=64.8

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCee-EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFL-KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~-~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....++|||+|||+++++++|+++|+.||.|. ++++++++.++.+++||||+|.+.++|.+|+..+++
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   74 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKING   74 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTT
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcC
Confidence            344678999999999999999999999999999 999999988999999999999999999999998886

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=8.3e-17  Score=104.57  Aligned_cols=66  Identities=15%  Similarity=0.136  Sum_probs=60.9

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++|||+|||+++|+++|+++|+.||+|.++.+++++. |.++|||||+|.+.++|.+|+. +++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~   73 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPG   73 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCC
Confidence            34568999999999999999999999999999999999975 9999999999999999999998 554

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.7e-16  Score=102.18  Aligned_cols=69  Identities=22%  Similarity=0.454  Sum_probs=63.8

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+..+.++|||+|||.++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|+. +++
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~   73 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHF   73 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCC
Confidence            344567899999999999999999999999999999999998889999999999999999999998 765

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

Probab=99.70  E-value=1.9e-16  Score=102.06  Aligned_cols=69  Identities=19%  Similarity=0.300  Sum_probs=64.1

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+.++|||+|||.++++++|+++|+.||.|.++.++.++ +|.+++||||+|.+.++|.+|+..+++
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g   80 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDG   80 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCC
Confidence            344567899999999999999999999999999999999997 899999999999999999999999886

>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=99.69  E-value=9.5e-17  Score=100.81  Aligned_cols=67  Identities=34%  Similarity=0.598  Sum_probs=62.7

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..+++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   70 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG   70 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC
Confidence            3578999999999999999999999999999999999988899999999999999999999999886

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.8e-16  Score=104.99  Aligned_cols=72  Identities=31%  Similarity=0.478  Sum_probs=66.1

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ......+.++|||+|||.++++++|+++|+.||.|.++++++++.++.+++||||+|.+.++|.+|+..+++
T Consensus        10 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~   81 (116)
T 2cqd_A           10 GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP   81 (116)
T ss_dssp             CCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC
T ss_pred             CCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC
Confidence            344455678999999999999999999999999999999999988899999999999999999999998875

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

Probab=99.69  E-value=1.9e-16  Score=101.03  Aligned_cols=67  Identities=25%  Similarity=0.523  Sum_probs=63.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++++|||+|||.++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|+..+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   69 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNG   69 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCC
Confidence            4578999999999999999999999999999999999988899999999999999999999998886

>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=99.69  E-value=1.1e-16  Score=103.93  Aligned_cols=74  Identities=24%  Similarity=0.384  Sum_probs=68.6

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+.+++++|+++|++||.|..+.+.        +|||||+|.+.++|.+|++.||+   ..++|++|+|
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v   77 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNG---KDLEGENIEI   77 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTT---EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCC---CccCCCEEEE
Confidence            345799999999999999999999999999999885        45999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        78 ~~a~~   82 (103)
T 2dgu_A           78 VFAKP   82 (103)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.69  E-value=1.7e-16  Score=104.82  Aligned_cols=72  Identities=35%  Similarity=0.580  Sum_probs=66.8

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+..+.++|||+|||.++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|+..+++
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   79 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG   79 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            344556788999999999999999999999999999999999988899999999999999999999999886

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=3.3e-17  Score=106.10  Aligned_cols=77  Identities=22%  Similarity=0.422  Sum_probs=72.5

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+.+++++|+++|+.||.|..+.+.+++ ++.++|||||+|.+.++|.+|+.  ++   ..++|+.|.|.+
T Consensus         9 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~---~~~~g~~l~v~~   82 (102)
T 2xs2_A            9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQ---INFHGKKLKLGP   82 (102)
T ss_dssp             EEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CC---CEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CC---CeECCEEEEEEE
Confidence            4689999999999999999999999999999999998 89999999999999999999999  88   899999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        83 a~~   85 (102)
T 2xs2_A           83 AIR   85 (102)
T ss_dssp             EEE
T ss_pred             CCc
Confidence            763

>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=99.69  E-value=8.3e-17  Score=104.83  Aligned_cols=71  Identities=18%  Similarity=0.470  Sum_probs=65.8

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+.+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|+..+++.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~   78 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQ   78 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Confidence            34556789999999999999999999999999999999999888999999999999999999999988863

>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=99.69  E-value=1.3e-16  Score=100.68  Aligned_cols=74  Identities=11%  Similarity=0.095  Sum_probs=68.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++| .|..+.+.      .++|||||+|.+.++|.+|++.|||   ..++|++|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g---~~~~g~~l~V~   73 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQ---YSFRGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTT---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCC---CeECCcEEEEE
Confidence            35689999999999999999999999 99998884      4689999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        74 ~a~~   77 (88)
T 1wg1_A           74 LQPT   77 (88)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9864

>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=99.69  E-value=1.3e-16  Score=99.25  Aligned_cols=66  Identities=39%  Similarity=0.717  Sum_probs=62.6

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..+++.
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~   66 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ   66 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCC
Confidence            368999999999999999999999999999999999889999999999999999999999998863

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.69  E-value=8e-17  Score=105.68  Aligned_cols=72  Identities=25%  Similarity=0.433  Sum_probs=60.4

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ...+++.+.++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|+..++
T Consensus        17 ~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~   88 (109)
T 2rs2_A           17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   88 (109)
T ss_dssp             ---------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC
Confidence            344556678899999999999999999999999999999999998889999999999999999999997653

>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=99.69  E-value=1.4e-16  Score=101.99  Aligned_cols=67  Identities=22%  Similarity=0.416  Sum_probs=63.4

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ++++|||+|||.++++++|+++|+.||.|.+++++.++.+|.++|||||+|.+.++|.+|+..+++.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   67 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGY   67 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCC
Confidence            3679999999999999999999999999999999999888999999999999999999999998863

>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=99.69  E-value=2e-16  Score=103.83  Aligned_cols=69  Identities=17%  Similarity=0.260  Sum_probs=64.9

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      .++.+.++|||+|||+++++++|+++|+.||.|.++.+++++.++.++|||||+|.+.++|.+|+..++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   78 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS   78 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHC
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhc
Confidence            345567899999999999999999999999999999999998889999999999999999999999988

>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=99.69  E-value=5.7e-17  Score=107.03  Aligned_cols=66  Identities=20%  Similarity=0.355  Sum_probs=62.3

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+ .+++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g   88 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTG   88 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCC
Confidence            44578999999999999999999999999999999999888999999999999999999999 8886

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.69  E-value=5.9e-17  Score=109.63  Aligned_cols=73  Identities=14%  Similarity=0.313  Sum_probs=65.8

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeE--EEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLK--AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~--i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .........++|||+|||+++++++|+++|+.||.|..  |++++++.+|.++|||||+|.+. +|.+|+..+++.
T Consensus        15 ~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~   89 (131)
T 2m2b_A           15 SEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQAL   89 (131)
T ss_dssp             CCCCCSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCC
Confidence            33344466789999999999999999999999999976  99999998999999999999999 999999999974

>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=99.69  E-value=2.4e-16  Score=102.46  Aligned_cols=67  Identities=24%  Similarity=0.413  Sum_probs=63.1

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.++.++ +|.+++||||+|.+.++|.+|+..+++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g   78 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHG   78 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcC
Confidence            3457899999999999999999999999999999999997 899999999999999999999998886

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-16  Score=101.04  Aligned_cols=73  Identities=19%  Similarity=0.360  Sum_probs=68.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.+        +||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus         8 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~   76 (90)
T 2dnp_A            8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNG---KEVKGKRINVE   76 (90)
T ss_dssp             CSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCC---CEECCcEEEEE
Confidence            457999999999999999999999999999998863        4999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        77 ~a~~   80 (90)
T 2dnp_A           77 LSTK   80 (90)
T ss_dssp             ESCC
T ss_pred             ECCC
Confidence            9875

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.3e-16  Score=100.83  Aligned_cols=74  Identities=16%  Similarity=0.311  Sum_probs=68.0

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccC--CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~--g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ...++|||+|||+.+++++|+++|++|  |.|..+.+.        +|||||+|.+.++|.+|+..|||   ..++|++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l   81 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNG---KVLDGSPI   81 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSS---EEETTEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCC---CEeCCcEE
Confidence            345799999999999999999999999  889888763        67999999999999999999999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.++.+
T Consensus        82 ~v~~a~~   88 (99)
T 2cpd_A           82 EVTLAKP   88 (99)
T ss_dssp             EEECCCC
T ss_pred             EEEECCC
Confidence            9999875

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

Probab=99.68  E-value=4.3e-17  Score=104.36  Aligned_cols=76  Identities=17%  Similarity=0.208  Sum_probs=69.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~~l~v~   86 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQG---AEIDGRSVSLY   86 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTE---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCC---CEECCeEEEEE
Confidence            35799999999999999999999999988766     22677899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        87 ~a~~   90 (96)
T 1fjc_A           87 YTGE   90 (96)
T ss_dssp             ECSS
T ss_pred             EcCC
Confidence            9864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=6.7e-17  Score=108.19  Aligned_cols=88  Identities=13%  Similarity=0.047  Sum_probs=76.2

Q ss_pred             HHHHHHHHHcCCCceEEecCCCCCCCHHHHHHHhccCCCe----eEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc
Q psy7847          75 QDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSF----LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        75 ~~a~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i----~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                      ..+.+.+. -....+|||+|||+++++++|+++|++||.|    ..|.++.+. ++.++|+|||+|.+.++|.+|++. |
T Consensus        12 ~~~~~~~~-~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~   88 (123)
T 2dha_A           12 NEVAQFLS-KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-H   88 (123)
T ss_dssp             HHHHHHHH-CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-T
T ss_pred             hhHHhhcc-CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-C
Confidence            34445553 3456899999999999999999999999875    688888885 899999999999999999999996 8


Q ss_pred             CCCccccCCeeEEEEeec
Q psy7847         151 EFPHLFVGDLKTRSSITL  168 (170)
Q Consensus       151 ~~~~~~~~~~~i~v~~~~  168 (170)
                      +   ..++++.|+|..+.
T Consensus        89 ~---~~l~gR~i~V~~a~  103 (123)
T 2dha_A           89 K---DLLGKRYIELFRST  103 (123)
T ss_dssp             T---EESSSCEECCEEEC
T ss_pred             C---CeeCCeEEEEEECC
Confidence            8   99999999998775

>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=99.68  E-value=3.5e-17  Score=103.71  Aligned_cols=64  Identities=20%  Similarity=0.292  Sum_probs=59.3

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCC--CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g--~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++|||+|||.++++++|+++|+.||  .+.+++++.++.+|.++|||||+|.+.++|.+|++.+++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g   67 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPK   67 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGG
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCC
Confidence            5799999999999999999999999  999999999998999999999999999999999998886

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

Probab=99.68  E-value=1.7e-16  Score=103.37  Aligned_cols=68  Identities=21%  Similarity=0.362  Sum_probs=64.0

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..+++
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   87 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG   87 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcC
Confidence            34567899999999999999999999999999999999988899999999999999999999998886

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.7e-16  Score=102.68  Aligned_cols=70  Identities=34%  Similarity=0.573  Sum_probs=65.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+.++|||+|||+++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|++.+++
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   76 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG   76 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            3455678999999999999999999999999999999999988899999999999999999999999886

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.51  E-value=2.2e-18  Score=114.25  Aligned_cols=81  Identities=25%  Similarity=0.274  Sum_probs=75.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeE--------EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLK--------AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV  157 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~  157 (170)
                      ...+|||+|||+.+++++|+++|++||.|..        +.+..++.++.++|||||+|.+.++|.+|+..|||   ..+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~   82 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG---KEF   82 (116)
Confidence            4568999999999999999999999999998        88988877889999999999999999999999999   999


Q ss_pred             CCeeEEEEeecc
Q psy7847         158 GDLKTRSSITLK  169 (170)
Q Consensus       158 ~~~~i~v~~~~~  169 (170)
                      +|++|+|.++.+
T Consensus        83 ~g~~l~V~~a~~   94 (116)
T 2lcw_A           83 SGNPIKVSFATR   94 (116)
Confidence            999999999864

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

Probab=99.68  E-value=2.5e-16  Score=102.64  Aligned_cols=71  Identities=17%  Similarity=0.344  Sum_probs=65.1

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEec-CCCCCcCCEEEEEeCCHHHHHHHHHHc-CC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRD-KRTNKTKGFGFVSFKDPQDFIRANKEM-ND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~-~~~~~~~~~afv~f~~~~~a~~~~~~~-~~   86 (170)
                      .......++|||+|||.++++++|+++|+.||.|.++.++++ +.++.+++||||+|.+.++|.+|+..+ ++
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~   81 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS   81 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccC
Confidence            344556789999999999999999999999999999999998 778999999999999999999999998 65

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.3e-16  Score=102.36  Aligned_cols=70  Identities=41%  Similarity=0.630  Sum_probs=64.8

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhc-CCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSK-YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~-~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .++.+.++|||+|||+++++++|+++|+. ||.|.++.++.++ +|.++|||||+|.+.++|.+|+..+++.
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   74 (104)
T 2dhg_A            4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGA   74 (104)
T ss_dssp             CCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCC
Confidence            34456789999999999999999999999 9999999999998 9999999999999999999999988863

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

Probab=99.68  E-value=1.2e-16  Score=103.39  Aligned_cols=70  Identities=27%  Similarity=0.442  Sum_probs=65.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|++.+++
T Consensus         7 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   76 (102)
T 2cqb_A            7 GMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE   76 (102)
T ss_dssp             CSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            3445678999999999999999999999999999999999988899999999999999999999998886

>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=99.68  E-value=5.8e-17  Score=108.82  Aligned_cols=79  Identities=18%  Similarity=0.119  Sum_probs=71.2

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCee--EEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFL--KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~--~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ....+|||+|||+++++++|+++|+.| .|.  .|.+++|+. +.++|||||+|.+.++|.+|++ +++   ..++|+.|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~---~~l~gR~I  113 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHK---ERIGHRYI  113 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTT---CCBTTBCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCC---CEECCEEE
Confidence            345799999999999999999999999 666  899999885 9999999999999999999998 478   89999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|..+.+
T Consensus       114 ~V~~a~~  120 (126)
T 2hgm_A          114 EVFKSSQ  120 (126)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9988753

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.67  E-value=5e-16  Score=104.46  Aligned_cols=77  Identities=19%  Similarity=0.273  Sum_probs=69.0

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccE-EEEEecCHHHHHHHHHHhcCCCccccCC--ee
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF-GFVSFKDPQDFIRANKEMNEFPHLFVGD--LK  161 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~l~~~~~~~~~~--~~  161 (170)
                      +.-..|||+||++.+++++|+++|++||.|..|.+..+.     +|+ |||+|.+.++|.+|++.|||   ..+.|  +.
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG---~~i~g~~~~   97 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDG---QNIYNACCT   97 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTT---CEEETTEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCC---CeecCCCcE
Confidence            445688999999999999999999999999999887643     577 99999999999999999999   88877  99


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      |+|.|+..
T Consensus        98 LrI~~ak~  105 (130)
T 3zzy_A           98 LRIDFSKL  105 (130)
T ss_dssp             EEEEECSC
T ss_pred             EEEEecCC
Confidence            99999864

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.7e-16  Score=101.49  Aligned_cols=68  Identities=29%  Similarity=0.541  Sum_probs=63.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEE-EEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i-~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.++|||+|||+++++++|+++|+.||.|.++ .+++++.++.+++||||+|.+.++|.+|+..+++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~   71 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ   71 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCC
Confidence            457899999999999999999999999999999 99999889999999999999999999999988863

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.5e-16  Score=101.37  Aligned_cols=70  Identities=31%  Similarity=0.563  Sum_probs=64.1

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+.+.++|||+|||+++++++|+++|+.||.|.++.++.+  ++.+++||||+|.+.++|.+|+..+++.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~   78 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGR   78 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCC
Confidence            344557889999999999999999999999999999999998  7899999999999999999999988863

>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=99.67  E-value=1.7e-16  Score=104.09  Aligned_cols=72  Identities=22%  Similarity=0.314  Sum_probs=67.9

Q ss_pred             CceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..+|||+|||+. +++++|+++|++||.|..+.+        ++|||||+|.+.++|.+|++.||+   ..++|+.|+|.
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g---~~~~g~~l~V~   95 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENG---RVLAGQTLDIN   95 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTT---CEETTEECCEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCC---CEECCeEEEEE
Confidence            479999999999 999999999999999999988        478999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        96 ~a~~   99 (110)
T 1wf1_A           96 MAGE   99 (110)
T ss_dssp             ESCC
T ss_pred             ECCC
Confidence            9863

>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=99.67  E-value=2.2e-16  Score=100.81  Aligned_cols=70  Identities=31%  Similarity=0.535  Sum_probs=63.6

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+.+.++|||+|||+++++++|+++|+.||.|.++.+++++ ++.+++||||+|.+.++|.+|+..+++.
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   80 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGI   80 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTC
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCC
Confidence            344567899999999999999999999999999999999997 4899999999999999999999988863

>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=99.67  E-value=3.6e-16  Score=103.65  Aligned_cols=68  Identities=31%  Similarity=0.627  Sum_probs=63.9

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..+.++|||+|||.++++++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|+..+++
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g   70 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNG   70 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCC
Confidence            34567899999999999999999999999999999999997 899999999999999999999999886

>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=99.67  E-value=9.9e-17  Score=103.58  Aligned_cols=72  Identities=24%  Similarity=0.487  Sum_probs=59.7

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecC-CCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK-RTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~-~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.......++|||+|||.++++++|+++|+.|| |.++.+++++ .+|.++|||||+|.+.++|.+|+ .+++.
T Consensus        11 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~   83 (100)
T 2j76_E           11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEE   83 (100)
T ss_dssp             ---------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTC
T ss_pred             CCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCC
Confidence            3444556688999999999999999999999999 9999999987 58999999999999999999999 88863

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.6e-16  Score=101.60  Aligned_cols=77  Identities=13%  Similarity=0.119  Sum_probs=69.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEE-EEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA-KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+ .++.++..    |.|||+|.+.++|.+|+..|||   ..++|++|+|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g---~~~~g~~l~V   86 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNG---FQLENFTLKV   86 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTT---CBCSSCBCEE
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCC---CEECCcEEEE
Confidence            35799999999999999999999999999999 47777532    3499999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        87 ~~a~~   91 (96)
T 2e44_A           87 AYIPD   91 (96)
T ss_dssp             EECCC
T ss_pred             EEcCc
Confidence            99875

>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=99.67  E-value=4.1e-16  Score=101.70  Aligned_cols=71  Identities=24%  Similarity=0.319  Sum_probs=65.1

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .....+.++|||+|||+++++++|+++|+.||.|.++.++.++ +|.+++||||+|.+.++|.+|+..+++.
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   93 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV   93 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            3445567899999999999999999999999999999999997 9999999999999999999999998863

>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=99.67  E-value=3.2e-16  Score=102.77  Aligned_cols=69  Identities=17%  Similarity=0.406  Sum_probs=64.4

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..+++.
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~   91 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA   91 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence            345688999999999999999999999999999999999888999999999999999999999998863

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

Probab=99.66  E-value=2.8e-16  Score=109.39  Aligned_cols=78  Identities=21%  Similarity=0.342  Sum_probs=72.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+++++++|+++|+.||.|..+.+.+++ .+.++|+|||+|.+.++|.+|++.+||   ..++|+.|+|.++
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~---~~~~g~~i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNG---KQIENNIVKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCC---CccCCCeeEEEEc
Confidence            479999999999999999999999999999999887 577899999999999999999999999   9999999999987


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      ..
T Consensus        77 ~~   78 (166)
T 3md3_A           77 FQ   78 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.66  E-value=2.8e-16  Score=109.42  Aligned_cols=66  Identities=14%  Similarity=0.235  Sum_probs=62.4

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCC--CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g--~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++|||+|||+++++++|+++|+.||  .|.+++++.++.+|.++|||||+|.+.++|.+|+..+++
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng  121 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPG  121 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC
Confidence            457999999999999999999999999  999999999999999999999999999999999999986

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

Probab=99.66  E-value=4.4e-16  Score=106.20  Aligned_cols=70  Identities=24%  Similarity=0.385  Sum_probs=65.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++...++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+++
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  106 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG  106 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            3445678999999999999999999999999999999999988899999999999999999999999886

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=3.7e-16  Score=101.62  Aligned_cols=69  Identities=33%  Similarity=0.523  Sum_probs=64.0

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+..+.++|||+|||+++++++|+++|+.||.|.++.+++++.++.+++||||+|.+.++|.+|+.. ++
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~   79 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RP   79 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CC
Confidence            3455678999999999999999999999999999999999988899999999999999999999987 54

>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=99.66  E-value=3.8e-16  Score=108.86  Aligned_cols=75  Identities=19%  Similarity=0.237  Sum_probs=67.9

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC--eeEEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD--LKTRSS  165 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~--~~i~v~  165 (170)
                      .+|||+||++.+++++|+++|++||.|..|.+..+.    ++|+|||+|.+.++|.+|++.|||   ..+.+  +.|+|.
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG---~~i~g~g~~L~V~  119 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDG---QNIYNACCTLRID  119 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTT---BCSSSSCSCEEEE
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCC---CEecCCCcEEEEE
Confidence            578999999999999999999999999999886542    578999999999999999999999   88855  999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+..
T Consensus       120 ~Ak~  123 (164)
T 1sjr_A          120 FSKL  123 (164)
T ss_dssp             ECSS
T ss_pred             EecC
Confidence            9864

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.66  E-value=7.6e-16  Score=96.16  Aligned_cols=79  Identities=9%  Similarity=0.172  Sum_probs=68.5

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----CceEEecCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----DFRLFCGDLG   96 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----~~~l~v~nlp   96 (170)
                      .+..|+|+||++.+|+++|+++|.+||+|.++.+..      ++|||||+|.+.++|.+|++.+|+    .++|.|.   
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~---   76 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAE---   76 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE---
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE---
Confidence            367899999999999999999999999999999865      579999999999999999999996    3566653   


Q ss_pred             CCCCHHHHHHHhc
Q psy7847          97 NDVTDELLIRTFS  109 (170)
Q Consensus        97 ~~~~~~~l~~~f~  109 (170)
                       .+++.++..+|+
T Consensus        77 -~A~e~~~~~~~~   88 (89)
T 2wbr_A           77 -SPSENEVQSIMQ   88 (89)
T ss_dssp             -CCCHHHHHHHHC
T ss_pred             -ECCHHHHHHHhh
Confidence             237888888875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.66  E-value=6.2e-16  Score=100.22  Aligned_cols=68  Identities=24%  Similarity=0.398  Sum_probs=62.8

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+.++|||+|||.++++++|+++|+.|| |.++.+++++.++.++|||||+|.+.++|.+|+ .+++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g   77 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDG   77 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTT
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCC
Confidence            3445678999999999999999999999997 999999999888999999999999999999999 7876

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

Probab=99.66  E-value=6.2e-16  Score=105.35  Aligned_cols=71  Identities=27%  Similarity=0.441  Sum_probs=65.7

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....+.++|||+|||+++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|++.+++
T Consensus        57 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  127 (140)
T 2ku7_A           57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE  127 (140)
T ss_dssp             CSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTE
T ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCC
Confidence            33455678999999999999999999999999999999999988899999999999999999999998885

>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=99.66  E-value=5.3e-16  Score=100.74  Aligned_cols=66  Identities=26%  Similarity=0.514  Sum_probs=61.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC-CCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~-~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||+++++++|+++|+.|| |.++.+++++.+ |.++|||||+|.+.++|.+|+ .+++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g   78 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNE   78 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGT
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCC
Confidence            34568999999999999999999999999 999999999877 899999999999999999999 8876

>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=99.66  E-value=2.9e-16  Score=103.72  Aligned_cols=70  Identities=13%  Similarity=0.159  Sum_probs=63.7

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCe-eEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSF-LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v-~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +...+.+.++|||+|||+++++++|+++|+.||.+ .++.++.++ +|.++|||||+|.+.++|.+|+.. ++
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~   78 (114)
T 2cpy_A            8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HR   78 (114)
T ss_dssp             CCSCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CS
T ss_pred             CCCCCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CC
Confidence            33456678899999999999999999999999999 899999997 999999999999999999999977 54

>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=99.66  E-value=5.1e-17  Score=111.46  Aligned_cols=78  Identities=18%  Similarity=0.328  Sum_probs=69.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEE--------EEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA--------KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV  157 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~--------~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~  157 (170)
                      ...+|||+|||+.+++++|+++|+.||.|..+        .+.   .++.++|||||+|.+.++|.+|+..|||   ..+
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng---~~~  117 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANG---YVL  117 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTT---BEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCC---CEe
Confidence            35799999999999999999999999998763        222   2577899999999999999999999999   999


Q ss_pred             CCeeEEEEeecc
Q psy7847         158 GDLKTRSSITLK  169 (170)
Q Consensus       158 ~~~~i~v~~~~~  169 (170)
                      +|++|+|.++..
T Consensus       118 ~g~~l~V~~a~~  129 (143)
T 3egn_A          118 FGKPMVVQFARS  129 (143)
T ss_dssp             TTEECEEEECCC
T ss_pred             CCcEEEEEECCC
Confidence            999999999864

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=8.1e-16  Score=99.64  Aligned_cols=68  Identities=25%  Similarity=0.367  Sum_probs=62.6

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      .....+.++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (103)
T 2cqg_A            9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ   76 (103)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS
T ss_pred             CCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc
Confidence            34445678999999999999999999999999999999999988899999999999999999999984

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

Probab=99.66  E-value=3.6e-16  Score=100.38  Aligned_cols=68  Identities=28%  Similarity=0.439  Sum_probs=62.6

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCC---CCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR---TNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~---~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.++|||+|||.++++++|+++|+.||.|.++.++.++.   ++.+++||||+|.+.++|.+|+..+++.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~   73 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH   73 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCC
Confidence            4578999999999999999999999999999999999875   5588999999999999999999998863

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=5.5e-16  Score=102.09  Aligned_cols=71  Identities=25%  Similarity=0.293  Sum_probs=65.2

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCee--------EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~--------~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+..+.++|||+|||.++++++|+++|+.||.|.        .++++.++.++.++|||||+|.+.++|.+|+..+++.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            3445678999999999999999999999999998        6999999889999999999999999999999998863

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.65  E-value=1.4e-15  Score=101.82  Aligned_cols=69  Identities=23%  Similarity=0.324  Sum_probs=64.5

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ......++|||+|||.++++++|+++|+.||.|.++.+..++ +|.++|||||+|.+.++|.+|+..+++
T Consensus        30 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g   98 (124)
T 2kt5_A           30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKG   98 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCC
Confidence            345667899999999999999999999999999999999998 899999999999999999999998886

>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=99.65  E-value=1.3e-15  Score=100.38  Aligned_cols=69  Identities=13%  Similarity=0.372  Sum_probs=64.2

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+.++|||+|||+++++++|+++|+.||.|.++++++++ ++.++|||||+|.+.++|.+|+..+++.
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   89 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK   89 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCC
Confidence            34567899999999999999999999999999999999997 8999999999999999999999998864

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

Probab=99.65  E-value=5.5e-16  Score=112.54  Aligned_cols=79  Identities=20%  Similarity=0.371  Sum_probs=72.4

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++.||+   ..++|+.|+|.+
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~---~~~~g~~l~v~~  104 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS---VMLGGRNIKVGR  104 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSS---CCCC-CCCEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccC---CeeCCeeEEEec
Confidence            46999999999999999999999999999999999988899999999999999999999999999   999999999987


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus       105 ~~  106 (216)
T 2qfj_A          105 PS  106 (216)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.65  E-value=6.8e-16  Score=112.05  Aligned_cols=75  Identities=21%  Similarity=0.254  Sum_probs=70.0

Q ss_pred             CCceEEecCCC-CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...+|||+||| ..+++++|+++|++||.|..+.+++++     +|+|||+|.+.++|.+|++.|||   ..+.|++|+|
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng---~~~~g~~l~v   74 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNN---NFMFGQKMNV   74 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCC---CEECCceEEE
Confidence            45789999999 799999999999999999999998753     79999999999999999999999   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      .++.
T Consensus        75 ~~s~   78 (205)
T 3tyt_A           75 CVSK   78 (205)
T ss_dssp             EECS
T ss_pred             EEcc
Confidence            9974

>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=99.65  E-value=3.1e-16  Score=100.67  Aligned_cols=70  Identities=13%  Similarity=0.173  Sum_probs=64.2

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .....++|||+|||+++++++|+++|+.||.|.++.++.++.+|.+++||||+|.+.++|.+|+..+++.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   80 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   80 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            3445688999999999999999999999999998888888888999999999999999999999999863

>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=99.65  E-value=5.2e-16  Score=97.79  Aligned_cols=65  Identities=20%  Similarity=0.390  Sum_probs=61.7

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .++|||+|||.++++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|.+|+ .+++.
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~   70 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDES   70 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCC
Confidence            578999999999999999999999999999999999889999999999999999999999 88863

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=3.4e-16  Score=104.18  Aligned_cols=79  Identities=11%  Similarity=0.136  Sum_probs=71.0

Q ss_pred             ceEEecCC----CCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecC----H-HH---HHHHHH--HhcCCC
Q psy7847          88 FRLFCGDL----GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD----P-QD---FIRANK--EMNEFP  153 (170)
Q Consensus        88 ~~l~v~nl----p~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~----~-~~---a~~a~~--~l~~~~  153 (170)
                      ..|+|+||    |+.+++.+|+.+|+.||.|..+.+..|+.++.++|||||+|.+    + ++   |.+|+.  .+||  
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng--   80 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSG--   80 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTC--
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcC--
Confidence            47999999    9999999999999999999999999999999999999999995    3 22   888888  7899  


Q ss_pred             ccccCCeeEEEEeecc
Q psy7847         154 HLFVGDLKTRSSITLK  169 (170)
Q Consensus       154 ~~~~~~~~i~v~~~~~  169 (170)
                       ..++|++|+|.+-..
T Consensus        81 -~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           81 -CFIMGFKFEVILNKH   95 (136)
T ss_dssp             -EEETTEEEEEEECCT
T ss_pred             -CeecCcEEEEEECcc
Confidence             999999999998653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.65  E-value=4.6e-16  Score=96.54  Aligned_cols=64  Identities=19%  Similarity=0.300  Sum_probs=58.7

Q ss_pred             CcEEEEcCCCCCc------cHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDV------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~------t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++|||+|||.++      ++++|+++|++||.|.++.+++  .+|.++|||||+|.+.++|.+|+..+++.
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~lng~   70 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADGY   70 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTTSSSC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHHhcCc
Confidence            4689999999999      7899999999999999999873  57899999999999999999999988863

>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=99.65  E-value=1.9e-15  Score=97.85  Aligned_cols=71  Identities=24%  Similarity=0.459  Sum_probs=63.2

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ....+.+.++|||+|||+++++++|+++|+.||.|.++.++.++.  .+++||||+|.+.++|.+|+..+++.
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cq3_A            8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGT   78 (103)
T ss_dssp             CSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            344556678999999999999999999999999999999998853  38999999999999999999988863

>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=99.65  E-value=8.1e-16  Score=110.05  Aligned_cols=80  Identities=25%  Similarity=0.398  Sum_probs=74.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++. ++   ..++|+.|+|.
T Consensus        12 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~---~~~~g~~l~v~   87 (196)
T 1l3k_A           12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RP---HKVDGRVVEPK   87 (196)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CS---CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CC---CEECCEEeeee
Confidence            357999999999999999999999999999999999988899999999999999999999986 88   89999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        88 ~~~~   91 (196)
T 1l3k_A           88 RAVS   91 (196)
T ss_dssp             ECCC
T ss_pred             cccC
Confidence            8753

>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=99.65  E-value=7.9e-16  Score=100.02  Aligned_cols=68  Identities=19%  Similarity=0.164  Sum_probs=61.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeE-EEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~-i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+....++|||+|||+++++++|+++|+.||.|.+ +.++.+ .+|.++|||||+|.+.++|.+|+.. ++
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~   78 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HK   78 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-Cc
Confidence            34456789999999999999999999999999987 888888 6899999999999999999999987 54

>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=99.65  E-value=3e-16  Score=103.28  Aligned_cols=75  Identities=20%  Similarity=0.245  Sum_probs=66.5

Q ss_pred             CCceEEe--cCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc-----C
Q psy7847          86 DDFRLFC--GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV-----G  158 (170)
Q Consensus        86 ~~~~l~v--~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~-----~  158 (170)
                      ...+|||  +||++.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|||   ..+     .
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG---~~~~~~lg~   94 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNG---KEVVDDLGQ   94 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTT---CEEECTTSC
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCC---CEEccccCC
Confidence            3568999  779999999999999999999999887542      78999999999999999999999   665     6


Q ss_pred             CeeEEEEeecc
Q psy7847         159 DLKTRSSITLK  169 (170)
Q Consensus       159 ~~~i~v~~~~~  169 (170)
                      +++|.|.++..
T Consensus        95 g~~l~v~~a~~  105 (114)
T 2cq2_A           95 KITLYLNFVEK  105 (114)
T ss_dssp             EEECEEEEESC
T ss_pred             CcEEEEEeccc
Confidence            89999998753

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=6.6e-16  Score=100.26  Aligned_cols=63  Identities=11%  Similarity=0.063  Sum_probs=57.7

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.+..+|||+|||+++++++|+++|++||.|.+++++++      +|||||+|.+.++|.+|++.+++
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~   74 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS   74 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcc
Confidence            4556889999999999999999999999999999999875      58999999999999999998764

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=2.1e-16  Score=96.98  Aligned_cols=63  Identities=29%  Similarity=0.488  Sum_probs=59.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ++|||+|||+++++++|+++|++||.|.++.+++++.+|.++|+|||+|.+.++|.+|+..++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC
Confidence            479999999999999999999999999999999998889999999999999999999998776

>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=99.64  E-value=7.7e-16  Score=103.27  Aligned_cols=68  Identities=21%  Similarity=0.362  Sum_probs=64.1

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||+++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|++.+++
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g   86 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNG   86 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            34567899999999999999999999999999999999988999999999999999999999999886

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=3.1e-16  Score=95.83  Aligned_cols=62  Identities=27%  Similarity=0.466  Sum_probs=58.4

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|++|++ +++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~   62 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHF   62 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCC
Confidence            58999999999999999999999999999999998889999999999999999999997 654

>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=99.64  E-value=5.5e-16  Score=97.43  Aligned_cols=67  Identities=22%  Similarity=0.466  Sum_probs=62.0

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCC-cCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK-TKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~-~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..++|||+|||.++++++|+++|+.||.|.++.++.++.++. ++|+|||+|.+.++|.+|+..+++.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   70 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGG   70 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCC
Confidence            467999999999999999999999999999999999876665 8999999999999999999998863

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=6.9e-16  Score=98.43  Aligned_cols=75  Identities=16%  Similarity=0.138  Sum_probs=66.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|+.||.|..|  ..++.++.   ||||+|.+.++|.+|+. |||   ..++|+.|+|.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g---~~~~g~~l~V~   77 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQ---HSLGGHRLRVR   77 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSC---CEETTEECCCB
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCC---eEECCEEEEEE
Confidence            34699999999999999999999999999987  44544443   99999999999999999 999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        78 ~a~~   81 (94)
T 2e5g_A           78 PREQ   81 (94)
T ss_dssp             CSCC
T ss_pred             ECCc
Confidence            8763

>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=99.64  E-value=1.8e-16  Score=102.82  Aligned_cols=66  Identities=27%  Similarity=0.516  Sum_probs=62.9

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +.++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.+++
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   72 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG   72 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSS
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            457899999999999999999999999999999999988899999999999999999999998886

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

Probab=99.64  E-value=1.8e-15  Score=97.06  Aligned_cols=73  Identities=21%  Similarity=0.287  Sum_probs=67.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|+  .+++++|+++|++||.|..+.+.      .++|||||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g---~~~~g~~l~v~   82 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNG---TQVESVQLKVN   82 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTT---EEETTEEEEEE
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCC---CeECCeEEEEE
Confidence            4579999995  89999999999999999999884      3588999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        83 ~a~~   86 (97)
T 1x5p_A           83 IARK   86 (97)
T ss_dssp             CCSS
T ss_pred             ECCC
Confidence            9865

>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=99.64  E-value=1.6e-15  Score=98.21  Aligned_cols=70  Identities=26%  Similarity=0.427  Sum_probs=62.6

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+..+.++|||+|||+++++++|+++|+.||.|.++.+++++  +.+++||||+|.+.++|.+|+..+++
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g   77 (103)
T 2cqi_A            8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNG   77 (103)
T ss_dssp             CCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCC
Confidence            34455668899999999999999999999999999999999985  33689999999999999999998886

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

Probab=99.64  E-value=1.4e-15  Score=100.19  Aligned_cols=70  Identities=23%  Similarity=0.337  Sum_probs=64.2

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ......++|||+|||.++++++|+++|+.||.|.++.++.++ ++.+++||||+|.+.++|.+|+..+++.
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~   79 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQ   79 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            344567899999999999999999999999999999999997 6999999999999999999999988863

>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=99.64  E-value=1.3e-15  Score=96.26  Aligned_cols=74  Identities=20%  Similarity=0.314  Sum_probs=63.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|++||.|..+.++++     ++|||||+|.+.++|.+    +++. ...++|+.|+|.
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~-~~~~~g~~v~v~   79 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGE-DLIIKGISVHIS   79 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTC-EEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCC-CcccCCEEEEEE
Confidence            4579999999999999999999999999999998775     68999999999999883    5663 345679999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        80 ~a~~   83 (89)
T 3d2w_A           80 NAEP   83 (89)
T ss_dssp             ECC-
T ss_pred             EcCC
Confidence            9864

>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=99.64  E-value=2.6e-16  Score=100.45  Aligned_cols=69  Identities=13%  Similarity=0.182  Sum_probs=62.4

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +...++|||+|||+++++++|+++|+.||.|.++.++.++.++.+++||||+|.+.++|.+|++.+++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~   80 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   80 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCC
Confidence            334689999999999999999999999999998999998888999999999999999999999988863

>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=99.64  E-value=4.3e-16  Score=103.13  Aligned_cols=72  Identities=19%  Similarity=0.196  Sum_probs=65.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee-----
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK-----  161 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~-----  161 (170)
                      .++|||+|||+.+++++|+++|++||.|..+.++.+       |||||+|.+.++|.+|++.|||   ..++|+.     
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g---~~~~gr~~~~~~   85 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN---TKFRSHEGETAY   85 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTT---CBCCCTTSCCCB
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCC---CEECCcEeeeEE
Confidence            478999999999999999999999999999998764       8999999999999999999999   9999988     


Q ss_pred             EEEEeec
Q psy7847         162 TRSSITL  168 (170)
Q Consensus       162 i~v~~~~  168 (170)
                      |+|..+.
T Consensus        86 i~v~~~~   92 (115)
T 3beg_B           86 IRVKVDG   92 (115)
T ss_dssp             CEEEECC
T ss_pred             EEeccCC
Confidence            6666543

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

Probab=99.64  E-value=2.7e-16  Score=106.96  Aligned_cols=75  Identities=27%  Similarity=0.379  Sum_probs=68.1

Q ss_pred             ccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          12 WIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        12 ~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+..+..+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|.+|+..+++
T Consensus        37 ~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g  111 (135)
T 2lea_A           37 YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG  111 (135)
T ss_dssp             SCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTT
T ss_pred             cCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCC
Confidence            344555566678999999999999999999999999999999999988899999999999999999999998886

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.64  E-value=2.2e-15  Score=98.13  Aligned_cols=81  Identities=11%  Similarity=0.082  Sum_probs=71.1

Q ss_pred             CCceEEecCCCC-----CCCHHHHHHHhccCCCeeEEEEeecCC-CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          86 DDFRLFCGDLGN-----DVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        86 ~~~~l~v~nlp~-----~~~~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      ...+|++.|+..     +-++++|++.|++||.|..+.+++++. .+.++|+|||+|.+.++|.+|++.|||   ..++|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG---~~~~G   83 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG---RYFGG   83 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTT---CEETT
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCC---CEECC
Confidence            457899999863     237899999999999999999998864 367899999999999999999999999   99999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      +.|+|+++.+
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            9999999864

>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=99.64  E-value=5.9e-16  Score=100.37  Aligned_cols=68  Identities=13%  Similarity=0.170  Sum_probs=60.7

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+...++|||+|||+++++++|+++|+.||.+ ++.+++++ +|+++|||||+|.+.++|.+|++ +++
T Consensus         9 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~   76 (102)
T 1wez_A            9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDK   76 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCC
Confidence            3445667899999999999999999999999954 99999997 89999999999999999999995 454

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=7.6e-16  Score=100.95  Aligned_cols=72  Identities=24%  Similarity=0.434  Sum_probs=64.1

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+..+....++|||+|||.++++++|+++|+.||.|.++.+++++  +.++|||||+|.+.++|.+|+..+++.
T Consensus        21 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~   92 (109)
T 2err_A           21 MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGT   92 (109)
T ss_dssp             -CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTC
T ss_pred             CCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCC
Confidence            455556678899999999999999999999999999999999885  458999999999999999999988863

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=4.2e-16  Score=103.14  Aligned_cols=64  Identities=28%  Similarity=0.489  Sum_probs=60.6

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      .+.++|||+|||.++++++|+++|+.||.|.++.++.++.++.++|||||+|.+.++|.+|+..
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~   88 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA   88 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh
Confidence            3457899999999999999999999999999999999988899999999999999999999976

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.63  E-value=2.6e-15  Score=100.39  Aligned_cols=73  Identities=11%  Similarity=0.088  Sum_probs=65.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccE-EEEEecCHHHHHHHHHHhcCCCccccCC--eeEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF-GFVSFKDPQDFIRANKEMNEFPHLFVGD--LKTRS  164 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~a~~~l~~~~~~~~~~--~~i~v  164 (170)
                      ..|||+||++.+++++|+++|++||.|..+.+.. +     .|+ |||+|.+.++|..|++.|||   ..+.|  +.|+|
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG---~~i~g~~~~l~V   96 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNG---ADIYAGCCTLKI   96 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTT---CCCBTTBSEEEE
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCC---CEecCCCeEEEE
Confidence            3578999999999999999999999999998864 2     285 99999999999999999999   88766  69999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .+|.+
T Consensus        97 ~~Ak~  101 (124)
T 2e5i_A           97 EYARP  101 (124)
T ss_dssp             ECCSC
T ss_pred             EEecC
Confidence            99864

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=7.5e-16  Score=100.99  Aligned_cols=66  Identities=18%  Similarity=0.274  Sum_probs=59.4

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....++|||+|||+++++++|+++|+.| .|.+|.++.++ +|+++|||||+|.+.++|.+|+ .+++
T Consensus        12 ~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~   77 (109)
T 2dnn_A           12 INPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNR   77 (109)
T ss_dssp             CCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCC
Confidence            34446799999999999999999999999 79999999996 5999999999999999999999 5664

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.63  E-value=2.1e-16  Score=105.81  Aligned_cols=65  Identities=20%  Similarity=0.375  Sum_probs=61.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +.++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+ .+++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g   99 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDE   99 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCC
Confidence            4679999999999999999999999999999999999889999999999999999999999 7776

>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=99.63  E-value=1.5e-15  Score=105.53  Aligned_cols=68  Identities=26%  Similarity=0.311  Sum_probs=64.4

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|.++.++.++.+++||||+|.+.++|.+|+..+++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g  103 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING  103 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            45678999999999999999999999999999999999988899999999999999999999999886

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

Probab=99.63  E-value=1.9e-15  Score=95.77  Aligned_cols=66  Identities=29%  Similarity=0.419  Sum_probs=61.2

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.++++  ++.+++||||+|.+.++|.+|+..+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g   70 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNG   70 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            345789999999999999999999999999999999884  788999999999999999999998886

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.63  E-value=9.2e-16  Score=101.97  Aligned_cols=68  Identities=15%  Similarity=0.124  Sum_probs=62.0

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCC---eeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPS---FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~---v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ......++|||+|||+++++++|+++|+.||.   |.+++++.++. |+++|||||+|.+.++|.+|+. +++
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g   82 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDR   82 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTT
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            34456789999999999999999999999998   89999999974 9999999999999999999998 775

>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=99.63  E-value=5.6e-16  Score=103.81  Aligned_cols=69  Identities=20%  Similarity=0.292  Sum_probs=61.6

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ......++|||+|||+++++++|+++|+.||.|.++.++.+..+|.++|||||+|.+.++|.+|+. +++
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g   88 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHK   88 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCS
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCC
Confidence            345567899999999999999999999999999886666666789999999999999999999998 775

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.63  E-value=1.4e-15  Score=98.96  Aligned_cols=68  Identities=19%  Similarity=0.287  Sum_probs=61.5

Q ss_pred             CCCCCCcEEEEcCCCCCc------cHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDV------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~------t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+...+++|||+|||.++      ++++|+++|+.||.|.++.+++  .+|.++|||||+|.+.++|.+|+..+++
T Consensus        10 ~~~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~l~g   83 (105)
T 2nlw_A           10 EADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKNADG   83 (105)
T ss_dssp             SCCSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHHCSS
T ss_pred             CCCCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            344457899999999999      8899999999999999999883  5789999999999999999999999886

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.8e-15  Score=95.46  Aligned_cols=70  Identities=21%  Similarity=0.125  Sum_probs=62.7

Q ss_pred             Cce-EEecCCCCCCCHHH----HHHHhccCC-CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          87 DFR-LFCGDLGNDVTDEL----LIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        87 ~~~-l~v~nlp~~~~~~~----l~~~f~~~g-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      ..+ |||+|||..+++++    |+++|++|| .|..|       ++   |+|||.|.+.++|.+|++.|||   ..+.|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G---~~l~gr   74 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMEN---EDVFGN   74 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTT---CCSSSS
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcC---CccCCc
Confidence            344 99999999999888    668999994 99888       22   9999999999999999999999   999999


Q ss_pred             eEEEEeecc
Q psy7847         161 KTRSSITLK  169 (170)
Q Consensus       161 ~i~v~~~~~  169 (170)
                      +|+|++|..
T Consensus        75 ~i~v~~A~~   83 (96)
T 2diu_A           75 RIIVSFTPK   83 (96)
T ss_dssp             CCEEESSCC
T ss_pred             eEEEEecCC
Confidence            999999864

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.2e-15  Score=100.80  Aligned_cols=64  Identities=14%  Similarity=0.349  Sum_probs=58.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCC---CCcccEEEEEecCHHHHHHHHHHhc
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                      ..++|||+|||+.+++++|+++|++||.|. +.++.+..+   +.++|||||+|.+.++|.+|++.|+
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~   73 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL   73 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh
Confidence            457899999999999999999999999999 877777655   6899999999999999999999984

>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=99.62  E-value=1.6e-15  Score=105.52  Aligned_cols=68  Identities=29%  Similarity=0.410  Sum_probs=64.3

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|+..+++
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g  134 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG  134 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            34578999999999999999999999999999999999988999999999999999999999999886

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=2.3e-15  Score=95.36  Aligned_cols=66  Identities=17%  Similarity=0.259  Sum_probs=61.5

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+...++|||+|||+++++++|+++|+.| .|.++.++++ .+|.++|+|||+|.+.++|.+|+. +++
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g   71 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNR   71 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCS
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCC
Confidence            44567899999999999999999999999 8999999999 689999999999999999999999 886

>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=99.62  E-value=2.5e-15  Score=105.45  Aligned_cols=83  Identities=20%  Similarity=0.340  Sum_probs=72.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCC--CcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ..++|||+|||+++++++|+++|++||.|..+.+++++..+  .++|||||+|.+.++|.+|++.||+.......++++.
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            35789999999999999999999999999999999998665  7899999999999999999999999433333367888


Q ss_pred             EEeec
Q psy7847         164 SSITL  168 (170)
Q Consensus       164 v~~~~  168 (170)
                      +.++.
T Consensus        82 ~~~~~   86 (175)
T 3nmr_A           82 MKPAD   86 (175)
T ss_dssp             EEECG
T ss_pred             Ecccc
Confidence            77764

>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=99.62  E-value=1.1e-15  Score=102.49  Aligned_cols=66  Identities=21%  Similarity=0.206  Sum_probs=59.4

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCee--EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFL--KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~--~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      ..++.+.++|||+|||+++|+++|+++|+.| .+.  +|+++.++. |+++|||||+|.+.++|.+|++.
T Consensus        36 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~  103 (126)
T 2hgm_A           36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK  103 (126)
T ss_dssp             TTCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH
Confidence            3445667899999999999999999999999 566  899999975 99999999999999999999975

>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=99.62  E-value=7.6e-16  Score=104.79  Aligned_cols=68  Identities=16%  Similarity=0.117  Sum_probs=62.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCC---eeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPS---FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~---v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +++.+.++|||+|||+++|+++|+++|+.||.   |.+|++++++. |+++|||||+|.+.++|.+|++ +++
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g  109 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDR  109 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCC
Confidence            34556789999999999999999999999999   89999999975 9999999999999999999998 774

>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=99.62  E-value=1.4e-15  Score=95.34  Aligned_cols=70  Identities=19%  Similarity=0.384  Sum_probs=64.8

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccC----C-------CeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcc
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKY----P-------SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL  155 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~----g-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  155 (170)
                      .++|||+|||+.+++++|+++|++|    |       .|..+.+.++      +|||||+|.+.++|.+|+ .|||   .
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g---~   75 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDG---I   75 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTT---C
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCC---C
Confidence            4699999999999999999999999    8       8999988654      799999999999999999 9999   9


Q ss_pred             ccCCeeEEEEe
Q psy7847         156 FVGDLKTRSSI  166 (170)
Q Consensus       156 ~~~~~~i~v~~  166 (170)
                      .++|+.|+|+.
T Consensus        76 ~~~g~~l~V~r   86 (87)
T 2hzc_A           76 IFQGQSLKIRR   86 (87)
T ss_dssp             EETTEECEEEC
T ss_pred             EECCeEEEEeC
Confidence            99999999874

>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=99.62  E-value=1.8e-15  Score=100.47  Aligned_cols=65  Identities=11%  Similarity=0.058  Sum_probs=58.2

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ......++++|||+|||+++++++|+++|++||.|.++.++++      +|||||+|.+.++|.+|++.++
T Consensus        24 ~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~   88 (119)
T 2ad9_A           24 SRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYT   88 (119)
T ss_dssp             TTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHH
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhc
Confidence            3444556889999999999999999999999999999999875      5899999999999999998765

>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=99.62  E-value=7.5e-16  Score=100.62  Aligned_cols=68  Identities=18%  Similarity=0.162  Sum_probs=62.0

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCC---eeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPS---FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~---v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+....++|||+|||+++++++|+++|+.||.   |.++.++.++. |.++|||||+|.+.++|.+|+. +++
T Consensus         6 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~   76 (107)
T 2lmi_A            6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHR   76 (107)
T ss_dssp             CCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTT
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCc
Confidence            44566889999999999999999999999887   89999999975 9999999999999999999998 665

>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=99.62  E-value=8.5e-15  Score=95.76  Aligned_cols=68  Identities=25%  Similarity=0.394  Sum_probs=60.7

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....+.++|||+|||.++++++|+++|+.||.|.++.+..   ++.+++||||+|.+.++|.+|++.+++
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g   83 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDG   83 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCC
Confidence            34455678999999999999999999999999999999955   456899999999999999999999886

>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=99.61  E-value=1e-15  Score=97.37  Aligned_cols=75  Identities=19%  Similarity=0.261  Sum_probs=65.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCC-eeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ..++|||+|||+.+++++|+++|++||. +..+.+.       ++|||||+|.+.++|.+|++.|||.  ..++|++|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~--~~~~g~~l~v   77 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGK--VELHGKIMEV   77 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTT--CEETTEECEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCC--eeECCEEEEE
Confidence            3578999999999999999999999999 6665552       3789999999999999999999982  4678999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .++.+
T Consensus        78 ~~a~~   82 (93)
T 2cqh_A           78 DYSVS   82 (93)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99865

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.61  E-value=2e-15  Score=97.07  Aligned_cols=65  Identities=15%  Similarity=0.140  Sum_probs=57.3

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .....++++|||+|||.++++++|+++|++||.|.++++++.      +|+|||+|.+.++|..|+..+++
T Consensus        15 ~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~   79 (100)
T 3r27_A           15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAAD   79 (100)
T ss_dssp             --CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHH
T ss_pred             cccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcC
Confidence            334557889999999999999999999999999999999753      58999999999999999998764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=1.6e-15  Score=100.17  Aligned_cols=65  Identities=14%  Similarity=0.364  Sum_probs=59.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC---CCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT---NKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~---~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      ....++|||+|||+++++++|+++|+.||.|. +.++.++.+   |.++|||||+|.+.++|.+|++.+
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            34578999999999999999999999999999 888877766   799999999999999999999988

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.60  E-value=4.1e-16  Score=100.87  Aligned_cols=63  Identities=25%  Similarity=0.464  Sum_probs=59.6

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHH
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK   82 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~   82 (170)
                      ....++|||+|||.++++++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh
Confidence            3346889999999999999999999999999999999998 99999999999999999999998

>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=99.60  E-value=2.5e-15  Score=98.27  Aligned_cols=66  Identities=21%  Similarity=0.373  Sum_probs=61.6

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCC-eeEEEEE-ecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVV-RDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~-v~~i~~~-~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      .+.++|||+|||.++++++|+++|+.||. |.++.++ .++.+|.++|||||+|.+.++|.+|+..++
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~   73 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLM   73 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhh
Confidence            35789999999999999999999999998 9999998 787788999999999999999999999885

>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=99.60  E-value=5.2e-16  Score=98.11  Aligned_cols=64  Identities=27%  Similarity=0.528  Sum_probs=60.8

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.+ |.+|+..+++.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~   65 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNT   65 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCC
Confidence            57999999999999999999999999999999999888999999999999999 99999998863

>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=99.60  E-value=2.3e-15  Score=105.03  Aligned_cols=77  Identities=26%  Similarity=0.495  Sum_probs=71.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.  +   ..++|+.|.+.+
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~---~~~~g~~i~v~~   77 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--Q---HILDGKVIDPKR   77 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--C---CEETTEECCCEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--c---cccCCeEccccc
Confidence            46899999999999999999999999999999999988899999999999999999999994  5   678899998887


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        78 ~~   79 (167)
T 2cjk_A           78 AI   79 (167)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>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=99.60  E-value=3.7e-15  Score=95.39  Aligned_cols=65  Identities=12%  Similarity=0.140  Sum_probs=59.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHH----HHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~----~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||.++++++|+    ++|+.||.|.++.++.++.+   ++||||+|.+.++|.+|+..+|+
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g   74 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHR   74 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCC
Confidence            3456789999999999999999    99999999999999988644   88999999999999999999986

>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=99.60  E-value=4.6e-15  Score=95.93  Aligned_cols=61  Identities=13%  Similarity=0.116  Sum_probs=55.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..++++|||+|||.++++++|+++|++||.|.++.++++      +|||||+|.+.++|..|++.++
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~   72 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYS   72 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhc
Confidence            345789999999999999999999999999999988764      6899999999999999998764

>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=99.60  E-value=6.3e-15  Score=95.79  Aligned_cols=62  Identities=11%  Similarity=0.078  Sum_probs=56.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ...++++|||+|||.++++++|+++|++||.|.++.++++      ++||||+|.+.++|.+|++.++
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~   72 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAA   72 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhc
Confidence            3456789999999999999999999999999999998764      6899999999999999998765

>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=99.59  E-value=1.2e-15  Score=100.77  Aligned_cols=73  Identities=18%  Similarity=0.240  Sum_probs=60.1

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .......+.++|||+|||.++++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|.+|+..+++
T Consensus        17 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g   89 (115)
T 2cpx_A           17 SSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG   89 (115)
T ss_dssp             CCCCCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTT
T ss_pred             cccCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            3344455678999999999999999999999999885443322223788999999999999999999999886

>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=99.59  E-value=5.2e-15  Score=103.80  Aligned_cols=67  Identities=18%  Similarity=0.417  Sum_probs=63.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.++|||+|||+++++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|.+|+..+++
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g  136 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG  136 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCC
Confidence            4467899999999999999999999999999999999988999999999999999999999999986

>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=99.59  E-value=7.4e-16  Score=94.07  Aligned_cols=60  Identities=25%  Similarity=0.521  Sum_probs=57.6

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      +|||+|||+++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|.+|+..
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~   60 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK   60 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh
Confidence            589999999999999999999999999999999988899999999999999999999975

>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=99.59  E-value=3.3e-15  Score=96.66  Aligned_cols=62  Identities=10%  Similarity=0.052  Sum_probs=56.4

Q ss_pred             CCCCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++++|||+|||+ ++++++|+++|++||.|.++.++++      ++||||+|.+.++|..|++.+++
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~   74 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTT   74 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcC
Confidence            34678999999999 9999999999999999999999865      37999999999999999998764

>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=99.59  E-value=3.3e-15  Score=98.16  Aligned_cols=70  Identities=16%  Similarity=0.230  Sum_probs=62.2

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHH---HHhhcCCCeeEEEEEecCCCC---CcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLI---RTFSKYPSFLKAKVVRDKRTN---KTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~---~~f~~~g~v~~i~~~~~~~~~---~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+.++|||+|||+++++++|+   ++|++||.|.++.+++++.++   .++|||||+|.+.++|.+|++.+++.
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~   86 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV   86 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTE
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCC
Confidence            34457799999999999999999   999999999999999887654   45699999999999999999998863

>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=99.59  E-value=1.6e-15  Score=95.53  Aligned_cols=74  Identities=22%  Similarity=0.296  Sum_probs=64.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+.+++++|+++|++||.|..+.+.++     ++|||||+|.+.++|++|    ++. ...+++++|+|.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~----~~~-~~~~~g~~l~v~   73 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL----CGE-DLIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT----TTC-EEEETTEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH----hcC-CceeCCEEEEEE
Confidence            4579999999999999999999999999999998765     589999999999999754    552 356799999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        74 ~a~~   77 (88)
T 1wf0_A           74 NAEP   77 (88)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9865

>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=99.59  E-value=7.4e-15  Score=105.62  Aligned_cols=77  Identities=12%  Similarity=0.023  Sum_probs=70.5

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+.+++++|+++|++||.|..+.++++. .+.++|+|||+|.+.++|.+|+..+ +   ..++|++|+|.+
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~---~~~~Gr~l~V~~  183 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-G---QKYKETDLLILF  183 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-T---CEETTEECEEEE
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-C---CeECCEEEEEEE
Confidence            3689999999999999999999999999999999887 5889999999999999999999855 4   579999999998


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus       184 ~~  185 (193)
T 2voo_A          184 KD  185 (193)
T ss_dssp             TT
T ss_pred             hH
Confidence            64

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=1.3e-15  Score=101.87  Aligned_cols=64  Identities=19%  Similarity=0.113  Sum_probs=58.7

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCe----eEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSF----LKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v----~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      ....++|||+|||+++|+++|+++|+.||.|    .+|.++.++ +|+++|||||+|.+.++|.+|++.
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~   87 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK   87 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh
Confidence            4567899999999999999999999999975    689999984 899999999999999999999975

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.6e-15  Score=97.88  Aligned_cols=59  Identities=31%  Similarity=0.604  Sum_probs=54.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+|||+|||+++++++|+++|+.||.|.++.++.+     +++||||+|.+.++|.+|+..+++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g   59 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDG   59 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCC
Confidence            47999999999999999999999999999999876     679999999999999999997764

>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=99.58  E-value=1.3e-14  Score=94.77  Aligned_cols=61  Identities=21%  Similarity=0.265  Sum_probs=56.9

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++|||+|||+++++++|+++|+.||.|.++.++.+       +||||+|.+.++|.+|++.+++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g   72 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN   72 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCc
Confidence            345789999999999999999999999999999999875       8999999999999999999986

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.58  E-value=4.7e-16  Score=100.43  Aligned_cols=67  Identities=27%  Similarity=0.410  Sum_probs=59.8

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+...++|||+|||.++++++|+++|+.||.+.. .++.++.+|.++|||||+|.+.++|.+|++ +++
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g   79 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTG   79 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGG
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCC
Confidence            4456789999999999999999999999998877 666666678999999999999999999998 875

>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=99.58  E-value=3.2e-15  Score=110.23  Aligned_cols=67  Identities=19%  Similarity=0.280  Sum_probs=62.4

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCC--CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYP--SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g--~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..++|||+|||+++|+++|+++|+.||  .|.+|+|++++.+|.++|||||+|.+.++|.+|++.+++.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~  135 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR  135 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCC
Confidence            456899999999999999999999999  9999999999989999999999999999999999988864

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.58  E-value=8.8e-15  Score=95.73  Aligned_cols=66  Identities=23%  Similarity=0.439  Sum_probs=57.0

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .....+...++|||+|||.++++++|+++|+.||.|.++.+.        +|||||+|.+.++|.+|+..+++.
T Consensus        23 ~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~   88 (108)
T 2jvo_A           23 HRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGK   88 (108)
T ss_dssp             -----CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCC
Confidence            344556678899999999999999999999999999999987        589999999999999999998863

>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=99.57  E-value=1.3e-14  Score=109.57  Aligned_cols=79  Identities=22%  Similarity=0.315  Sum_probs=72.3

Q ss_pred             CCCceEEecCCCCCCCHHHHH----HHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          85 NDDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~----~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      ...++|||+|||+.+++++|+    ++|+.||.|..|.+.+   ++.++|||||+|.+.++|.+|++.|||   ..+.|+
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g---~~~~g~   80 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG---FPFYDK   80 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcC---CeeCCc
Confidence            446799999999999999966    8999999999998875   577899999999999999999999999   999999


Q ss_pred             eEEEEeecc
Q psy7847         161 KTRSSITLK  169 (170)
Q Consensus       161 ~i~v~~~~~  169 (170)
                      .|+|.|+..
T Consensus        81 ~l~v~~a~~   89 (282)
T 3pgw_A           81 PMRIQYAKT   89 (282)
T ss_pred             EEEEEEecc
Confidence            999999854

>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=99.57  E-value=1.8e-14  Score=92.28  Aligned_cols=63  Identities=21%  Similarity=0.401  Sum_probs=57.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.+.++|||+|||.++++++|+++|+.||.|.++.+..+      ++||||+|.+.++|.+|++.+++
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g   75 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRG   75 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCC
Confidence            3445789999999999999999999999999999988754      68999999999999999998885

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

Probab=99.57  E-value=8.9e-15  Score=94.33  Aligned_cols=66  Identities=26%  Similarity=0.349  Sum_probs=58.8

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+.++|||+|||.++++++|+++|+.||.|   +++.+ .++.+++||||+|.+.++|.+|+..+++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g   75 (101)
T 2fc9_A           10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNK   75 (101)
T ss_dssp             CCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSS
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCC
Confidence            345568999999999999999999999999966   56666 5789999999999999999999998886

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.57  E-value=6.8e-15  Score=108.70  Aligned_cols=76  Identities=17%  Similarity=0.232  Sum_probs=69.3

Q ss_pred             CCCceEEecCCCCCC---------CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcc
Q psy7847          85 NDDFRLFCGDLGNDV---------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL  155 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~  155 (170)
                      ....+|||+||+..+         ++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|++.|||   .
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g---~  202 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSN---Q  202 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTT---C
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCC---C
Confidence            456799999999998         79999999999999999999854      79999999999999999999999   7


Q ss_pred             cc------------CCeeEEEEeecc
Q psy7847         156 FV------------GDLKTRSSITLK  169 (170)
Q Consensus       156 ~~------------~~~~i~v~~~~~  169 (170)
                      .+            .|+.|.|.||..
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~  228 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANE  228 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC-
T ss_pred             EEeccccccccccCCCCEEEEEEccC
Confidence            77            899999999864

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

Probab=99.57  E-value=1.1e-14  Score=97.86  Aligned_cols=66  Identities=14%  Similarity=0.157  Sum_probs=58.6

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHH----HHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~----~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..+.++|||+|||+++++++|+    ++|++||.|.+|.+.+   ++.++|||||+|.+.++|..|+..+++
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng   94 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQG   94 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCC
Confidence            34557899999999999999876    6999999999987753   678999999999999999999999987

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

Probab=99.57  E-value=1.2e-14  Score=93.81  Aligned_cols=70  Identities=33%  Similarity=0.554  Sum_probs=62.0

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+...+.+.++|||+|||.++++++|+++|+.|+   .+.++.++.++.+++||||+|.+.++|.+|+..+++
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   76 (102)
T 2fc8_A            7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED   76 (102)
T ss_dssp             TTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC
Confidence            3445556788999999999999999999999774   788888888899999999999999999999999886

>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=99.57  E-value=1.9e-15  Score=103.19  Aligned_cols=67  Identities=12%  Similarity=0.142  Sum_probs=58.2

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+...++|||+|||+++|+++|+++|+.|| +.+|.++.++ +|.++|||||+|.+.++|.+|+ .+++
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al-~~~g  107 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-SKDR  107 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHT-TCCS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHH-hhCC
Confidence            3455678999999999999999999999999 6799999997 4999999999999999999999 5664

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=2.4e-14  Score=90.39  Aligned_cols=61  Identities=23%  Similarity=0.485  Sum_probs=56.3

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.+.++|||+|||.++++++|+++|+.||.|.++.++        ++||||+|.+.++|.+|+..+++
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g   64 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHH   64 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcC
Confidence            34567899999999999999999999999999999987        47999999999999999998886

>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=99.56  E-value=1e-14  Score=107.36  Aligned_cols=76  Identities=20%  Similarity=0.217  Sum_probs=71.1

Q ss_pred             CCCceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          85 NDDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        85 ~~~~~l~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      +...+|||+|||+ .+++++|+++|+.||.|..+.+.+++     +|||||+|.+.++|.+|++.|||   ..++|++|+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g---~~~~g~~l~  103 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNG---HKLHGKPIR  103 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTT---CBCSSSBCE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCC---CeECCeEEE
Confidence            3467999999999 99999999999999999999998875     78999999999999999999999   999999999


Q ss_pred             EEeec
Q psy7847         164 SSITL  168 (170)
Q Consensus       164 v~~~~  168 (170)
                      |.++.
T Consensus       104 v~~a~  108 (229)
T 2adc_A          104 ITLSK  108 (229)
T ss_dssp             EECCS
T ss_pred             EEEec
Confidence            99885

>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=99.56  E-value=2.4e-14  Score=89.31  Aligned_cols=64  Identities=25%  Similarity=0.375  Sum_probs=57.4

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc-CC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM-ND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~-~~   86 (170)
                      ..+.+.++|||+|||.++++++|+++|+.||.|.++.++++      +++|||+|.+.++|.+|+..+ ++
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~   71 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNK   71 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTT
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCC
Confidence            34456789999999999999999999999999999999874      589999999999999999988 54

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.56  E-value=1.5e-14  Score=102.61  Aligned_cols=68  Identities=24%  Similarity=0.333  Sum_probs=63.6

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +...++|||+|||+++++++|+++|+.||.|.+|.+..++ ++.++|||||+|.+.++|.+|+..+++.
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~  152 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGV  152 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCC
Confidence            4456899999999999999999999999999999999997 8999999999999999999999988863

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

Probab=99.56  E-value=3.2e-14  Score=91.13  Aligned_cols=66  Identities=14%  Similarity=0.138  Sum_probs=57.5

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+...++|||+|||+++++++|+++|+.||.|. +.++.+    .+++||||+|.+.++|.+|+..+++.
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~   79 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGL   79 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCC
Confidence            3445578999999999999999999999999986 666653    67899999999999999999998863

>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=99.55  E-value=1.2e-14  Score=91.76  Aligned_cols=58  Identities=22%  Similarity=0.391  Sum_probs=49.8

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHH
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR   79 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~   79 (170)
                      ..+.+.++|||+|||+++++++|+++|++||.|.+++++++     ++|||||+|.+.++|.+
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH
Confidence            34556789999999999999999999999999999999864     78999999999999984

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.55  E-value=1.2e-14  Score=95.44  Aligned_cols=65  Identities=14%  Similarity=0.146  Sum_probs=57.9

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+...++|||+|||+++++++|+++|+.|| .|..+.+..    +.++|||||+|.+.++|.+|++.+++
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng   89 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNN   89 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCC
Confidence            355678999999999999999999999999 899988853    35789999999999999999999986

>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=99.55  E-value=2.2e-14  Score=92.15  Aligned_cols=65  Identities=29%  Similarity=0.420  Sum_probs=58.4

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ....+.++|||+|||+++++++|+++|+.||.|.++.+.++      ++||||+|.+.++|.+|++.+++.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~   74 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNM   74 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCC
Confidence            34456789999999999999999999999999999999854      589999999999999999998863

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

Probab=99.54  E-value=3.5e-14  Score=91.48  Aligned_cols=64  Identities=16%  Similarity=0.219  Sum_probs=57.7

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+...++|||+|||.++++++|+++|+.||.|.++++.      .++|||||+|.+.++|.+|+..+++
T Consensus        22 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g   85 (101)
T 2la4_A           22 SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALAN   85 (101)
T ss_dssp             TSCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTT
T ss_pred             cCCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCC
Confidence            334557899999999999999999999999999999987      3468999999999999999999886

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.54  E-value=9.6e-15  Score=104.84  Aligned_cols=75  Identities=20%  Similarity=0.224  Sum_probs=70.1

Q ss_pred             CceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      .++|||+|||+ .+++++|+++|+.||.|..+.+.+++     +|||||+|.+.++|.+|+..|||   ..++|++|+|.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~---~~~~g~~l~v~   74 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNG---HKLHGKPIRIT   74 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTT---CCCSSCCCEEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCC---CeecCeEEEEE
Confidence            46899999999 99999999999999999999998764     78999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        75 ~a~~   78 (198)
T 1qm9_A           75 LSKH   78 (198)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            8853

>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=99.54  E-value=4e-14  Score=90.75  Aligned_cols=64  Identities=30%  Similarity=0.526  Sum_probs=55.9

Q ss_pred             CCCCCCCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          16 TCEDENDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .....+.++|||+|||. ++++++|+++|+.||.|.++.+.        +|||||+|.+.++|.+|+..+++.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~   80 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQE   80 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTS
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCC
Confidence            33345678999999998 99999999999999999999883        689999999999999999988863

>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=99.54  E-value=2.9e-14  Score=92.81  Aligned_cols=80  Identities=15%  Similarity=0.028  Sum_probs=68.3

Q ss_pred             CceEEecCC--CCCCC--------HHHHHHHhccCCCeeEEEEeecCCC--CCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          87 DFRLFCGDL--GNDVT--------DELLIRTFSKYPSFLKAKVVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        87 ~~~l~v~nl--p~~~~--------~~~l~~~f~~~g~i~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                      .++|.+.|+  |....        +++|++.|++||.|..+.+++++..  +.++|+|||+|.+.++|.+|++.|||   
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG---   81 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG---   81 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT---
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC---
Confidence            457788887  33332        4799999999999999999988743  35799999999999999999999999   


Q ss_pred             cccCCeeEEEEeecc
Q psy7847         155 LFVGDLKTRSSITLK  169 (170)
Q Consensus       155 ~~~~~~~i~v~~~~~  169 (170)
                      ..++|++|+|++...
T Consensus        82 ~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           82 RKFANRVVVTKYCDP   96 (105)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEeCCCEEEEEEeCH
Confidence            999999999999764

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.30  E-value=5.1e-16  Score=102.75  Aligned_cols=69  Identities=26%  Similarity=0.351  Sum_probs=63.8

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeE--------EEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLK--------AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~--------i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..+.++|||+|||.++++++|+++|+.||.|.+        +.++.++.++.++|||||+|.+.++|.+|+..+++
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   79 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   79 (116)
Confidence            3456789999999999999999999999999998        89999988899999999999999999999998886

>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=3.2e-15  Score=97.16  Aligned_cols=71  Identities=17%  Similarity=0.286  Sum_probs=61.1

Q ss_pred             cCCCCCCCHHHHHHHh------------ccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          93 GDLGNDVTDELLIRTF------------SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        93 ~nlp~~~~~~~l~~~f------------~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      .+||..+++++|++.|            ++||.|..+.+.++. .+.++|+|||+|.+.++|.+|+..|||   ..++|+
T Consensus        21 ~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng---~~~~Gr   96 (104)
T 1jmt_A           21 DGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNN---RWFNGQ   96 (104)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTT---CEETTE
T ss_pred             CCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCC---CEECCE
Confidence            3455556666665555            999999999999876 478899999999999999999999999   999999


Q ss_pred             eEEEEee
Q psy7847         161 KTRSSIT  167 (170)
Q Consensus       161 ~i~v~~~  167 (170)
                      +|+|.|+
T Consensus        97 ~i~v~~s  103 (104)
T 1jmt_A           97 PIHAELS  103 (104)
T ss_dssp             ECCEEEC
T ss_pred             EEEEEEc
Confidence            9999986

>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=99.54  E-value=2.3e-14  Score=94.08  Aligned_cols=61  Identities=13%  Similarity=0.191  Sum_probs=55.7

Q ss_pred             CCCCcEEEEcCCCCC-ccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          19 DENDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~-~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..++++|||+|||++ +++++|+++|++||.|.++.+++      +++||||+|.+.++|..|++.++
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~   83 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCL   83 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhc
Confidence            556889999999998 99999999999999999999974      36899999999999999998765

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=4.3e-14  Score=89.61  Aligned_cols=62  Identities=18%  Similarity=0.465  Sum_probs=56.4

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+.++|||+|||.++++++|+++|+.||.|.++.+++        +||||+|.+.++|.+|+..+++
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g   66 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDN   66 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCC
Confidence            4455678999999999999999999999999999999873        3999999999999999999886

>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=99.53  E-value=8.4e-15  Score=93.68  Aligned_cols=66  Identities=24%  Similarity=0.422  Sum_probs=59.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHH----HHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLI----RTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~----~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..++++|||+|||.++++++|+    ++|+.||.|.++.+.+   +|.++|||||+|.+.++|.+|+..+++
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g   73 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG   73 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCC
Confidence            34567899999999999999999    9999999999998873   567889999999999999999999887

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

Probab=99.53  E-value=5e-14  Score=90.03  Aligned_cols=62  Identities=31%  Similarity=0.502  Sum_probs=54.6

Q ss_pred             CCCCCCcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+..+.++|||+|||+ ++++++|+++|+.||.|.++.+.        +|||||+|.+.++|..|+..+++
T Consensus         5 ~~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g   67 (96)
T 2kvi_A            5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQ   67 (96)
T ss_dssp             ----CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTC
T ss_pred             ccCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCC
Confidence            3455688999999998 99999999999999999999984        58999999999999999999886

>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=99.52  E-value=3.8e-14  Score=92.65  Aligned_cols=63  Identities=25%  Similarity=0.583  Sum_probs=58.3

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+...++|||+|||.++++++|+++|+.||.|.++.++++      ++||||+|.+.++|.+|+..+++
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g   83 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG   83 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCC
Confidence            4556789999999999999999999999999999999876      68999999999999999999886

>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=99.52  E-value=7.1e-14  Score=91.90  Aligned_cols=77  Identities=17%  Similarity=0.192  Sum_probs=66.3

Q ss_pred             CCceEEecCCCCCCC-----------HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          86 DDFRLFCGDLGNDVT-----------DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~-----------~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                      ...+|+|.||.....           +++|+++|++||.|..+.+ .++   .++|+|||+|.+.++|.+|+..|||   
T Consensus        14 ~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng---   86 (112)
T 2dit_A           14 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG---   86 (112)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT---
T ss_pred             CceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC---
Confidence            357899999944332           6899999999999999966 443   3799999999999999999999999   


Q ss_pred             cccCCeeEEEEeecc
Q psy7847         155 LFVGDLKTRSSITLK  169 (170)
Q Consensus       155 ~~~~~~~i~v~~~~~  169 (170)
                      ..++|++|+|.++.+
T Consensus        87 ~~~~gr~l~v~~a~~  101 (112)
T 2dit_A           87 RWFGGRQITAQAWDG  101 (112)
T ss_dssp             CEETTEECEEEECCS
T ss_pred             CEECCcEEEEEEeCC
Confidence            999999999999865

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

Probab=99.52  E-value=4.1e-14  Score=99.10  Aligned_cols=70  Identities=21%  Similarity=0.325  Sum_probs=64.9

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+...++|||+|||.++++++|+++|+.||.|.++.+.+++.+|.++|+|||+|.+.++|.+|+..+++.
T Consensus        90 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  159 (172)
T 2g4b_A           90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM  159 (172)
T ss_dssp             CCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTC
T ss_pred             CCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCC
Confidence            3445789999999999999999999999999999999999888999999999999999999999998873

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.1e-13  Score=88.13  Aligned_cols=62  Identities=16%  Similarity=0.153  Sum_probs=54.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++|||+|||.++++++|+++|+.||.|.+|  +.++.+|.   ||||+|.+.++|.+|+. +++
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g   66 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQ   66 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCC
Confidence            3456799999999999999999999999999987  55554554   99999999999999999 876

>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=99.51  E-value=5.2e-14  Score=97.11  Aligned_cols=66  Identities=32%  Similarity=0.548  Sum_probs=59.7

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .......++|||+|||+++++++|+++|+.||.|.+++++++     ++|||||+|.+.++|.+|+..+++
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g  132 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG  132 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSS
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCC
Confidence            334456789999999999999999999999999999999875     579999999999999999999886

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=4.8e-14  Score=89.01  Aligned_cols=62  Identities=21%  Similarity=0.415  Sum_probs=56.3

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+.++|||+|||.++++++|+++|+.||.|.++.+++        +||||+|.+.++|.+|+..+++
T Consensus         4 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g   65 (90)
T 2dnp_A            4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNG   65 (90)
T ss_dssp             CSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCC
Confidence            3455678999999999999999999999999999999974        3899999999999999999886

>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=99.51  E-value=5.7e-14  Score=105.26  Aligned_cols=75  Identities=27%  Similarity=0.432  Sum_probs=69.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|+.||.|..+.+.++      +|||||+|.+.++|.+|+..+||   ..++|+.|+|.
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g---~~i~g~~l~v~   91 (261)
T 3sde_A           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDG---TILKSRPLRIR   91 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCC---cEECCceeEee
Confidence            3569999999999999999999999999999988653      78999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        92 ~a~~   95 (261)
T 3sde_A           92 FATH   95 (261)
T ss_dssp             ECCC
T ss_pred             eccc
Confidence            9864

>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=99.51  E-value=3.5e-14  Score=93.40  Aligned_cols=64  Identities=20%  Similarity=0.269  Sum_probs=56.9

Q ss_pred             CCCCcEEEE--cCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCc
Q psy7847          19 DENDFRLFC--GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDF   88 (170)
Q Consensus        19 ~~~~~~v~v--~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~   88 (170)
                      ..+.++|||  +|||.++++++|+++|++||.|.++.++.      .+|||||+|.+.++|.+|++.+|+..
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~   87 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKE   87 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCE
Confidence            345778999  77999999999999999999999988754      26899999999999999999999853

>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=99.51  E-value=4.9e-15  Score=104.26  Aligned_cols=79  Identities=24%  Similarity=0.293  Sum_probs=68.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|+.||.+.. .++.+..++.++|||||+|.+.++|.+|++ |||   ..++|++|+|.
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g---~~~~g~~l~v~   86 (175)
T 1fje_B           12 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTG---LKVFGNEIKLE   86 (175)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGG---EEETTEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCC---CEeCCeEEEEe
Confidence            4679999999999999999999999987665 233344467789999999999999999995 999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        87 ~~~~   90 (175)
T 1fje_B           87 KPKG   90 (175)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9864

>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=99.51  E-value=3.2e-14  Score=93.46  Aligned_cols=61  Identities=15%  Similarity=0.191  Sum_probs=55.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.      +++||||+|.+.++|.+|+..+|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~   69 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYS   69 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCC
Confidence            467899999999999999999999999999998864      4689999999999999999999873

>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=99.50  E-value=8.4e-14  Score=91.15  Aligned_cols=60  Identities=27%  Similarity=0.391  Sum_probs=55.1

Q ss_pred             CCCCcEEEEcCCCCC-ccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~-~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....++|||+|||++ +++++|+++|+.||.|.++.+        +++||||+|.+.++|.+|+..+++
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g   84 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENG   84 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTT
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCC
Confidence            334589999999999 999999999999999999988        468999999999999999999886

>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=99.50  E-value=6.7e-14  Score=112.05  Aligned_cols=69  Identities=25%  Similarity=0.458  Sum_probs=64.6

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+..+|||+|||+++|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..+|+.
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~  167 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGK  167 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCC
Confidence            344679999999999999999999999999999999999889999999999999999999999999874

>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=99.50  E-value=3e-14  Score=94.19  Aligned_cols=61  Identities=21%  Similarity=0.266  Sum_probs=54.7

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.+       +||||+|.+.++|.+|++.+++.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~   74 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT   74 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCC
Confidence            34689999999999999999999999999999999765       89999999999999999998863

>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=99.50  E-value=8.7e-14  Score=90.01  Aligned_cols=60  Identities=30%  Similarity=0.529  Sum_probs=55.0

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||+++++++|+++|+.||.|.++.++        ++||||+|.+.++|.+|+..+++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g   67 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNG   67 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCC
Confidence            3457899999999999999999999999999999886        35899999999999999999886

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

Probab=99.49  E-value=1.3e-13  Score=98.70  Aligned_cols=68  Identities=22%  Similarity=0.386  Sum_probs=64.3

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +...++|||+|||.++++++|+++|+.||.|.++.+.+++.+|.++|||||+|.+.++|.+|+..+++
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  178 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG  178 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCC
Confidence            35678999999999999999999999999999999999988899999999999999999999999886

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=2.9e-13  Score=86.84  Aligned_cols=62  Identities=19%  Similarity=0.349  Sum_probs=55.2

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcC--CCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKY--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~--g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+.++|||+|||.++++++|+++|+.|  |.|.++.+.        ++||||+|.+.++|.+|+..+++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g   73 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNG   73 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSS
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCC
Confidence            334567899999999999999999999999  889888764        46999999999999999998886

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

Probab=99.48  E-value=2.4e-14  Score=91.41  Aligned_cols=63  Identities=19%  Similarity=0.293  Sum_probs=56.3

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.++|||+|||.++++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..+++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g   75 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQG   75 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence            4457899999999999999999999999977665     24788999999999999999999998885

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=9e-14  Score=88.70  Aligned_cols=65  Identities=15%  Similarity=0.101  Sum_probs=56.9

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEE-EEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAK-VVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~-~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ....++|||+|||+++++++|+++|+.||.|.+++ ++.++.++.    |||+|.+.++|.+|+..+++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~   77 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGF   77 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCC
Confidence            34578999999999999999999999999999994 777754443    999999999999999988863

>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=99.47  E-value=1.8e-13  Score=90.80  Aligned_cols=81  Identities=11%  Similarity=0.154  Sum_probs=69.9

Q ss_pred             CCceEEecCCCC--CC---CHHHHHHHhccCCCeeEEEEeecCC----CCCcccEEEEEecCHHHHHHHHHHhcCCCccc
Q psy7847          86 DDFRLFCGDLGN--DV---TDELLIRTFSKYPSFLKAKVVRDKR----TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF  156 (170)
Q Consensus        86 ~~~~l~v~nlp~--~~---~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  156 (170)
                      ...+|++.|+-.  ++   .+++|++.|++||.|..+.+++++.    ++.++|++||+|.+.++|.+|++.|||   ..
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnG---r~   95 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG---RW   95 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTT---CE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCC---CE
Confidence            567899999842  22   3689999999999999999998864    345679999999999999999999999   99


Q ss_pred             cCCeeEEEEeecc
Q psy7847         157 VGDLKTRSSITLK  169 (170)
Q Consensus       157 ~~~~~i~v~~~~~  169 (170)
                      ++|+.|+|++...
T Consensus        96 f~GR~i~v~~~~~  108 (118)
T 3ue2_A           96 FAGRKVVAEVYDQ  108 (118)
T ss_dssp             ETTEECEEEEECH
T ss_pred             ECCcEEEEEEcCh
Confidence            9999999999753

>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=99.47  E-value=5.8e-14  Score=88.27  Aligned_cols=56  Identities=25%  Similarity=0.398  Sum_probs=50.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHH
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA   80 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~   80 (170)
                      .++++|||+|||.++++++|+++|+.||.|.+++++.+     ++|||||+|.+.++|+++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH
Confidence            35789999999999999999999999999999998754     689999999999999764

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.47  E-value=7.2e-14  Score=92.99  Aligned_cols=64  Identities=13%  Similarity=0.158  Sum_probs=56.1

Q ss_pred             cEEEEcCC----CCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCC----HHH----HHHHHH--HcCC
Q psy7847          23 FRLFCGDL----GNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD----PQD----FIRANK--EMND   86 (170)
Q Consensus        23 ~~v~v~nL----p~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~----~~~----a~~~~~--~~~~   86 (170)
                      ..|||+||    |+++++++|+++|+.||+|.++.++.|+.||.++|||||+|.+    +++    |.+|+.  .+++
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng   80 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSG   80 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTC
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcC
Confidence            57999999    9999999999999999999999999999999999999999996    433    677777  4454

>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=99.47  E-value=2.3e-14  Score=98.15  Aligned_cols=69  Identities=22%  Similarity=0.383  Sum_probs=58.5

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEE------EEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKA------KVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i------~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+.++|||+|||+++++++|+++|+.||.|..+      .+.. ..+|.++|||||+|.+.++|.+|+..+|+
T Consensus        40 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng  114 (143)
T 3egn_A           40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL-MKEGRMKGQAFIGLPNEKAAAKALKEANG  114 (143)
T ss_dssp             CCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEE-EEETTTEEEEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEe-ccCCCcccEEEEEeCCHHHHHHHHHHhCC
Confidence            335567899999999999999999999999998764      1211 13688999999999999999999999987

>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=99.47  E-value=8.3e-14  Score=88.41  Aligned_cols=61  Identities=23%  Similarity=0.369  Sum_probs=53.8

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCC-eeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~-v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +...++|||+|||.++++++|+++|+.||. +..+.+.       +++||||+|.+.++|.+|+..+++
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g   66 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSG   66 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccC
Confidence            445789999999999999999999999999 6666553       368999999999999999999987

>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=99.46  E-value=2.4e-13  Score=94.67  Aligned_cols=65  Identities=20%  Similarity=0.291  Sum_probs=57.3

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +..-.+|||+|||+++++++|+++|++||.|.+|.+...    .+++||||+|.+.++|.+|++.+++.
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~  107 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQ  107 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTB
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            444566999999999999999999999999999998653    25689999999999999999999873

>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=99.46  E-value=2.2e-13  Score=97.86  Aligned_cols=63  Identities=14%  Similarity=0.115  Sum_probs=59.0

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      .++|||+|||+++++++|+++|+.||.|.+++++++. +|.++|||||+|.+.++|.+|+..++
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~  171 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG  171 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC
Confidence            5789999999999999999999999999999999985 68999999999999999999997654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=9.8e-13  Score=87.85  Aligned_cols=59  Identities=14%  Similarity=0.175  Sum_probs=52.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCE-EEEEeCCHHHHHHHHHHcCCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF-GFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~-afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..|||+|||+.+++++|+++|++||.|.+|.+.. +     .|+ |||+|.+.++|..|++.|++.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~   85 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGA   85 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCC
Confidence            3478999999999999999999999999999865 2     276 999999999999999999973

>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=99.45  E-value=1.6e-13  Score=85.85  Aligned_cols=61  Identities=21%  Similarity=0.433  Sum_probs=55.1

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcC----C-------CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKY----P-------SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~----g-------~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.++|||+|||+++++++|+++|+.|    |       .+.++.+.++      +|||||+|.+.++|.+|+ .+++.
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~   75 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGI   75 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCC
Confidence            357899999999999999999999999    8       8999988754      689999999999999999 88863

>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=99.45  E-value=2e-13  Score=85.83  Aligned_cols=59  Identities=14%  Similarity=0.167  Sum_probs=54.6

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++|||+|||+++++++|+++|++| .|.++.+.      .++|||||+|.+.++|.+|+..+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g   62 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQ   62 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCC
Confidence            46789999999999999999999999 89999884      5679999999999999999999986

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.44  E-value=5e-13  Score=89.79  Aligned_cols=64  Identities=22%  Similarity=0.361  Sum_probs=56.4

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCE-EEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF-GFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~-afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.+--+|||+||++.+|+++|+++|++||.|.+|.+....     +++ |||+|.+.++|..|++.|++.
T Consensus        25 ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~   89 (130)
T 3zzy_A           25 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQ   89 (130)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCC
Confidence            3444568899999999999999999999999999887642     577 999999999999999999974

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

Probab=99.43  E-value=1.3e-12  Score=83.48  Aligned_cols=61  Identities=20%  Similarity=0.297  Sum_probs=54.7

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.+.++|||+||  ++++++|+++|+.||.|.++.+.      .+++||||+|.+.++|.+|+..+++
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g   71 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNG   71 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCC
Confidence            3446789999996  99999999999999999999884      4578999999999999999999886

>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=99.38  E-value=1.1e-12  Score=101.60  Aligned_cols=77  Identities=16%  Similarity=0.127  Sum_probs=63.1

Q ss_pred             CCceEEecC--CCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCe--e
Q psy7847          86 DDFRLFCGD--LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL--K  161 (170)
Q Consensus        86 ~~~~l~v~n--lp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~--~  161 (170)
                      ...+|||+|  |++.+++++|+++|++||.|..+.+..      ++|||||+|.+.++|++|++.|||....-..|+  .
T Consensus        17 ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             CCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            457999998  578999999999999999999887743      479999999999999999999999544222344  5


Q ss_pred             EEEEeec
Q psy7847         162 TRSSITL  168 (170)
Q Consensus       162 i~v~~~~  168 (170)
                      +.++++.
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            7777764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.38  E-value=2.4e-12  Score=82.87  Aligned_cols=63  Identities=19%  Similarity=0.174  Sum_probs=55.8

Q ss_pred             CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847          97 NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus        97 ~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ..+++++|+++|++||.|..+.++.     .++|||||+|.+.++|..|++.+++     +.+++|+|.|+..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~~~~-----~~g~~l~V~~a~~   89 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEVG-----LVDNPLKISWLEG   89 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHTCCB-----CSSSBCEEECSSC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHhcCC-----CCCCeEEEEEccC
Confidence            5799999999999999999999873     5699999999999999999998555     4689999999864

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=3.1e-12  Score=80.63  Aligned_cols=56  Identities=20%  Similarity=0.205  Sum_probs=49.6

Q ss_pred             CCcE-EEEcCCCCCccHHH----HHHHhhcCC-CeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFR-LFCGDLGNDVTDEL----LIRTFSKYP-SFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~-v~v~nLp~~~t~~~----l~~~f~~~g-~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++.+ |||+|||.++++++    |+++|+.|| .|.+|       ++   |+|||.|.+.++|.+|++.+++
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G   68 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMEN   68 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTT
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcC
Confidence            4555 99999999999988    558999994 99888       33   9999999999999999999997

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.37  E-value=3.6e-12  Score=82.81  Aligned_cols=68  Identities=12%  Similarity=0.068  Sum_probs=59.1

Q ss_pred             CCCcEEEEcCCCC-----CccHHHHHHHhhcCCCeeEEEEEecCCC-CCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGN-----DVTDELLIRTFSKYPSFLKAKVVRDKRT-NKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~-----~~t~~~l~~~f~~~g~v~~i~~~~~~~~-~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+++.|+|+||..     +-++++|++.|++||.|.++.+++++.+ +.++|+|||+|.+.++|.+|+..+|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~   79 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGR   79 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCC
Confidence            4578999999962     2378999999999999999999998643 688999999999999999999999974

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.36  E-value=1.5e-12  Score=85.80  Aligned_cols=76  Identities=11%  Similarity=0.058  Sum_probs=63.1

Q ss_pred             CceEEecCCCCCC----------CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccc
Q psy7847          87 DFRLFCGDLGNDV----------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF  156 (170)
Q Consensus        87 ~~~l~v~nlp~~~----------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  156 (170)
                      .++|.+.|+=..-          .+++|++.|++||.|..+.+.++.    ++|+|||+|.+.++|.+|++.|||   ..
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG---~~   79 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHG---RW   79 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTT---CE
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCC---CE
Confidence            4566676653211          246899999999999999886653    589999999999999999999999   99


Q ss_pred             cCCeeEEEEeecc
Q psy7847         157 VGDLKTRSSITLK  169 (170)
Q Consensus       157 ~~~~~i~v~~~~~  169 (170)
                      ++|+.|+|+|+..
T Consensus        80 f~GR~i~v~~~~~   92 (114)
T 3s6e_A           80 FAGKMITAAYVPL   92 (114)
T ss_dssp             ETTEECEEEEECH
T ss_pred             ECCEEEEEEEEcH
Confidence            9999999999753

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.31  E-value=7.3e-12  Score=92.49  Aligned_cols=63  Identities=21%  Similarity=0.358  Sum_probs=57.5

Q ss_pred             CCCCcEEEEcCCCCCc---------cHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDV---------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~---------t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ....++|||+|||.++         ++++|+++|+.||.|.+|+++.+      +|||||+|.+.++|+.|++.+++.
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~  202 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQ  202 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCC
Confidence            4467899999999998         79999999999999999999864      689999999999999999999974

>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=99.26  E-value=1.9e-11  Score=94.71  Aligned_cols=64  Identities=19%  Similarity=0.259  Sum_probs=56.7

Q ss_pred             CCCCCcEEEEcC--CCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGD--LGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~n--Lp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...++.+|||+|  |+..+|+++|+++|++||.|.++.+..      ++|||||+|.+.++|++|++.+|+.
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~   79 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGK   79 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCC
Confidence            355678999999  578999999999999999999887743      4699999999999999999999985

>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=99.23  E-value=8.7e-11  Score=76.97  Aligned_cols=68  Identities=18%  Similarity=0.217  Sum_probs=56.1

Q ss_pred             CCCCCCCcEEEEcCCCCCc-----------cHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847          16 TCEDENDFRLFCGDLGNDV-----------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~-----------t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      ...+.++++|+|+||....           ++++|+++|++||.|.++.+ .++   .++|||||+|.+.++|.+|+..+
T Consensus         9 ~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~l   84 (112)
T 2dit_A            9 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTL   84 (112)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHc
Confidence            3456678899999994332           26899999999999999966 443   37999999999999999999999


Q ss_pred             CCC
Q psy7847          85 NDD   87 (170)
Q Consensus        85 ~~~   87 (170)
                      |+.
T Consensus        85 ng~   87 (112)
T 2dit_A           85 DGR   87 (112)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            973

>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=99.18  E-value=7.5e-11  Score=76.52  Aligned_cols=67  Identities=18%  Similarity=0.095  Sum_probs=57.2

Q ss_pred             CCcEEEEcCC--CCCcc--------HHHHHHHhhcCCCeeEEEEEecCCC--CCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDL--GNDVT--------DELLIRTFSKYPSFLKAKVVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nL--p~~~t--------~~~l~~~f~~~g~v~~i~~~~~~~~--~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++.|.|.|+  |.+..        +++|++.|++||.|.++.+++++.+  +.++|+|||+|.+.++|.+|+..+|+.
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            5778999998  44443        4799999999999999999988744  367899999999999999999999974

>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=99.14  E-value=2.1e-11  Score=78.99  Aligned_cols=60  Identities=20%  Similarity=0.317  Sum_probs=52.1

Q ss_pred             EcCCCCCccHHHHHHHh------------hcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          27 CGDLGNDVTDELLIRTF------------SKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        27 v~nLp~~~t~~~l~~~f------------~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.|||.++++++|++.|            ++||.|.++.+++++ ++.++|||||+|.+.++|.+|+..+|+.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~   91 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNR   91 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCC
Confidence            56777788888777666            999999999999886 5789999999999999999999999974

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.14  E-value=2.7e-10  Score=75.38  Aligned_cols=75  Identities=19%  Similarity=0.151  Sum_probs=64.7

Q ss_pred             CCceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecC-HHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD-PQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~-~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      ....|+|+||++. +++++|+++|+.||.|.+|.+.+++.      .|||.|.+ ..+|..|+..+|. ....+++..++
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~-~~~~i~g~~~~   89 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANN-GNLQLRNKEVT   89 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTT-SCBCTTSSSEE
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhc-CCcEEeCcEEE
Confidence            3579999999999 99999999999999999999988753      49999999 8999999999952 12888888888


Q ss_pred             EEee
Q psy7847         164 SSIT  167 (170)
Q Consensus       164 v~~~  167 (170)
                      +.+.
T Consensus        90 ~evL   93 (121)
T 1owx_A           90 WEVL   93 (121)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            8764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.13  E-value=1.6e-10  Score=72.11  Aligned_cols=71  Identities=14%  Similarity=0.200  Sum_probs=60.1

Q ss_pred             CceEEecCCC----CCCCH----HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccC
Q psy7847          87 DFRLFCGDLG----NDVTD----ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVG  158 (170)
Q Consensus        87 ~~~l~v~nlp----~~~~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~  158 (170)
                      .-|++|...+    ..+..    .+|.+.|++||.+..+++..++        +||+|.+.++|.+|++ |||   ..++
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG---~~v~   74 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNG---KELL   74 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTT---CEET
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCC---eEeC
Confidence            3467776665    23333    6799999999999999998774        8999999999999999 999   9999


Q ss_pred             CeeEEEEeecc
Q psy7847         159 DLKTRSSITLK  169 (170)
Q Consensus       159 ~~~i~v~~~~~  169 (170)
                      |+.|+|+++.+
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999999875

>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=99.11  E-value=2.7e-10  Score=75.41  Aligned_cols=67  Identities=12%  Similarity=0.138  Sum_probs=57.5

Q ss_pred             CCcEEEEcCCC--CC---ccHHHHHHHhhcCCCeeEEEEEecCC----CCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLG--ND---VTDELLIRTFSKYPSFLKAKVVRDKR----TNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp--~~---~t~~~l~~~f~~~g~v~~i~~~~~~~----~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++.|+|+|+-  .+   --+++|++.|++||.|.++.+++++.    ++.++|++||+|.+.++|.+|+..+|+.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr   94 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR   94 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCC
Confidence            57899999993  22   23689999999999999999999864    3567899999999999999999999974

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.10  E-value=1e-09  Score=70.47  Aligned_cols=60  Identities=18%  Similarity=0.157  Sum_probs=50.2

Q ss_pred             CcEEEEcCCC-------CCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLG-------NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp-------~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+++.|.-.+       .++++++|+++|++||.|.++.++     +.++|||||+|.+.++|..|+..+++
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~   76 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG   76 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC
Confidence            4456665443       468999999999999999999987     36789999999999999999987553

>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=99.04  E-value=6.4e-10  Score=81.16  Aligned_cols=96  Identities=9%  Similarity=0.050  Sum_probs=74.8

Q ss_pred             eCCHHHHHHHHHHcCC-----CceEEecCCC-----CCCCHHHHHHHhccCCCeeEEEEeecCC----CCCcccEEEEEe
Q psy7847          71 FKDPQDFIRANKEMND-----DFRLFCGDLG-----NDVTDELLIRTFSKYPSFLKAKVVRDKR----TNKTKGFGFVSF  136 (170)
Q Consensus        71 f~~~~~a~~~~~~~~~-----~~~l~v~nlp-----~~~~~~~l~~~f~~~g~i~~~~~~~~~~----~~~~~g~afv~f  136 (170)
                      ..+.+.....+..+-.     ...+.+.++-     ..-.+++|.+.|++||.|..+.+.++..    ++.++|++||+|
T Consensus       103 ~~~~~~l~~~l~~~l~~~~~~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f  182 (222)
T 3dxb_A          103 ALSKGQLKEFLDANLAGSAMESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEF  182 (222)
T ss_dssp             CCCHHHHHHHHHHHSCCSCCBCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEE
T ss_pred             ccChHHHHHHHHhhccccccccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEE
Confidence            4567777777765443     2244444332     2345789999999999999999986653    347899999999


Q ss_pred             cCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         137 KDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       137 ~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      .+.++|.+|++.|||   ..++||.|.+++...
T Consensus       183 ~~~~~a~~a~~~l~g---r~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          183 SIASETHKAIQALNG---RWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             SSHHHHHHHHHHHTT---CBSSSSBCEEEECCH
T ss_pred             CCHHHHHHHHHHhcC---ceECCeEEEEEEcCH
Confidence            999999999999999   999999999998753

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.97  E-value=2.4e-09  Score=70.77  Aligned_cols=65  Identities=22%  Similarity=0.216  Sum_probs=56.7

Q ss_pred             CCCCCCCcEEEEcCCCCC-ccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCC-HHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD-PQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~-~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~-~~~a~~~~~~~~~   86 (170)
                      +-.-.....|+|+||+.+ ++.++|+++|+.||+|..|.+.++..      .|||.|.+ .++|..++..++.
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~   78 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANN   78 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTT
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhc
Confidence            334456788999999999 99999999999999999999987753      59999999 8999999998853

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=6.8e-10  Score=69.65  Aligned_cols=73  Identities=14%  Similarity=0.163  Sum_probs=61.1

Q ss_pred             CCceEEecCCCCC-----CCH----HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccc
Q psy7847          86 DDFRLFCGDLGND-----VTD----ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLF  156 (170)
Q Consensus        86 ~~~~l~v~nlp~~-----~~~----~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~  156 (170)
                      ..-|++|..++..     +..    .+|.+.|++||.+..+++..|+        +||+|.+.++|.+|++ |||   ..
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG---~~   81 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDG---MK   81 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGG---SE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCC---ee
Confidence            3457888777632     322    5688999999999999998774        9999999999999999 999   99


Q ss_pred             cCCeeEEEEeeccC
Q psy7847         157 VGDLKTRSSITLKG  170 (170)
Q Consensus       157 ~~~~~i~v~~~~~~  170 (170)
                      ++|+.|+|++..++
T Consensus        82 v~Gr~L~V~~k~~~   95 (95)
T 1ufw_A           82 VKGRAVKISGPSSG   95 (95)
T ss_dssp             ETTEEEEEECCCCC
T ss_pred             eCCeEEEEeccCCC
Confidence            99999999987764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.82  E-value=1.9e-08  Score=65.96  Aligned_cols=82  Identities=11%  Similarity=0.031  Sum_probs=60.5

Q ss_pred             CCCCcEEEEcCCC--CC--------ccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC-
Q psy7847          19 DENDFRLFCGDLG--ND--------VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD-   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp--~~--------~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~-   87 (170)
                      +.+++.|.|.|+=  .+        --+++|++.|++||.|.++.+.++.    .+|++||+|.+.++|.+|+..+|+. 
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4457788899882  22        1236889999999999999986652    5899999999999999999999974 


Q ss_pred             ---ceEEecCCCCCCCHHHHHHHh
Q psy7847          88 ---FRLFCGDLGNDVTDELLIRTF  108 (170)
Q Consensus        88 ---~~l~v~nlp~~~~~~~l~~~f  108 (170)
                         +.|.+.-    ..++...+.|
T Consensus        80 f~GR~i~v~~----~~~~~y~~~f   99 (114)
T 3s6e_A           80 FAGKMITAAY----VPLPTYHNLF   99 (114)
T ss_dssp             ETTEECEEEE----ECHHHHHHHC
T ss_pred             ECCEEEEEEE----EcHHHHHHhC
Confidence               3444432    3444555555

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.52  E-value=1.1e-06  Score=56.24  Aligned_cols=82  Identities=16%  Similarity=0.102  Sum_probs=71.6

Q ss_pred             HHHHHHHHHcCC---CceEEecCCCCCCCHHHHHHHhccC-----CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q psy7847          75 QDFIRANKEMND---DFRLFCGDLGNDVTDELLIRTFSKY-----PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN  146 (170)
Q Consensus        75 ~~a~~~~~~~~~---~~~l~v~nlp~~~~~~~l~~~f~~~-----g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~  146 (170)
                      .++.+.+..-+.   .+++-+-|||..+++..++.+..++     |.+..+.+..|.      +-|+|+|.+...|-+|.
T Consensus         6 qeVk~il~s~~~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKas   79 (117)
T 2l9w_A            6 NEVKRLLASRNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKML   79 (117)
T ss_dssp             HHHHHHHHCCCTTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHH
T ss_pred             HHHHHHHhccCCccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHH
Confidence            456666665544   5789999999999999999999999     999999888774      46999999999999999


Q ss_pred             HHhcCCCccccCCeeEEEE
Q psy7847         147 KEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus       147 ~~l~~~~~~~~~~~~i~v~  165 (170)
                      -.+||   ..+.|++|++.
T Consensus        80 LaL~G---~ef~gr~Lr~g   95 (117)
T 2l9w_A           80 MILNG---SQFQGKVIRSG   95 (117)
T ss_dssp             HHHSS---EEETTEEEEEE
T ss_pred             hhcCC---eeecCeEEEec
Confidence            99999   99999999985

>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=98.35  E-value=6.8e-06  Score=51.55  Aligned_cols=71  Identities=17%  Similarity=0.230  Sum_probs=58.2

Q ss_pred             ccccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc--CCCce
Q psy7847          12 WIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM--NDDFR   89 (170)
Q Consensus        12 ~~~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~--~~~~~   89 (170)
                      ...+...+...+.++| ++|+++.-.||.++|+.|| -..|+.+.|.       .|||.|.+++.|..++..+  +...+
T Consensus         6 l~g~d~~p~r~HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~k~~~y~   76 (100)
T 1whv_A            6 SGGPDLQPKRDHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVQIAVNTSKYAESYR   76 (100)
T ss_dssp             CCCSCCCCCCCSEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEETT-------EEEEECSCHHHHHHHHHHHHHCCSSE
T ss_pred             cCCCCCCCCCCeEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcccCCceE
Confidence            3455566677778888 9999999999999999999 4568888774       6999999999999999866  66566


Q ss_pred             EE
Q psy7847          90 LF   91 (170)
Q Consensus        90 l~   91 (170)
                      +.
T Consensus        77 i~   78 (100)
T 1whv_A           77 IQ   78 (100)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.31  E-value=2.4e-06  Score=53.21  Aligned_cols=70  Identities=13%  Similarity=0.186  Sum_probs=52.1

Q ss_pred             CCcEEEEcCCCC----CccH----HHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----c
Q psy7847          21 NDFRLFCGDLGN----DVTD----ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----F   88 (170)
Q Consensus        21 ~~~~v~v~nLp~----~~t~----~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~   88 (170)
                      +..+|+|.-.|.    +.-+    .+|.+.|..||.+..+++..++        +||+|.+.++|.+|+. +++.    +
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            455777766652    2333    6789999999999999998875        8999999999999998 8874    4


Q ss_pred             eEEecCCCCCC
Q psy7847          89 RLFCGDLGNDV   99 (170)
Q Consensus        89 ~l~v~nlp~~~   99 (170)
                      +|.|.--.++|
T Consensus        77 ~LkV~lkt~dW   87 (91)
T 2dnr_A           77 TITIALKSPSG   87 (91)
T ss_dssp             EEEEEECCCSS
T ss_pred             EEEEEeCCCCc
Confidence            55554333333

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.24  E-value=2.3e-06  Score=62.10  Aligned_cols=54  Identities=13%  Similarity=0.141  Sum_probs=47.5

Q ss_pred             ccHHHHHHHhhcCCCeeEEEEEecCC----CCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          34 VTDELLIRTFSKYPSFLKAKVVRDKR----TNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        34 ~t~~~l~~~f~~~g~v~~i~~~~~~~----~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      -.+++|++.|++||.|.++.+.++..    ++.++|++||+|.+.++|.+|+..+++.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr  198 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGR  198 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCc
Confidence            45689999999999999999986653    3488999999999999999999999984

>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=98.03  E-value=3e-05  Score=48.40  Aligned_cols=68  Identities=15%  Similarity=0.234  Sum_probs=56.1

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCC--CcCCEEEEEeCCHHHHHHHHHHcCCCceEEe
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANKEMNDDFRLFC   92 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~--~~~~~afv~f~~~~~a~~~~~~~~~~~~l~v   92 (170)
                      .+|.|++||+.+|++++.+.++....+........+.+.  ...+-|||.|.+.+++.......++  .+|+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g--~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDG--YVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTT--CEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCC--cEEE
Confidence            478999999999999999999999888777776665443  3356799999999999999998887  3555

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.96  E-value=4.9e-06  Score=52.10  Aligned_cols=59  Identities=12%  Similarity=0.177  Sum_probs=48.1

Q ss_pred             CCCcEEEEcCCCCC-----ccH----HHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGND-----VTD----ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~-----~t~----~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .++.+|+|.-++.+     .-+    .+|.+.|..||.+..+++..++        +||+|.+.++|.+|+. +++.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~   80 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGS
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCe
Confidence            34678888877643     222    5688999999999999999885        9999999999999998 8863

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.93  E-value=8.3e-05  Score=47.15  Aligned_cols=72  Identities=22%  Similarity=0.229  Sum_probs=57.9

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhc-----CCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH-cC---C-----
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSK-----YPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE-MN---D-----   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~-----~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~-~~---~-----   86 (170)
                      -..+|.|.|||+++.++.|.-+|+.     -|.+.++....        ..|+|+|.+...|++.++. -|   +     
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            3568999999999999999999975     24788877644        4699999999999999987 22   2     


Q ss_pred             -------CceEEecCCCCCCC
Q psy7847          87 -------DFRLFCGDLGNDVT  100 (170)
Q Consensus        87 -------~~~l~v~nlp~~~~  100 (170)
                             ..+|++.+||+.++
T Consensus        79 ~P~~~~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           79 RPAPPRAPARLLLQGLPPGTS   99 (104)
T ss_dssp             EECCCCCCCCCCCCSCCCCCC
T ss_pred             EcCCCCCcceEeeecCCCCCC
Confidence                   35888888888765

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.93  E-value=5.3e-05  Score=47.28  Aligned_cols=64  Identities=14%  Similarity=0.242  Sum_probs=53.9

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC--cccEEEEEecCHHHHHHHHHHhcCC
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK--TKGFGFVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~a~~~l~~~  152 (170)
                      .|.|++||+.+|++++.+.++....+.+..+...+.+..  ..+.|+|.|.+.+++....+.++|.
T Consensus         3 KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~   68 (91)
T 1uw4_A            3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGY   68 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCc
Confidence            688999999999999999999998888877766654332  2346999999999999999999993

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.87  E-value=3.1e-05  Score=49.26  Aligned_cols=74  Identities=11%  Similarity=0.030  Sum_probs=61.2

Q ss_pred             CceEEecCCCCCCC-----HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          87 DFRLFCGDLGNDVT-----DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        87 ~~~l~v~nlp~~~~-----~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                      ..+|++.||+.++-     ++.++.+|..|+.+......+.-      ....|.|.+.++|.+|-..||+   ..++|+.
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~---~~f~g~~   75 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHK---TEFLGKE   75 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTT---SEETTEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhcc---ceecCce
Confidence            45899999987652     36789999999988877666542      2578999999999999999999   9999999


Q ss_pred             EEEEeecc
Q psy7847         162 TRSSITLK  169 (170)
Q Consensus       162 i~v~~~~~  169 (170)
                      +++-++.+
T Consensus        76 ~r~YFgq~   83 (104)
T 1wey_A           76 MKLYFAQT   83 (104)
T ss_dssp             CEEECCCC
T ss_pred             eEEEecCC
Confidence            99998753

>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=97.66  E-value=5.7e-05  Score=47.49  Aligned_cols=54  Identities=19%  Similarity=0.249  Sum_probs=47.0

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      +.++| ++|+++.-.||.++|+.|| ...|+.+.|.       .|||.|.+++.|..++..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 9999999999999999999 5678888774       69999999999999998763

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.58  E-value=0.0004  Score=44.49  Aligned_cols=69  Identities=16%  Similarity=0.128  Sum_probs=59.7

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcC-----CCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----Cce
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKY-----PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----DFR   89 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~-----g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----~~~   89 (170)
                      .+..+++-+-|||-.++++.|+.+.+.+     |.+..+.+..|-      +-|+|+|.|..+|-+|.-.++|    .++
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            4457899999999999999999999999     999999998874      4599999999999999988887    356


Q ss_pred             EEec
Q psy7847          90 LFCG   93 (170)
Q Consensus        90 l~v~   93 (170)
                      |.++
T Consensus        92 Lr~g   95 (117)
T 2l9w_A           92 IRSG   95 (117)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            6654

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.54  E-value=0.00016  Score=45.51  Aligned_cols=70  Identities=13%  Similarity=0.241  Sum_probs=49.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCC--CCcCCEEEEEeCCHHHHHHHHHHcCCCceEEe
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNDDFRLFC   92 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~--~~~~~~afv~f~~~~~a~~~~~~~~~~~~l~v   92 (170)
                      .+-+|.|+.||+.+|++++.+.++..-.+........+.+  ...-+-|||.|.+.+++.......++  .+|+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g--~~F~   79 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDG--YIFL   79 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTT--EEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCC--cEEE
Confidence            4568999999999999998888776555433333322222  12346789999999999999988876  4444

>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=97.52  E-value=0.00036  Score=43.74  Aligned_cols=54  Identities=19%  Similarity=0.275  Sum_probs=44.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                      +.+++ ++|+.+-..||.++|+.||. ..|.++-|-       .|||.|.+++.|..|++.+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45666 99999999999999999984 445555543       79999999999999998763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.52  E-value=0.00015  Score=45.52  Aligned_cols=67  Identities=12%  Similarity=0.193  Sum_probs=51.7

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCC--cccEEEEEecCHHHHHHHHHHhcC
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNK--TKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      +....|.|+.||+.+|++++.+.++..-.+.+..+...+.+..  .-..|+|.|.+.++...-.+.++|
T Consensus         7 ~~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g   75 (97)
T 2l08_A            7 HHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDG   75 (97)
T ss_dssp             CCCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTT
T ss_pred             ccceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCC
Confidence            4466899999999999999999998876665544443332222  223589999999999999999999

>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=97.40  E-value=0.00032  Score=44.10  Aligned_cols=53  Identities=19%  Similarity=0.254  Sum_probs=44.8

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhc
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                      .+++ ++|+.+-..||.++|+.|| -..|.++-|-       .|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4566 9999999999999999998 4566666553       79999999999999999764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.22  E-value=0.0034  Score=39.73  Aligned_cols=67  Identities=19%  Similarity=0.187  Sum_probs=52.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhcc---C--CCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSK---Y--PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK  161 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~---~--g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~  161 (170)
                      +.+|.|.|||+.++++.|.-.|+.   .  |.+..+....        +-|+|+|.+.+.|++.++.- .   ..+.+..
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~-~---H~L~~~~   75 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQA-D---HELHGAQ   75 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCS-C---CBSSSSB
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCC-c---ceecCeE
Confidence            468999999999999999999976   2  4566665532        36899999999999998841 2   5667777


Q ss_pred             EEEE
Q psy7847         162 TRSS  165 (170)
Q Consensus       162 i~v~  165 (170)
                      |+|.
T Consensus        76 LsV~   79 (104)
T 2dhx_A           76 LSLR   79 (104)
T ss_dssp             CEEE
T ss_pred             EEEE
Confidence            7763

>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=96.80  E-value=0.0053  Score=39.97  Aligned_cols=62  Identities=11%  Similarity=0.196  Sum_probs=49.9

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      ...|.|-+.|+.. ...+.+.|++||.|......    .+  ..+-.|.|.++.+|++|+. .||   ..+++
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~--~NWihI~Y~s~~~A~rAL~-kNG---~ii~g   85 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NT--GNWMHIRYQSKLQARKALS-KDG---RIFGE   85 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SS--SSEEEEEESSHHHHHHHHT-TTT---CEETT
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CC--CCeEEEEeCCHHHHHHHHH-hCC---eEecC
Confidence            5678888999985 66688889999999988762    12  3478899999999999999 588   77764

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.04  E-value=0.0033  Score=50.40  Aligned_cols=55  Identities=5%  Similarity=0.104  Sum_probs=42.3

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHH
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK   82 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~   82 (170)
                      .+.|+|. .|...++.+|.++|++||+|.++.+..++     .-||.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            4689996 79999999999999999999999887654     2699999999999988874

>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=95.67  E-value=0.078  Score=34.44  Aligned_cols=59  Identities=12%  Similarity=0.194  Sum_probs=46.6

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      +....+.|.|-+.|+.. ...|...|+.||.|.+....      ...-+-+|.|.+..+|++|+..
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~k   78 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK   78 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTT
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHh
Confidence            34456789999999986 45677789999999887761      1235899999999999999965

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.50  E-value=0.0077  Score=48.32  Aligned_cols=56  Identities=5%  Similarity=0.100  Sum_probs=41.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHH
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK  147 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~  147 (170)
                      ..+.++|. .|...++.+|.+.|++||.|..+.+..+.     .-||.|+|.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHh
Confidence            34689997 79999999999999999999999887654     2599999999988886654

>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=95.41  E-value=0.073  Score=43.25  Aligned_cols=67  Identities=16%  Similarity=0.193  Sum_probs=50.8

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCCceEE
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDDFRLF   91 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~~~l~   91 (170)
                      .+.+..++.++++ +|..+...+|.+.|+.||. .+|+.+.+.       .|||.|.+.+.|..++..+.....+.
T Consensus       434 d~~~~R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~~~~~~~  500 (507)
T 3d45_A          434 DLQPKRDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSKYAESYR  500 (507)
T ss_dssp             CCCCCGGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHTTCSSCE
T ss_pred             CCCCCcCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHHhCCceE
Confidence            3334455677776 8999999999999999994 456665542       59999999999999999885443333

>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=94.96  E-value=0.084  Score=33.40  Aligned_cols=67  Identities=13%  Similarity=0.192  Sum_probs=52.6

Q ss_pred             CcEEEEcCCCCCc-cH----HHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC------ceE
Q psy7847          22 DFRLFCGDLGNDV-TD----ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD------FRL   90 (170)
Q Consensus        22 ~~~v~v~nLp~~~-t~----~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~------~~l   90 (170)
                      ..+|+|.||+.++ ..    +.++++|..|++.......+.-      +-..|.|.++++|.+|-..+|+.      .++
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4579999998865 22    5778999999998888776652      24789999999999999999874      466


Q ss_pred             EecC
Q psy7847          91 FCGD   94 (170)
Q Consensus        91 ~v~n   94 (170)
                      |.+.
T Consensus        79 YFgq   82 (104)
T 1wey_A           79 YFAQ   82 (104)
T ss_dssp             ECCC
T ss_pred             EecC
Confidence            6654

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.45  E-value=0.085  Score=34.83  Aligned_cols=76  Identities=12%  Similarity=0.224  Sum_probs=49.4

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeE-EEEeecC--------C-CC----CcccEEEEEecCHHHHHHHHHHhc
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDK--------R-TN----KTKGFGFVSFKDPQDFIRANKEMN  150 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~--------~-~~----~~~g~afv~f~~~~~a~~a~~~l~  150 (170)
                      ++..-+.|-+.|++.+. .+-+.|++||.|.. ....++.        . ..    ....+..|+|.++.+|.+|+. .|
T Consensus         5 ~~e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-EN   82 (132)
T ss_dssp             ---CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TT
T ss_pred             cCceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hC
Confidence            34456777788776554 56678999999865 2111100        0 00    124578999999999999999 68


Q ss_pred             CCCccccCCeeEEEE
Q psy7847         151 EFPHLFVGDLKTRSS  165 (170)
Q Consensus       151 ~~~~~~~~~~~i~v~  165 (170)
                      |   ..++|.-|-|-
T Consensus        83 G---~ii~G~mIGV~   94 (132)
T 3p3d_A           83 G---AVFNGVLLGVI   94 (132)
T ss_dssp             T---CEETTEECEEE
T ss_pred             C---eEeCcEEEEEE
Confidence            8   88888755443

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=91.52  E-value=0.73  Score=37.38  Aligned_cols=54  Identities=19%  Similarity=0.245  Sum_probs=43.9

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      .++++ +|..+...+|.++|+.||. .+|.++.+       ..|||.|.+.++|..+++.++.
T Consensus       442 vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          442 VLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             EEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             EEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            55554 8889999999999999995 45555543       3699999999999999998865

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=88.73  E-value=0.41  Score=31.56  Aligned_cols=84  Identities=14%  Similarity=0.251  Sum_probs=52.5

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeE-EEEEe------------cCCCC-CcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVR------------DKRTN-KTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~-i~~~~------------~~~~~-~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...|.|=+.|++.+. .+.+.|++||.|.+ ....+            .++.+ ....+..|+|.++.+|.+|+......
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            456888899887765 56678999998765 21111            01111 12468899999999999999643321


Q ss_pred             c-eEEecCCCCCCCHHHHHHHh
Q psy7847          88 F-RLFCGDLGNDVTDELLIRTF  108 (170)
Q Consensus        88 ~-~l~v~nlp~~~~~~~l~~~f  108 (170)
                      . -.+|+-.|.  ++..++++-
T Consensus        86 i~G~mIGV~Py--~~~~ve~l~  105 (132)
T 3p3d_A           86 FNGVLLGVIPY--TKDAVERLQ  105 (132)
T ss_dssp             ETTEECEEEEC--CHHHHHHHC
T ss_pred             eCcEEEEEEEC--CHHHHHHHh
Confidence            1 125666666  566666554

---

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	170
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-15
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-06
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-10
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-09
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	7e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	6e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	5e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-08
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	9e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-07
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	8e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	4e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	9e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	6e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-06
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	9e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	9e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	1e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-05
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	8e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-05
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	9e-05
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-04
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-04
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-04
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-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	7e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-04
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.001
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.001
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.001
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.003
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.004

>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 = 67.7 bits (164), Expect = 3e-15
 Identities = 35/159 (22%), Positives = 62/159 (38%), Gaps = 26/159 (16%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 2   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 78  IRANKEMN--------------------------DDFRLFCGDLGNDVTDELLIRTFSKY 111
             A                                  ++F G +  D  +  L   F +Y
Sbjct: 62  DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 121

Query: 112 PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN 150
                 +++ D+ + K +GF FV+F D     +   +  
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKY 160

>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 = 47.3 bits (111), Expect = 8e-08
 Identities = 23/80 (28%), Positives = 37/80 (46%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           KE     +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 142 FIRANKEMNEFPHLFVGDLK 161
              A           V + K
Sbjct: 61  VDAAMNARPHKVDGRVVEPK 80

>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 = 42.3 bits (98), Expect = 6e-06
 Identities = 14/77 (18%), Positives = 30/77 (38%)

Query: 12  WIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSF 71
             ++        ++F G +  D  +  L   F +Y      +++ D+ + K +GF FV+F
Sbjct: 87  DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

Query: 72  KDPQDFIRANKEMNDDF 88
            D     +   +     
Sbjct: 147 DDHDSVDKIVIQKYHTV 163

>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 = 52.6 bits (126), Expect = 2e-10
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 1/74 (1%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQD 76
          + +   ++   ++        +   FS +      ++ +    T   +GFGFV F   QD
Sbjct: 4  KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 77 FIRANKEMNDDFRL 90
            +A   +     L
Sbjct: 64 AKKAFNALCHSTHL 77

>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 = 50.7 bits (121), Expect = 1e-09
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 1/68 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANK 147
           ++   ++        +   FS +      ++ +    T   +GFGFV F   QD  +A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 148 EMNEFPHL 155
            +    HL
Sbjct: 70  ALCHSTHL 77

>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 = 50.7 bits (121), Expect = 8e-10
 Identities = 24/61 (39%), Positives = 34/61 (55%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+ +V+F+ P D  RA   M
Sbjct: 3  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 85 N 85
          N
Sbjct: 63 N 63

>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 = 50.7 bits (121), Expect = 8e-10
 Identities = 24/61 (39%), Positives = 34/61 (55%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+ GDL  DVT+ +L   FS     L  +V RD  T ++ G+ +V+F+ P D  RA   M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 150 N 150
           N
Sbjct: 63  N 63

>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 = 50.0 bits (119), Expect = 2e-09
 Identities = 17/71 (23%), Positives = 32/71 (45%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           + +     L    L    T++ L   FS +   L  +V +D +T  +KGFGFV F + + 
Sbjct: 3   RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 62

Query: 142 FIRANKEMNEF 152
            ++   + +  
Sbjct: 63  QVKVMSQRHMI 73

>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 = 48.4 bits (115), Expect = 7e-09
 Identities = 17/66 (25%), Positives = 31/66 (46%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
          +    L    L    T++ L   FS +   L  +V +D +T  +KGFGFV F + +  ++
Sbjct: 6  QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 80 ANKEMN 85
             + +
Sbjct: 66 VMSQRH 71

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-09
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E E   +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++ 
Sbjct: 2  EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 61

Query: 78 IRANKEMN 85
            A     
Sbjct: 62 DAAMNARP 69

>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 = 48.5 bits (115), Expect = 6e-09
 Identities = 21/69 (30%), Positives = 34/69 (49%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           KE     +LF G L  + TDE L   F ++ +     V+RD  T +++GFGFV++   ++
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 142 FIRANKEMN 150
              A     
Sbjct: 61  VDAAMNARP 69

>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 = 49.6 bits (118), Expect = 2e-09
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +LF G L N + D+ +    + +       +V+D  T  +KG+ F  + D     +A   
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 84 MN 85
          +N
Sbjct: 63 LN 64

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 2e-09
 Identities = 15/62 (24%), Positives = 28/62 (45%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +LF G L N + D+ +    + +       +V+D  T  +KG+ F  + D     +A   
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 149 MN 150
           +N
Sbjct: 63  LN 64

>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 = 49.6 bits (118), Expect = 3e-09
 Identities = 20/68 (29%), Positives = 34/68 (50%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E   D  L+  +L   +TD+ L   F KY S ++  ++RDK T + +G  FV +   ++ 
Sbjct: 2  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 78 IRANKEMN 85
            A   +N
Sbjct: 62 QEAISALN 69

>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 = 48.4 bits (115), Expect = 7e-09
 Identities = 19/65 (29%), Positives = 33/65 (50%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
            D  L+  +L   +TD+ L   F KY S ++  ++RDK T + +G  FV +   ++   A
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 146 NKEMN 150
              +N
Sbjct: 65  ISALN 69

>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 = 48.4 bits (115), Expect = 5e-09
 Identities = 15/65 (23%), Positives = 32/65 (49%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L  D  +E +   F  +      ++  D +TNK +GF F++FK+ +   +  ++
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 84 MNDDF 88
             + 
Sbjct: 61 KYHNV 65

>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 = 48.4 bits (115), Expect = 6e-09
 Identities = 15/62 (24%), Positives = 31/62 (50%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L  D  +E +   F  +      ++  D +TNK +GF F++FK+ +   +  ++
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 149 MN 150
             
Sbjct: 61  KY 62

>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 = 49.3 bits (117), Expect = 5e-09
 Identities = 19/72 (26%), Positives = 33/72 (45%)

Query: 79  RANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 138
           R  +E     +LF G L  + T+E L   + ++       V+RD  + +++GFGFV+F  
Sbjct: 12  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 71

Query: 139 PQDFIRANKEMN 150
             +   A     
Sbjct: 72  MAEVDAAMAARP 83

>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 = 48.9 bits (116), Expect = 6e-09
 Identities = 19/71 (26%), Positives = 32/71 (45%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E E   +LF G L  + T+E L   + ++       V+RD  + +++GFGFV+F    + 
Sbjct: 16 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 75

Query: 78 IRANKEMNDDF 88
            A        
Sbjct: 76 DAAMAARPHSI 86

>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 = 47.3 bits (112), Expect = 1e-08
 Identities = 18/65 (27%), Positives = 31/65 (47%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D     +   +
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 84 MNDDF 88
             + 
Sbjct: 62 SRHEL 66

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.9 bits (111), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L    T E L   F ++    +  V+RD  T +++GFGFV+F D     +   +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 149 MN 150
             
Sbjct: 62  SR 63

>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 = 47.3 bits (112), Expect = 1e-08
 Identities = 18/65 (27%), Positives = 31/65 (47%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L  D T + L   FSK+   +   +  D  T +++GFGFV FK+ +   +   +
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 84 MNDDF 88
               
Sbjct: 61 KEHKL 65

>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 = 46.9 bits (111), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 31/62 (50%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L  D T + L   FSK+   +   +  D  T +++GFGFV FK+ +   +   +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 149 MN 150
             
Sbjct: 61  KE 62

>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 = 47.6 bits (113), Expect = 2e-08
 Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 13 IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
          +KK+C       L+ G+L    T+E +   FSK     K  +  DK      GF FV + 
Sbjct: 4  LKKSC------TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 57

Query: 73 DPQDFIRANKEMN 85
             D   A + +N
Sbjct: 58 SRADAENAMRYIN 70

>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 = 47.6 bits (113), Expect = 2e-08
 Identities = 18/62 (29%), Positives = 26/62 (41%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+ G+L    T+E +   FSK     K  +  DK      GF FV +    D   A + 
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 149 MN 150
           +N
Sbjct: 69  IN 70

>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 = 46.6 bits (110), Expect = 3e-08
 Identities = 17/65 (26%), Positives = 33/65 (50%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
            D  L+   L   +T + L + FS+Y   + ++++ D+ T  ++G GF+ F    +   A
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 146 NKEMN 150
            K +N
Sbjct: 65  IKGLN 69

>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 = 46.6 bits (110), Expect = 3e-08
 Identities = 17/64 (26%), Positives = 33/64 (51%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          D  L+   L   +T + L + FS+Y   + ++++ D+ T  ++G GF+ F    +   A 
Sbjct: 6  DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 65

Query: 82 KEMN 85
          K +N
Sbjct: 66 KGLN 69

>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 = 47.0 bits (111), Expect = 3e-08
 Identities = 22/71 (30%), Positives = 36/71 (50%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +D    ++F G L    TD  L + F  +    +A V+ D++T K++G+GFV+  D    
Sbjct: 6  KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 65

Query: 78 IRANKEMNDDF 88
           RA K+ N   
Sbjct: 66 ERACKDPNPII 76

>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 = 43.2 bits (101), Expect = 9e-07
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L    TD  L + F  +    +A V+ D++T K++G+GFV+  D     RA K+
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 149 MN 150
            N
Sbjct: 72  PN 73

>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 = 46.6 bits (110), Expect = 5e-08
 Identities = 17/87 (19%), Positives = 33/87 (37%), Gaps = 4/87 (4%)

Query: 8  PISSWIKKTCEDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 66
          P+   +     +E D R +FC  L   +    L   FS        +++ D+ + ++KG 
Sbjct: 3  PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 62

Query: 67 GFVSFKDPQDFIRANKEMNDDFRLFCG 93
           +V F + Q        +    +   G
Sbjct: 63 AYVEFCEIQS---VPLAIGLTGQRLLG 86

>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 = 45.0 bits (106), Expect = 2e-07
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 3/79 (3%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
            + E  D   +FC  L   +    L   FS        +++ D+ + ++KG  +V F + 
Sbjct: 11  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 70

Query: 140 QDFIRANKEMNEFPHLFVG 158
           Q        +       +G
Sbjct: 71  QS---VPLAIGLTGQRLLG 86

>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 = 45.8 bits (108), Expect = 8e-08
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 7  GPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGF 66
          GPIS       E   D  ++ G L   V++ LL   F +    +   + +D+ T + +G+
Sbjct: 1  GPIS-------ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 53

Query: 67 GFVSFKDPQDFIRANKEMN 85
          GFV F   +D   A K M+
Sbjct: 54 GFVEFLSEEDADYAIKIMD 72

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 1e-07
 Identities = 20/69 (28%), Positives = 34/69 (49%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
            E N D  ++ G L   V++ LL   F +    +   + +D+ T + +G+GFV F   +D
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 142 FIRANKEMN 150
              A K M+
Sbjct: 64  ADYAIKIMD 72

>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 = 45.1 bits (106), Expect = 1e-07
 Identities = 25/65 (38%), Positives = 39/65 (60%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           D+ +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++  D   A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 146 NKEMN 150
              MN
Sbjct: 64  MMAMN 68

>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 = 42.8 bits (100), Expect = 1e-06
 Identities = 24/65 (36%), Positives = 39/65 (60%)

Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          ++ +LF G L  D  ++ L + FSKY    +  VV+D+ T +++GFGFV+F++  D   A
Sbjct: 4  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 81 NKEMN 85
             MN
Sbjct: 64 MMAMN 68

>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 = 45.0 bits (106), Expect = 1e-07
 Identities = 8/67 (11%), Positives = 23/67 (34%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
                +   ++   V+ + ++  F  Y     +  ++        G   V+F+   +  
Sbjct: 6  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 79 RANKEMN 85
           A  ++N
Sbjct: 66 AAVIDLN 72

>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 = 44.7 bits (105), Expect = 2e-07
 Identities = 8/63 (12%), Positives = 23/63 (36%)

Query: 88  FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
             +   ++   V+ + ++  F  Y     +  ++        G   V+F+   +   A  
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 148 EMN 150
           ++N
Sbjct: 70  DLN 72

>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 = 44.2 bits (104), Expect = 2e-07
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 84 MN 85
           N
Sbjct: 61 YN 62

>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 = 44.2 bits (104), Expect = 2e-07
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +L   +L   V+D  +   F+++ +  KA V  D R+ ++ G   V F+   D ++A K+
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 149 MN 150
            N
Sbjct: 61  YN 62

>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 = 44.2 bits (104), Expect = 4e-07
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 79
          E +  L+  +L   +T E +   F KY      + +R   T +T+G  +V ++D  D   
Sbjct: 5  EVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKN 61

Query: 80 ANKEMN 85
          A   ++
Sbjct: 62 ACDHLS 67

>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 = 43.9 bits (103), Expect = 6e-07
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+  +L   +T E +   F KY      + +R   T +T+G  +V ++D  D   A   +
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 150 NEF 152
           + F
Sbjct: 67  SGF 69

>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 = 43.9 bits (103), Expect = 4e-07
 Identities = 19/70 (27%), Positives = 35/70 (50%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           N+  +D+  +   +L  D  +  L   F  + S  +  + +DK T ++KGF F+SF   +
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 141 DFIRANKEMN 150
           D  RA   ++
Sbjct: 62  DAARAIAGVS 71

>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 = 40.4 bits (94), Expect = 7e-06
 Identities = 17/68 (25%), Positives = 33/68 (48%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
            +++  +   +L  D  +  L   F  + S  +  + +DK T ++KGF F+SF   +D 
Sbjct: 4  RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 63

Query: 78 IRANKEMN 85
           RA   ++
Sbjct: 64 ARAIAGVS 71

>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 = 42.8 bits (100), Expect = 9e-07
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 6/67 (8%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +L+ G+L   VT + L + F         K+    +     G+ FV + D    IRA + 
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 84 MNDDFRL 90
          ++    L
Sbjct: 57 LSGKVEL 63

>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 = 42.4 bits (99), Expect = 1e-06
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 9/72 (12%)

Query: 84  MNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
           MN   +L+ G+L   VT + L + F         K+    +     G+ FV + D    I
Sbjct: 1   MN---KLYIGNLSPAVTADDLRQLFGDR------KLPLAGQVLLKSGYAFVDYPDQNWAI 51

Query: 144 RANKEMNEFPHL 155
           RA + ++    L
Sbjct: 52  RAIETLSGKVEL 63

>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 = 42.7 bits (100), Expect = 1e-06
 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 3/68 (4%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
             ND R++ G+L  D+  + +   F KY +    + +  K       F FV F+DP+D 
Sbjct: 10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEFEDPRDA 66

Query: 78 IRANKEMN 85
            A    +
Sbjct: 67 EDAVYGRD 74

>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 = 42.7 bits (100), Expect = 1e-06
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           N+D R++ G+L  D+  + +   F KY +    + +  K       F FV F+DP+D   
Sbjct: 12  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEFEDPRDAED 68

Query: 145 ANKEMN 150
           A    +
Sbjct: 69  AVYGRD 74

>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 = 42.8 bits (100), Expect = 1e-06
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKA--KVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          RLF G +      E ++   +K    +             K +GF FV ++  +    A 
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 82 KEMNDDFRLFCG 93
          +++        G
Sbjct: 63 RKLMPGRIQLWG 74

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 3e-06
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKA--KVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
           RLF G +      E ++   +K    +             K +GF FV ++  +    A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 147 KEMNEFPHLFVG 158
           +++        G
Sbjct: 63  RKLMPGRIQLWG 74

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 2e-06
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 6/70 (8%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           N+    +  ++CG + + +TD+L+ +TFS +   ++ +V  +K       + FV F   +
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHE 65

Query: 141 DFIRANKEMN 150
               A   +N
Sbjct: 66  SAAHAIVSVN 75

>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 = 41.1 bits (96), Expect = 4e-06
 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
             +  ++CG + + +TD+L+ +TFS +   ++ +V  +K       + FV F   +   
Sbjct: 15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAA 68

Query: 79 RANKEMN 85
           A   +N
Sbjct: 69 HAIVSVN 75

>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 = 41.5 bits (97), Expect = 2e-06
 Identities = 19/65 (29%), Positives = 29/65 (44%)

Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          ++  L    L  D+TD  L   F         +++RD +T  + G+ FV F    D  RA
Sbjct: 1  SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 81 NKEMN 85
           K +N
Sbjct: 61 IKVLN 65

>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 = 40.4 bits (94), Expect = 6e-06
 Identities = 19/64 (29%), Positives = 28/64 (43%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
           +  L    L  D+TD  L   F         +++RD +T  + G+ FV F    D  RA 
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 147 KEMN 150
           K +N
Sbjct: 62  KVLN 65

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 14/65 (21%), Positives = 28/65 (43%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G +  D  +  L   F +Y      +++ D+ + K +GF FV+F D     +   +
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 84 MNDDF 88
               
Sbjct: 64 KYHTV 68

>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 = 40.9 bits (95), Expect = 4e-06
 Identities = 14/62 (22%), Positives = 28/62 (45%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G +  D  +  L   F +Y      +++ D+ + K +GF FV+F D     +   +
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 149 MN 150
             
Sbjct: 64  KY 65

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 3e-06
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR---TNKTKGFGFVSFKDPQDFIRAN 81
          LF  +L    T+E L   FSK  +     + + K       + GFGFV +K P+   +A 
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 82 KEMN 85
          K++ 
Sbjct: 61 KQLQ 64

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.6 bits (97), Expect = 3e-06
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR---TNKTKGFGFVSFKDPQDFIRAN 146
           LF  +L    T+E L   FSK  +     + + K       + GFGFV +K P+   +A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 147 KEMN 150
           K++ 
Sbjct: 61  KQLQ 64

>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 = 42.0 bits (98), Expect = 3e-06
 Identities = 13/73 (17%), Positives = 22/73 (30%), Gaps = 6/73 (8%)

Query: 78  IRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 137
           I           +  G LGN V+   L+    K                  K + F  ++
Sbjct: 11  IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLV------DALLMPPNKPYSFARYR 64

Query: 138 DPQDFIRANKEMN 150
             ++  RA   +N
Sbjct: 65  TTEESKRAYVTLN 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 = 42.0 bits (98), Expect = 3e-06
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 8/88 (9%)

Query: 13  IKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFK 72
           I+          +  G LGN V+   L+    K                  K + F  ++
Sbjct: 11  IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLV------DALLMPPNKPYSFARYR 64

Query: 73  DPQDFIRANKEMNDDFRLFCGDLGNDVT 100
             ++  RA   +N   +    DLG  +T
Sbjct: 65  TTEESKRAYVTLNG--KEVVDDLGQKIT 90

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 3e-06
 Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 5/62 (8%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 78
          RL+ G++   +T+E ++  F+               V   + N+ K F F+ F+   +  
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 79 RA 80
          +A
Sbjct: 63 QA 64

>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 = 41.3 bits (96), Expect = 3e-06
 Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 5/62 (8%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKV-----VRDKRTNKTKGFGFVSFKDPQDFI 143
           RL+ G++   +T+E ++  F+               V   + N+ K F F+ F+   +  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 144 RA 145
           +A
Sbjct: 63  QA 64

>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 = 40.5 bits (94), Expect = 5e-06
 Identities = 18/62 (29%), Positives = 29/62 (46%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L    L    T+  L   FSKY       +V D+++ +++GF FV F++  D   A + 
Sbjct: 11 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 84 MN 85
           N
Sbjct: 71 AN 72

>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 = 40.5 bits (94), Expect = 5e-06
 Identities = 18/62 (29%), Positives = 29/62 (46%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L    L    T+  L   FSKY       +V D+++ +++GF FV F++  D   A + 
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 149 MN 150
            N
Sbjct: 71  AN 72

>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 = 41.0 bits (96), Expect = 5e-06
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 9/69 (13%)

Query: 18 EDENDFRLFCGDLGNDVTDE-LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
              + R+F G+L   V  +  +   FSKY   +   V         KGF FV + + ++
Sbjct: 11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERN 62

Query: 77 FIRANKEMN 85
             A    +
Sbjct: 63 ARAAVAGED 71

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 9/67 (13%)

Query: 85  NDDFRLFCGDLGNDVTDE-LLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 143
           + + R+F G+L   V  +  +   FSKY   +   V         KGF FV + + ++  
Sbjct: 13  SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNAR 64

Query: 144 RANKEMN 150
            A    +
Sbjct: 65  AAVAGED 71

>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 = 40.8 bits (95), Expect = 7e-06
 Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 5/75 (6%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           R+   +L   VT ++L + FSK+ + LK            +    + + DP     A   
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLS 64

Query: 149 MNEFPHLFVGDLKTR 163
           ++    ++      R
Sbjct: 65  LDGQN-IYNACCTLR 78

>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 = 40.8 bits (95), Expect = 7e-06
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 4/62 (6%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          R+   +L   VT ++L + FSK+ + LK            +    + + DP     A   
Sbjct: 9  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLS 64

Query: 84 MN 85
          ++
Sbjct: 65 LD 66

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 40.4 bits (94), Expect = 7e-06
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 9/80 (11%)

Query: 71  FKDPQDFIRANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 130
            +DP      +K++     L   +L  ++T++ L   F               +  K+KG
Sbjct: 4   LEDPCT----SKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKG 54

Query: 131 FGFVSFKDPQDFIRANKEMN 150
             ++ FK   D  +  +E  
Sbjct: 55  IAYIEFKSEADAEKNLEEKQ 74

>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 = 37.7 bits (87), Expect = 9e-05
 Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +      L   +L  ++T++ L   F               +  K+KG  ++ FK   D 
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADA 66

Query: 78 IRANKEMN 85
           +  +E  
Sbjct: 67 EKNLEEKQ 74

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 9e-06
 Identities = 14/82 (17%), Positives = 27/82 (32%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
            ++ +   +F  +L  D  +E L     ++      +VV    T  +KG  F  F   + 
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 142 FIRANKEMNEFPHLFVGDLKTR 163
             +     +         L  R
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGR 84

>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 = 38.3 bits (88), Expect = 5e-05
 Identities = 13/80 (16%), Positives = 25/80 (31%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          +      +F  +L  D  +E L     ++      +VV    T  +KG  F  F   +  
Sbjct: 4  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 63

Query: 78 IRANKEMNDDFRLFCGDLGN 97
           +     + +       L  
Sbjct: 64 QKCLAAASLEAEGGGLKLDG 83

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 25 LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          +F G+L  ++ ++LL  TFS +       K++RD  T  +KG+ F++F        A + 
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 84 MN 85
          MN
Sbjct: 61 MN 62

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 90  LFCGDLGNDVTDELLIRTFSKY-PSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           +F G+L  ++ ++LL  TFS +       K++RD  T  +KG+ F++F        A + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 149 MN 150
           MN
Sbjct: 61  MN 62

>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 = 40.0 bits (93), Expect = 1e-05
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 5/64 (7%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F G    D+T++ L   FS+Y       V+        + F FV+F D Q       E
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQY-----GDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE 61

Query: 149 MNEF 152
               
Sbjct: 62  DLII 65

>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 = 37.7 bits (87), Expect = 7e-05
 Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 5/63 (7%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           +F G    D+T++ L   FS+Y       V+        + F FV+F D Q       E
Sbjct: 7  GVFVGRCTGDMTEDELREFFSQY-----GDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE 61

Query: 84 MND 86
             
Sbjct: 62 DLI 64

>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 = 40.0 bits (93), Expect = 1e-05
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 18 EDENDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 76
          ED+   R L+ G+L  DVT+ L+++ FS+       K++ +        + FV F + +D
Sbjct: 3  EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRD 60

Query: 77 FIRANKEMN 85
             A   MN
Sbjct: 61 AAAALAAMN 69

>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 = 38.5 bits (89), Expect = 4e-05
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
                L+ G+L  DVT+ L+++ FS+       K++ +        + FV F + +D   
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAA 63

Query: 145 ANKEMN 150
           A   MN
Sbjct: 64  ALAAMN 69

>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 = 39.3 bits (91), Expect = 2e-05
 Identities = 21/62 (33%), Positives = 32/62 (51%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF  +L    ++E L + FS Y    +     D  T K KGF FV+F  P+  ++A  E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 84 MN 85
          ++
Sbjct: 70 VD 71

>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 = 39.3 bits (91), Expect = 2e-05
 Identities = 21/62 (33%), Positives = 32/62 (51%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           RLF  +L    ++E L + FS Y    +     D  T K KGF FV+F  P+  ++A  E
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 149 MN 150
           ++
Sbjct: 70  VD 71

>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 = 38.9 bits (90), Expect = 3e-05
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D   A   
Sbjct: 7  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 84 MN 85
          MN
Sbjct: 67 MN 68

>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 = 38.9 bits (90), Expect = 3e-05
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+ G L  +V D++L   F  +      ++  D  T K +GF FV F+  +D   A   
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 149 MN 150
           MN
Sbjct: 67  MN 68

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 20/62 (32%), Positives = 31/62 (50%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L    L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 84 MN 85
          +N
Sbjct: 64 LN 65

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 20/62 (32%), Positives = 31/62 (50%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L    L  ++T E     F         K+VRDK T ++ G+GFV++ DP+D  +A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 149 MN 150
           +N
Sbjct: 64  LN 65

>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 = 38.2 bits (88), Expect = 3e-05
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          ++F G L  + T E +   F ++     A ++ DK TN+ +GFGFV+F+      +   E
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CE 59

Query: 84 MND 86
          ++ 
Sbjct: 60 IHF 62

>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 = 38.2 bits (88), Expect = 3e-05
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
           ++F G L  + T E +   F ++     A ++ DK TN+ +GFGFV+F+      +   E
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CE 59

Query: 149 MN 150
           ++
Sbjct: 60  IH 61

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (89), Expect = 5e-05
 Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 9/70 (12%)

Query: 16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 75
             D  D  L   ++  D+  E      SK+    K  +          G   VSF+DP+
Sbjct: 18 HPMDFEDDPLVLNEIREDLRVE-----CSKFGQIRKLLLFDRHP----DGVASVSFRDPE 68

Query: 76 DFIRANKEMN 85
          +     + ++
Sbjct: 69 EADYCIQTLD 78

>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 = 36.8 bits (85), Expect = 2e-04
 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 9/65 (13%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           +D  L   ++  D+  E      SK+    K  +          G   VSF+DP++    
Sbjct: 23  EDDPLVLNEIREDLRVE-----CSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYC 73

Query: 146 NKEMN 150
            + ++
Sbjct: 74  IQTLD 78

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 5e-05
 Identities = 25/71 (35%), Positives = 39/71 (54%)

Query: 80  ANKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP 139
           + KE  +   LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 140 QDFIRANKEMN 150
                A + MN
Sbjct: 71  VSAQAAIQSMN 81

>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 = 37.8 bits (87), Expect = 8e-05
 Identities = 24/68 (35%), Positives = 36/68 (52%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
          E      LF   L  +  D+ L++ F  + + + AKV  DK+TN +K FGFVS+ +P   
Sbjct: 14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 73

Query: 78 IRANKEMN 85
            A + MN
Sbjct: 74 QAAIQSMN 81

>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 = 38.2 bits (88), Expect = 5e-05
 Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFV 69
          ED ++  ++   L + VT + L   F +                +  DK T K KG   V
Sbjct: 4  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 70 SFKDPQDFIRANKEMN 85
          S++DP     A +  +
Sbjct: 64 SYEDPPTAKAAVEWFD 79

>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 = 37.1 bits (85), Expect = 1e-04
 Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 83  EMNDDFRLFCGDLGNDVTDELLIRTFSKY--------PSFLKAKVVRDKRTNKTKGFGFV 134
           E +D+  ++   L + VT + L   F +                +  DK T K KG   V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 135 SFKDPQDFIRANKEMN 150
           S++DP     A +  +
Sbjct: 64  SYEDPPTAKAAVEWFD 79

>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 = 37.3 bits (86), Expect = 9e-05
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 147
            ++  +L   +  + L ++     S F +   +   R+ K +G  FV FK+      A +
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 148 EMNEFP----HLFVGDLKTRSSITLK 169
            M  FP     + +   KT S I  K
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDSDIIAK 90

>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 = 35.8 bits (82), Expect = 4e-04
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
           ++  +L   +  + L ++     S F +   +   R+ K +G  FV FK+      A +
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 83 EMN 85
           M 
Sbjct: 65 SMQ 67

>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 = 37.3 bits (86), Expect = 9e-05
 Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
           K      RLF G+L  D+T+E + + F KY    +         +K KGFGF+  +    
Sbjct: 3   KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEV------FIHKDKGFGFIRLETRTL 56

Query: 142 FIRANKEMN 150
              A  E++
Sbjct: 57  AEIAKVELD 65

>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 = 36.1 bits (83), Expect = 2e-04
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 6/62 (9%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
          RLF G+L  D+T+E + + F KY    +         +K KGFGF+  +       A  E
Sbjct: 10 RLFVGNLPPDITEEEMRKLFEKYGKAGEV------FIHKDKGFGFIRLETRTLAEIAKVE 63

Query: 84 MN 85
          ++
Sbjct: 64 LD 65

>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 = 37.3 bits (86), Expect = 9e-05
 Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 82  KEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQD 141
             M+    L+  +L    ++E++ + F+             +R  K + + FV F + +D
Sbjct: 3   DTMSSVKILYVRNLMLSTSEEMIEKEFNNIK------PGAVERVKKIRDYAFVHFSNRED 56

Query: 142 FIRANKEMN 150
            + A K +N
Sbjct: 57  AVEAMKALN 65

>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 = 36.5 bits (84), Expect = 2e-04
 Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 6/62 (9%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+  +L    ++E++ + F+             +R  K + + FV F + +D + A K 
Sbjct: 10 ILYVRNLMLSTSEEMIEKEFNNIK------PGAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 84 MN 85
          +N
Sbjct: 64 LN 65

>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 = 37.3 bits (86), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           +F  +L   + ++ L  TFS + + L  KVV D+  +K   +GFV F+  +   RA ++
Sbjct: 10 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIEK 67

Query: 84 MN 85
          MN
Sbjct: 68 MN 69

>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 = 37.3 bits (86), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F  +L   + ++ L  TFS + + L  KVV D+  +K   +GFV F+  +   RA ++
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIEK 67

Query: 149 MN 150
           MN
Sbjct: 68  MN 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 = 36.7 bits (84), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 29/61 (47%)

Query: 25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 84
          L+   L    TD+ L++    Y   +  K + DK TNK KG+GFV F  P    +A   +
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 85 N 85
           
Sbjct: 61 K 61

>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 = 36.7 bits (84), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 29/61 (47%)

Query: 90  LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM 149
           L+   L    TD+ L++    Y   +  K + DK TNK KG+GFV F  P    +A   +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 150 N 150
            
Sbjct: 61  K 61

>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 = 37.1 bits (85), Expect = 1e-04
 Identities = 10/66 (15%), Positives = 19/66 (28%), Gaps = 1/66 (1%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L      +DV  E   R       F         +  K+     ++F +P     A   
Sbjct: 7   GLIACVANDDVFSESETR-AKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65

Query: 149 MNEFPH 154
           +++   
Sbjct: 66  LHKTEF 71

>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 = 36.3 bits (83), Expect = 3e-04
 Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 1/62 (1%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L      +DV  E   R       F         +  K+     ++F +P     A   
Sbjct: 7  GLIACVANDDVFSESETR-AKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65

Query: 84 MN 85
          ++
Sbjct: 66 LH 67

>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 = 36.7 bits (84), Expect = 2e-04
 Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 24 RLFCGDLGNDVTDELLIRTF---SKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDF 77
           +F   L   + D  +++      K+    K  +        +       +V++   +D 
Sbjct: 10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 78 IRANKEMN 85
          +RA + +N
Sbjct: 70 LRAIQCVN 77

>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 = 36.7 bits (84), Expect = 2e-04
 Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 89  RLFCGDLGNDVTDELLIRTF---SKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDF 142
            +F   L   + D  +++      K+    K  +        +       +V++   +D 
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 143 IRANKEMN 150
           +RA + +N
Sbjct: 70  LRAIQCVN 77

>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 = 36.6 bits (84), Expect = 2e-04
 Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
                RL   ++     D  L + F ++   L  +++ ++R +K   FGFV+F++  D 
Sbjct: 7  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSADA 64

Query: 78 IRANKEMN 85
           RA ++++
Sbjct: 65 DRAREKLH 72

>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 = 36.6 bits (84), Expect = 2e-04
 Identities = 16/70 (22%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 81  NKEMNDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQ 140
           ++  +   RL   ++     D  L + F ++   L  +++ ++R +K   FGFV+F++  
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FGFVTFENSA 62

Query: 141 DFIRANKEMN 150
           D  RA ++++
Sbjct: 63  DADRAREKLH 72

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 12/81 (14%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 71  FKDPQDFIRANKEMNDDFR-LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTK 129
           +++PQ+  ++   +      +   +  ++  +E+      KY    +  V  +   +   
Sbjct: 10  YRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLV 68

Query: 130 GFGFVSFKDPQDFIRANKEMN 150
           G  +V F+  +D  +A  ++N
Sbjct: 69  GNVYVKFRREEDAEKAVIDLN 89

>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 = 36.9 bits (85), Expect = 2e-04
 Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 6  PGPISSWIKKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKG 65
            P +S             +   +  ++  +E+      KY    +  V  +   +   G
Sbjct: 11 RNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVG 69

Query: 66 FGFVSFKDPQDFIRANKEMN 85
            +V F+  +D  +A  ++N
Sbjct: 70 NVYVKFRREEDAEKAVIDLN 89

>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 = 36.2 bits (83), Expect = 2e-04
 Identities = 12/65 (18%), Positives = 29/65 (44%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           + + LF   +  +  ++ +   F  Y       +  D+RT  +KG+  V ++  +  + A
Sbjct: 6   EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 65

Query: 146 NKEMN 150
            + +N
Sbjct: 66  KEALN 70

>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 = 35.9 bits (82), Expect = 3e-04
 Identities = 12/63 (19%), Positives = 28/63 (44%)

Query: 23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK 82
          + LF   +  +  ++ +   F  Y       +  D+RT  +KG+  V ++  +  + A +
Sbjct: 8  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 83 EMN 85
           +N
Sbjct: 68 ALN 70

>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 = 36.3 bits (83), Expect = 3e-04
 Identities = 19/68 (27%), Positives = 37/68 (54%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           D +   +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  ++D +  
Sbjct: 4  VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 78 IRANKEMN 85
          + A + +N
Sbjct: 64 LSAMRNLN 71

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 7e-04
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            +F G++  + T+E L   FS+    +  ++V D+ T K KG+GF  ++D +  + A + 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 149 MN 150
           +N
Sbjct: 70  LN 71

>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 = 35.5 bits (81), Expect = 6e-04
 Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 1/67 (1%)

Query: 19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFI 78
              +  F G+L  DVT+E +   F                  + KGFG+  F+D    +
Sbjct: 12 KSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 79 RANKEMN 85
           A   +N
Sbjct: 72 SA-LSLN 77

>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 = 34.3 bits (78), Expect = 0.001
 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
           +  +  F G+L  DVT+E +   F                  + KGFG+  F+D    + 
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLS 72

Query: 145 ANKEMN 150
           A   +N
Sbjct: 73  A-LSLN 77

>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 = 34.9 bits (80), Expect = 7e-04
 Identities = 9/73 (12%), Positives = 24/73 (32%), Gaps = 10/73 (13%)

Query: 86  DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 145
           DD  +            +L   F++Y + LK  +           +  + ++      +A
Sbjct: 3   DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKA 55

Query: 146 NKEMNEFPHLFVG 158
              +++   +F  
Sbjct: 56  ---LSKDGRIFGE 65

>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 = 34.5 bits (79), Expect = 0.001
 Identities = 7/60 (11%), Positives = 19/60 (31%), Gaps = 7/60 (11%)

Query: 21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRA 80
          +D  +            +L   F++Y + LK  +           +  + ++      +A
Sbjct: 3  DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKA 55

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 7e-04
 Identities = 13/72 (18%), Positives = 30/72 (41%)

Query: 14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKD 73
                E +  L+  +L   VT+  L+  F+++       +     T + +G  F++F +
Sbjct: 10 SSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN 69

Query: 74 PQDFIRANKEMN 85
           +   +A   +N
Sbjct: 70 KEIAWQALHLVN 81

>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 = 34.8 bits (79), Expect = 0.001
 Identities = 12/62 (19%), Positives = 28/62 (45%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+  +L   VT+  L+  F+++       +     T + +G  F++F + +   +A   
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 149 MN 150
           +N
Sbjct: 80  VN 81

>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 = 34.4 bits (78), Expect = 0.001
 Identities = 7/64 (10%), Positives = 21/64 (32%)

Query: 22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 81
          +  L+  +     T   +            +  +   R N ++ F ++     +D     
Sbjct: 1  ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 82 KEMN 85
          +++N
Sbjct: 61 EKLN 64

>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 = 34.4 bits (78), Expect = 0.001
 Identities = 7/64 (10%), Positives = 21/64 (32%)

Query: 87  DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRAN 146
           +  L+  +     T   +            +  +   R N ++ F ++     +D     
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 147 KEMN 150
           +++N
Sbjct: 61  EKLN 64

>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 = 33.5 bits (76), Expect = 0.002
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 8/62 (12%)

Query: 24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 83
           L+      D+T  LL   FS + +        D   +  +   FV+++  +   +A  E
Sbjct: 7  TLYVYGE--DMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAE 58

Query: 84 MN 85
          +N
Sbjct: 59 LN 60

>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 = 33.5 bits (76), Expect = 0.002
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 8/62 (12%)

Query: 89  RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE 148
            L+      D+T  LL   FS + +        D   +  +   FV+++  +   +A  E
Sbjct: 7   TLYVYGE--DMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAE 58

Query: 149 MN 150
           +N
Sbjct: 59  LN 60

>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 = 33.6 bits (76), Expect = 0.002
 Identities = 10/66 (15%), Positives = 21/66 (31%), Gaps = 7/66 (10%)

Query: 85  NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIR 144
             DFR+    L    + + L     +                +  G G V +   +D   
Sbjct: 13  RSDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMGMVEYLRKEDMEY 65

Query: 145 ANKEMN 150
           A ++++
Sbjct: 66  ALRKLD 71

>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 = 33.6 bits (76), Expect = 0.003
 Identities = 11/69 (15%), Positives = 23/69 (33%), Gaps = 7/69 (10%)

Query: 18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
             +DFR+    L    + + L     +                +  G G V +   +D 
Sbjct: 11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMGMVEYLRKEDM 63

Query: 78 IRANKEMND 86
            A ++++D
Sbjct: 64 EYALRKLDD 72

>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 = 33.3 bits (75), Expect = 0.004
 Identities = 17/68 (25%), Positives = 31/68 (45%)

Query: 18  EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDF 77
           E +    L    +   V +  L + F +Y      K+V D+ T +++G+GFV F+     
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 78  IRANKEMN 85
            +A   +N
Sbjct: 98  QQAIAGLN 105

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	170
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.89
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.85
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.85
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.82
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.79
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.79
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.79
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.79
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.79
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.79
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.79
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.78
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.76
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.76
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.76
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.76
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.76
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.75
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.75
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.74
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.74
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.74
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.74
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.74
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.73
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.73
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.73
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.73
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.72
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.72
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.72
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.71
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.71
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.71
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.7
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.69
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.68
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.68
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.68
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.68
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.67
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.67
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.64
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.64
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.64
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.64
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.63
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.61
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.6
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.6
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.6
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.58
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.58
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.58
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.58
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.58
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.57
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.57
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.56
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.56
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.56
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.55
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.55
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.54
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.53
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.53
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.53
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.53
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.52
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.51
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.5
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.49
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.49
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.47
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.45
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.45
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.43
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.43
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.42
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.41
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.4
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
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	99.27
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.21
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.2
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.07
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.96
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	98.09
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.98
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.84
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.26
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.66
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.43
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	93.32
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	91.55

>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=100.00  E-value=1.9e-34  Score=204.67  Aligned_cols=148  Identities=25%  Similarity=0.418  Sum_probs=137.3

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC-----------
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND-----------   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~-----------   86 (170)
                      +|++.++|||+|||+++|+++|+++|++||.|.++.++++..+|.++|+|||.|.+.++|.+|+..++.           
T Consensus         2 ep~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (183)
T ss_dssp             CCHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhh
Confidence            344568999999999999999999999999999999999988999999999999999999999986653           


Q ss_pred             ---------------CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          87 ---------------DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        87 ---------------~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                                     ..+|||+|||+.+++++|+++|+.||.|..+.+..+..++.++|||||+|.+.++|.+|++ +++
T Consensus        82 ~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~  160 (183)
T d1u1qa_          82 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKY  160 (183)
T ss_dssp             CCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSC
T ss_pred             hhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCC
Confidence                           2599999999999999999999999999999999998889999999999999999999997 688


Q ss_pred             CCccccCCeeEEEEeecc
Q psy7847         152 FPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       152 ~~~~~~~~~~i~v~~~~~  169 (170)
                         ..++|++|+|++|.+
T Consensus       161 ---~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         161 ---HTVNGHNCEVRKALS  175 (183)
T ss_dssp             ---EEETTEEEEEEECCC
T ss_pred             ---CeECCEEEEEEecCC
Confidence               889999999999864

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.89  E-value=4.3e-23  Score=127.63  Aligned_cols=81  Identities=27%  Similarity=0.379  Sum_probs=77.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +.+|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng---~~~~g~~l~v~~   78 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG---ITVRNKRLKVSY   78 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            35799999999999999999999999999999999988899999999999999999999999999   999999999999


Q ss_pred             eccC
Q psy7847         167 TLKG  170 (170)
Q Consensus       167 ~~~~  170 (170)
                      |.+|
T Consensus        79 a~pg   82 (82)
T d1b7fa1          79 ARPG   82 (82)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9886

>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=3.7e-22  Score=123.32  Aligned_cols=80  Identities=28%  Similarity=0.384  Sum_probs=76.8

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+|||+|||+++++++|+++|++||.|..+.+.++...+.++|||||+|.+.++|+.|++.|||   ..++|++|+|+||
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g---~~~~g~~l~v~~A   79 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG---LRLQTKTIKVSYA   79 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCC---CEECCEEEEEEEe
Confidence            4799999999999999999999999999999999988899999999999999999999999999   9999999999999


Q ss_pred             ccC
Q psy7847         168 LKG  170 (170)
Q Consensus       168 ~~~  170 (170)
                      .++
T Consensus        80 kPs   82 (82)
T d1fxla1          80 RPS   82 (82)
T ss_dssp             CCC
T ss_pred             eCc
Confidence            874

>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=4.6e-22  Score=124.48  Aligned_cols=80  Identities=15%  Similarity=0.314  Sum_probs=76.9

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|.++|++||.|..+.+.+|+.++.++|||||+|.+.++|.+|++.|||   ..++|+.|+|+|
T Consensus         7 ~~~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_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNG---AEIMGQTIQVDW   83 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCC---CEECCEEEEEEE
Confidence            46899999999999999999999999999999999988999999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      |.+
T Consensus        84 a~~   86 (88)
T d1rk8a_          84 CFV   86 (88)
T ss_dssp             SEE
T ss_pred             ecC
Confidence            975

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=3.1e-22  Score=123.11  Aligned_cols=78  Identities=32%  Similarity=0.482  Sum_probs=75.2

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      .|||+|||+.+++++|.++|++||.|..+.+++|+.++.++|||||+|.+.++|..|++.|||   ..++|++|+|+||.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g---~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNF---DVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTT---CEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCC---CEECCEEEEEEEeC
Confidence            589999999999999999999999999999999998999999999999999999999999999   99999999999986


Q ss_pred             c
Q psy7847         169 K  169 (170)
Q Consensus       169 ~  169 (170)
                      +
T Consensus        79 ~   79 (80)
T d1cvja1          79 R   79 (80)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.86  E-value=5.4e-22  Score=124.45  Aligned_cols=80  Identities=26%  Similarity=0.379  Sum_probs=77.0

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +++|||+|||+++++++|+++|++||.|..+.+++|+.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|++
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~---~~i~g~~l~v~~   81 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE---SELFGRTIRVNL   81 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT---EEETTEEEEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCC---CEECCEEEEEEE
Confidence            56899999999999999999999999999999999998899999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      |.+
T Consensus        82 a~p   84 (89)
T d2cqba1          82 AKP   84 (89)
T ss_dssp             CCC
T ss_pred             eCC
Confidence            975

>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=99.86  E-value=1.5e-21  Score=123.32  Aligned_cols=82  Identities=24%  Similarity=0.268  Sum_probs=77.8

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|..|++.|||   ..++|++|+|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g---~~~~gr~i~V   81 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING---TRLDDRIIRT   81 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTT---SEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCC---CEECCEEEEE
Confidence            4567999999999999999999999999999999999998999999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +|+..
T Consensus        82 ~~a~~   86 (93)
T d1h2vz_          82 DWDAG   86 (93)
T ss_dssp             EEESC
T ss_pred             EEcCC
Confidence            99853

>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=6.1e-22  Score=123.12  Aligned_cols=79  Identities=23%  Similarity=0.337  Sum_probs=76.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+|||+|||+++++++|+++|++||.|..+.+.+|+.++.++|||||+|.+.++|..|++.|||   ..++|++|+|.+|
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   78 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG---MQLGDKKLLVQRA   78 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSS---CCCSSSCCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCC---CEECCEEEEEEEC
Confidence            3799999999999999999999999999999999988899999999999999999999999999   9999999999999


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      ..
T Consensus        79 ~~   80 (85)
T d2u2fa_          79 SV   80 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.1e-21  Score=124.06  Aligned_cols=82  Identities=24%  Similarity=0.369  Sum_probs=77.8

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      +...+|||+|||+.+++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|..|++.|||   ..++|+.|+|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V   83 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDM---IKLYGKPIRV   83 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSS---CBCSSCBCEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCC---CEECCEEEEE
Confidence            3457999999999999999999999999999999999988999999999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +||.+
T Consensus        84 ~~A~~   88 (93)
T d1x5ua1          84 NKASA   88 (93)
T ss_dssp             EETTT
T ss_pred             EEcCC
Confidence            99875

>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=99.86  E-value=1.6e-21  Score=122.45  Aligned_cols=81  Identities=23%  Similarity=0.331  Sum_probs=77.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|+.||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|+
T Consensus         7 ~~~~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           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG---FGYDHLILNVE   83 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTT---CEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            456899999999999999999999999999999999988899999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ||.+
T Consensus        84 ~akp   87 (90)
T d2cq0a1          84 WAKP   87 (90)
T ss_dssp             ESSC
T ss_pred             eeeC
Confidence            9976

>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=99.85  E-value=1.7e-21  Score=119.21  Aligned_cols=77  Identities=21%  Similarity=0.312  Sum_probs=73.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +|||+|||+++++++|+++|++||.|..+.+.+++ ++.++|||||+|.+.++|.+|++.|||   ..++|++|+|++++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG---VPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTT---CEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCC---CEECCEEEEEEEee
Confidence            69999999999999999999999999999999886 788999999999999999999999999   99999999999986


Q ss_pred             c
Q psy7847         169 K  169 (170)
Q Consensus       169 ~  169 (170)
                      .
T Consensus        78 S   78 (78)
T d1no8a_          78 S   78 (78)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.85  E-value=3.2e-21  Score=119.86  Aligned_cols=78  Identities=24%  Similarity=0.443  Sum_probs=73.0

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC--eeEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD--LKTRS  164 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~--~~i~v  164 (170)
                      ..+|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||   ..+.|  ++|+|
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~g~~~~l~V   82 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN---VIPEGGSQPLSV   82 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CCCTTCSSCCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCC---CEeCCCCeEEEE
Confidence            45799999999999999999999999999999999988999999999999999999999999999   66654  89999


Q ss_pred             Eee
Q psy7847         165 SIT  167 (170)
Q Consensus       165 ~~~  167 (170)
                      .||
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            986

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3e-21  Score=119.98  Aligned_cols=78  Identities=22%  Similarity=0.351  Sum_probs=73.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC--eeEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD--LKTRS  164 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~--~~i~v  164 (170)
                      ..+|||+|||+.+++++|+++|++||.|..+.+++|+.++.++|||||+|.+.++|.+|++.|||   ..++|  ++|+|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng---~~~~G~~~~i~V   82 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG---QKPSGATEPITV   82 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT---CCCTTCSSCCEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCC---CEeCCCCEEEEE
Confidence            35799999999999999999999999999999999988899999999999999999999999999   78876  67999


Q ss_pred             Eee
Q psy7847         165 SIT  167 (170)
Q Consensus       165 ~~~  167 (170)
                      +||
T Consensus        83 ~~A   85 (85)
T d1fxla2          83 KFA   85 (85)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>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=99.85  E-value=1.3e-21  Score=120.52  Aligned_cols=79  Identities=10%  Similarity=0.142  Sum_probs=69.1

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+++++++|+++|++||.|..+.+..+...+.++|||||+|.+.++|.+|++.|||   ..++|++|+|.++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g---~~~~g~~i~V~~a   78 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG---LKIEGYTLVTKVS   78 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTT---CEETTEECEEEEC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCC---CEECCEEEEEEEc
Confidence            5899999999999999999999999999888877777899999999999999999999999999   9999999999999


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .|
T Consensus        79 ~P   80 (81)
T d2ghpa1          79 NP   80 (81)
T ss_dssp             CC
T ss_pred             cC
Confidence            76

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=7.6e-21  Score=121.41  Aligned_cols=81  Identities=26%  Similarity=0.319  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +..+|||+|||+.+++++|+++|++||.|..+.+++|+.++.++|||||+|.+.++|..|++.||+   ..++|++|+|.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g---~~~~gr~i~V~   83 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG---QVFQGRMLHVL   83 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT---EESSSCEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            456899999999999999999999999999999999988999999999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        84 ~a~~   87 (99)
T d1whwa_          84 PSTI   87 (99)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9864

>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=99.84  E-value=4e-21  Score=120.62  Aligned_cols=80  Identities=34%  Similarity=0.502  Sum_probs=76.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|..|++.|||   ..++|++|+|++
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~---~~~~g~~l~V~~   81 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG---KSVDGRQIRVDQ   81 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT---CCTTSCCCEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCC---CEECCEEEEEEE
Confidence            46899999999999999999999999999999998888899999999999999999999999999   899999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        82 a~~   84 (90)
T d1x5sa1          82 AGK   84 (90)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            875

>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=99.84  E-value=7e-21  Score=120.44  Aligned_cols=81  Identities=15%  Similarity=0.240  Sum_probs=75.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCC-CCCcccEEEEEecCHHHHHHHHHHh-cCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEM-NEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l-~~~~~~~~~~~~i~  163 (170)
                      ...+|||+|||+.+++++|+++|++||.|..+.++++.. ++.++|||||+|.+.++|.+|++.| ||   ..++|++|+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~---~~~~Gr~l~   83 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS---THLYGRRLV   83 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC---CBSSSCBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCC---cEECCEEEE
Confidence            356899999999999999999999999999999988754 7889999999999999999999998 88   889999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |+||.+
T Consensus        84 V~~A~~   89 (94)
T d2cpha1          84 LEWADS   89 (94)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            999975

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=5.2e-21  Score=122.80  Aligned_cols=80  Identities=30%  Similarity=0.444  Sum_probs=76.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|+.||.+..+.+..++.++.++|||||+|.+.++|..|++.|||   ..++|++|+|+|
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng---~~~~g~~i~V~~   94 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG---FQIGMKRLKVQL   94 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT---CEETTEECEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            46899999999999999999999999999999999988999999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        95 a~~   97 (102)
T d2cpza1          95 KRS   97 (102)
T ss_dssp             CCC
T ss_pred             eCC
Confidence            875

>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=99.84  E-value=8.4e-21  Score=117.39  Aligned_cols=75  Identities=25%  Similarity=0.357  Sum_probs=72.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      .++|||+|||+.+++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g---~~~~gr~i~V   83 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG---MELDGRRIRV   83 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT---EEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCC---CEECCEEeEC
Confidence            46899999999999999999999999999999999988899999999999999999999999999   9999999987

>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=99.83  E-value=4.7e-21  Score=118.54  Aligned_cols=77  Identities=29%  Similarity=0.516  Sum_probs=72.4

Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeE-EEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          90 LFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        90 l~v~nlp~~~~~~~l~~~f~~~g~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      |||+|||+++++++|+++|++||.|.. +.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|+|+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g---~~~~gr~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNG---QYLCNRPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTT---CEETTEECEEEESC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCC---cEECCEEEEEEEec
Confidence            799999999999999999999999865 47888888899999999999999999999999999   99999999999987


Q ss_pred             c
Q psy7847         169 K  169 (170)
Q Consensus       169 ~  169 (170)
                      +
T Consensus        78 ~   78 (83)
T d1x5ta1          78 K   78 (83)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.83  E-value=8.1e-21  Score=117.97  Aligned_cols=77  Identities=29%  Similarity=0.424  Sum_probs=71.5

Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCC---CcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN---KTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        90 l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      |||+|||+++++++|+++|++||.|..+.+.+++.++   .++|||||+|.+.++|.+|++.|||   ..++|++|+|.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~---~~~~g~~i~V~~   77 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQG---HTVDGHKLEVRI   77 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTT---CEETTEECEEEC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            7999999999999999999999999999998886544   3689999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        78 a~~   80 (85)
T d2cpfa1          78 SER   80 (85)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

>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=99.83  E-value=3.2e-21  Score=117.56  Aligned_cols=76  Identities=24%  Similarity=0.395  Sum_probs=72.4

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+++++++|+++|++||.|..+.+++|+.++.++|||||+|.+.++|.+|++ +|+   ..++|++|+|.+|
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-QSR---HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTT---CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCC---CEECCeEEEEEEC
Confidence            369999999999999999999999999999999999899999999999999999999998 698   9999999999886

>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=8e-21  Score=122.37  Aligned_cols=79  Identities=24%  Similarity=0.405  Sum_probs=75.6

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+++++++|.++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|+++
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~---~~~~g~~i~V~~a   85 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG---REFSGRALRVDNA   85 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSS---BSCSSSCBEEEET
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCC---CEECCEEEEEEEC
Confidence            5799999999999999999999999999999999988899999999999999999999999999   9999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus        86 ~~   87 (104)
T d1p1ta_          86 AS   87 (104)
T ss_dssp             TC
T ss_pred             CC
Confidence            64

>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=99.82  E-value=2.9e-20  Score=115.15  Aligned_cols=77  Identities=26%  Similarity=0.423  Sum_probs=73.2

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|+.||.|..+.+++|+.++.++|||||+|.+.++|.+|++ +++   ..++|+.|+|..|
T Consensus         7 ~~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           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARP---HKVDGRVVEPKRA   82 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCS---CEETTEECEEEEC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCC---CEECCEEEEEEee
Confidence            589999999999999999999999999999999999899999999999999999999998 588   8899999999987


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.1e-20  Score=115.94  Aligned_cols=80  Identities=21%  Similarity=0.338  Sum_probs=73.6

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      ...++|||+|||+++++++|+++|++||.|..+.+.+++..  .+|||||+|.+.++|..|++.+||   ..++|++|+|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~---~~~~g~~i~v   80 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNG---RKILGKEVKV   80 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTT---EEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCC---CEECCEEEEE
Confidence            34579999999999999999999999999999999888643  488999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +||.+
T Consensus        81 ~~a~~   85 (90)
T d2cqia1          81 NWATT   85 (90)
T ss_dssp             EECCC
T ss_pred             EEcCC
Confidence            99865

>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=99.82  E-value=4.7e-20  Score=115.59  Aligned_cols=79  Identities=22%  Similarity=0.312  Sum_probs=73.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|+.||.|..+.+++|+.++.++|||||+|.+.++|.+|++  ++   ..++|+.|.|.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~--~~---~~l~Gr~i~v~   81 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QR---HMIDGRWCDCK   81 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SC---EEETTEEEEEE
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cC---CccCCEEeEEE
Confidence            35689999999999999999999999999999999999899999999999999999999998  34   57899999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        82 ~a~~   85 (90)
T d2cqga1          82 LPNS   85 (90)
T ss_dssp             CCCT
T ss_pred             eCCC
Confidence            9875

>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=1.8e-20  Score=113.64  Aligned_cols=75  Identities=25%  Similarity=0.392  Sum_probs=70.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|.++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++ +++   ..++|+.|+|..|
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-QKE---HKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCC---CCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCC---CEECCCEEEeeEC
Confidence            58999999999999999999999999999999999899999999999999999999998 788   8899999998654

>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=99.82  E-value=1.9e-20  Score=126.63  Aligned_cols=80  Identities=20%  Similarity=0.350  Sum_probs=76.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.+
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng---~~~~gr~l~V~~  118 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG---FNILNKRLKVAL  118 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTT---EECSSCEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            35899999999999999999999999999999999988899999999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus       119 a~~  121 (139)
T d1u6fa1         119 AAS  121 (139)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            854

>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=99.82  E-value=2.3e-20  Score=116.89  Aligned_cols=79  Identities=30%  Similarity=0.454  Sum_probs=73.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +..+|||+|||+++++++|+++|+.||.|..+.+..+.  +.++|||||+|.+.++|.+|++.|||   ..++|++|+|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g---~~~~g~~i~V~   81 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG---MLLNDRKVFVG   81 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSE---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            44589999999999999999999999999999998885  44789999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        82 ~a~~   85 (89)
T d1cvja2          82 RFKS   85 (89)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9875

>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=99.82  E-value=8.9e-20  Score=115.05  Aligned_cols=78  Identities=23%  Similarity=0.385  Sum_probs=73.2

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+.+++++|+++|++||.|..+.+..++  +.++|||||+|.+.++|.+|++.|||   ..++|++|+|.+
T Consensus        11 ~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~---~~~~g~~l~V~~   85 (93)
T d2cq3a1          11 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHG---TVVEGRKIEVNN   85 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCC---CEECCEEEEEEe
Confidence            4689999999999999999999999999999998885  44789999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      |.+
T Consensus        86 A~~   88 (93)
T d2cq3a1          86 ATA   88 (93)
T ss_dssp             CCS
T ss_pred             cCc
Confidence            975

>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=3.1e-20  Score=118.87  Aligned_cols=77  Identities=17%  Similarity=0.243  Sum_probs=73.7

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++ |||   ..++|++|+|.++
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g---~~~~G~~l~V~~a   94 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTG---QRLLGVPIIVQAS   94 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTT---EEETTEEEEEEEH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCC---CEECCEEEEEEEC
Confidence            589999999999999999999999999999999998889999999999999999999995 999   9999999999987


Q ss_pred             c
Q psy7847         168 L  168 (170)
Q Consensus       168 ~  168 (170)
                      .
T Consensus        95 ~   95 (101)
T d2cq4a1          95 Q   95 (101)
T ss_dssp             H
T ss_pred             C
Confidence            5

>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=99.81  E-value=2.8e-20  Score=112.80  Aligned_cols=75  Identities=23%  Similarity=0.369  Sum_probs=71.5

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|+.||.+..+.+..++.++.++|+|||+|.+.++|.+|++ +||   ..++|++|+|.+|
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-IHF---HEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSS---CCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCC---CEECCeEEEEEEC
Confidence            58999999999999999999999999999999888889999999999999999999997 999   9999999999876

>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=99.81  E-value=9.5e-20  Score=111.50  Aligned_cols=76  Identities=20%  Similarity=0.351  Sum_probs=72.4

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+++|+++|+++|++||.+..+.+..++.++.++|+|||+|.+.+++.+|++ +||   ..++|++|+|..|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~---~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKY---HTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSC---CEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCC---CEECCEEEEEEEC
Confidence            589999999999999999999999999999999999899999999999999999999996 899   9999999999987

>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=99.81  E-value=5.9e-20  Score=117.89  Aligned_cols=78  Identities=22%  Similarity=0.378  Sum_probs=74.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+++++++|+++|++||.|..+.+++|+.++.++|||||+|.+.++|.+|++ +++   ..++|++|.|.+|
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~---~~l~G~~i~V~~a   96 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARP---HSIDGRVVEPKRA   96 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCS---EEETTEEEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCC---CeECCEEEEEEEC
Confidence            589999999999999999999999999999999998888999999999999999999996 788   8999999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus        97 ~~   98 (103)
T d1x4ba1          97 VA   98 (103)
T ss_dssp             SS
T ss_pred             cc
Confidence            65

>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=99.81  E-value=5.6e-20  Score=118.10  Aligned_cols=78  Identities=28%  Similarity=0.474  Sum_probs=72.9

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|+.||.|..+.+++++.++.++|||||+|.+.++|.+|++.+|+    .++|++|+|.++
T Consensus        11 ~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~----~l~Gr~l~V~~a   86 (103)
T d2cqda1          11 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP----IIDGRKANVNLA   86 (103)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC----EETTEECEEEES
T ss_pred             cEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC----cCCCEEEEEEEc
Confidence            5799999999999999999999999999999999998899999999999999999999998765    479999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      ..
T Consensus        87 ~~   88 (103)
T d2cqda1          87 YL   88 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>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=1.2e-20  Score=114.38  Aligned_cols=75  Identities=24%  Similarity=0.426  Sum_probs=70.2

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++. ++   ..++|+.|+|.+|
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-KY---HNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SS---CCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CC---CEECCEEeEEEEC
Confidence            589999999999999999999999999999999998999999999999999999999974 66   7899999999875

>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=99.80  E-value=4.3e-20  Score=114.87  Aligned_cols=80  Identities=20%  Similarity=0.311  Sum_probs=69.4

Q ss_pred             CceEEecCCCCCCC-HHHHHHHhccCCCeeEEEEeec-CCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          87 DFRLFCGDLGNDVT-DELLIRTFSKYPSFLKAKVVRD-KRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        87 ~~~l~v~nlp~~~~-~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      .++|||+|||++++ +++|+++|++||.|..+.+..+ +.++.++|||||+|.+.++|.+|++ |||   ..++|++|+|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~---~~~~gr~l~V   79 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNR---SLLGNREISV   79 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTT---EEETTEEEEE
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCC---CEECCEEEEE
Confidence            46899999999986 5569999999999999998664 4578899999999999999999996 999   9999999999


Q ss_pred             EeeccC
Q psy7847         165 SITLKG  170 (170)
Q Consensus       165 ~~~~~~  170 (170)
                      +++.+.
T Consensus        80 ~~a~~k   85 (86)
T d2ghpa3          80 SLADKK   85 (86)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999763

>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=99.80  E-value=2.1e-19  Score=114.32  Aligned_cols=84  Identities=15%  Similarity=0.223  Sum_probs=76.4

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCC---ccccCCeeE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFP---HLFVGDLKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~---~~~~~~~~i  162 (170)
                      ..++|||+|||+++++++|+++|++||.+..+.+..++..+.++|||||+|.+.++|.+|++.+|+..   +..++|++|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            45789999999999999999999999999999999998889999999999999999999999998421   378999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|+++.+
T Consensus        87 ~v~~a~~   93 (98)
T d1x4ha1          87 KVDLAVT   93 (98)
T ss_dssp             EEECCCC
T ss_pred             EEEECCC
Confidence            9999865

>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=99.79  E-value=1.6e-19  Score=114.50  Aligned_cols=76  Identities=21%  Similarity=0.440  Sum_probs=71.1

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      +...+|||+|||..+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|||   ..++|++|+|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~---~~i~g~~l~v   86 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG---TTIEGHVVKC   86 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTT---CEETTEECEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCC---CEECCEEEEE
Confidence            34578999999999999999999999999999999875      78999999999999999999999   9999999999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      +|+.+
T Consensus        87 ~~ak~   91 (96)
T d1x4ga1          87 YWGKE   91 (96)
T ss_dssp             ECCCC
T ss_pred             EEcCC
Confidence            99865

>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=99.79  E-value=3.1e-19  Score=110.21  Aligned_cols=77  Identities=17%  Similarity=0.339  Sum_probs=69.4

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc-CCeeEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV-GDLKTR  163 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~-~~~~i~  163 (170)
                      +.+.+|||+|||.++++++|.++|+.||.|..+.+.+++     +|+|||+|.+.++|..|++.|||   ..+ +|++|+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g---~~~~~~~~i~   77 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQG---FKITPTHAMK   77 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTT---CBSSTTCBCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCC---cEeCCCcEEE
Confidence            456799999999999999999999999999999987653     78999999999999999999999   666 578999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |+||.+
T Consensus        78 v~~akk   83 (83)
T d2b0ga1          78 ITFAKK   83 (83)
T ss_dssp             EEECCC
T ss_pred             EEEecC
Confidence            999864

>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=99.79  E-value=9.7e-20  Score=109.54  Aligned_cols=71  Identities=30%  Similarity=0.459  Sum_probs=68.1

Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEE
Q psy7847          90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTR  163 (170)
Q Consensus        90 l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~  163 (170)
                      |||+|||+++++++|+++|++||.|..+.+.+++.++.++|+|||+|.+.++|.+|++.|||   ..++|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng---~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA---SGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH---HTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCC---CEECCEECc
Confidence            79999999999999999999999999999999988999999999999999999999999999   999998875

>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=99.79  E-value=2.2e-19  Score=110.89  Aligned_cols=71  Identities=25%  Similarity=0.371  Sum_probs=65.9

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+|.++++|||+|||+++|+++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|..|+..+++
T Consensus         3 r~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g   73 (83)
T d2cqca1           3 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG   73 (83)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCC
Confidence            34455678999999999999999999999999999999999988899999999999999999999999886

>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=99.79  E-value=3e-19  Score=116.67  Aligned_cols=76  Identities=20%  Similarity=0.218  Sum_probs=70.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +++|||+|||..+++++|+++|++||.|..|.+..+   +.++|||||+|.+.++|..|++.|||   ..++|+.|+|.+
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g---~~~~gr~l~V~~   80 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSG---FNVCNRYLVVLY   80 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTT---CEETTEECEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            468999999999999999999999999999988654   55689999999999999999999999   999999999999


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        81 a~   82 (114)
T d2f9da1          81 YN   82 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=1.6e-19  Score=112.97  Aligned_cols=76  Identities=17%  Similarity=0.247  Sum_probs=69.0

Q ss_pred             CceEEecCCCCCCCHHHH---HHHhccCCCeeEEEEeecCCCCC---cccEEEEEecCHHHHHHHHHHhcCCCccccCCe
Q psy7847          87 DFRLFCGDLGNDVTDELL---IRTFSKYPSFLKAKVVRDKRTNK---TKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDL  160 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l---~~~f~~~g~i~~~~~~~~~~~~~---~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~  160 (170)
                      ..+|||+|||+.+++++|   .++|++||.|..+.+.+++..+.   +.|||||+|.+.++|.+|++.|||   ..++|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng---~~~~gr   84 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN---VVVDGR   84 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTT---EEETTE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCC---CEECCE
Confidence            457999999999999999   67899999999999998875443   458999999999999999999999   999999


Q ss_pred             eEEEE
Q psy7847         161 KTRSS  165 (170)
Q Consensus       161 ~i~v~  165 (170)
                      +|+||
T Consensus        85 ~lkvS   89 (89)
T d2cpia1          85 TLKAS   89 (89)
T ss_dssp             EEEEE
T ss_pred             EEEEC
Confidence            99986

>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=99.79  E-value=2.5e-19  Score=111.32  Aligned_cols=75  Identities=27%  Similarity=0.416  Sum_probs=70.1

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +..+|||+|||+++++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|++.|||   ..++|++|+|+
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g---~~i~g~~l~V~   77 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDN---MPLRGKQLRVR   77 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTT---CCBTTBCCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            4468999999999999999999999999999998765      68999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ||..
T Consensus        78 ~A~~   81 (86)
T d2cpja1          78 FACH   81 (86)
T ss_dssp             ESSC
T ss_pred             ECCC
Confidence            9875

>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=99.79  E-value=3.3e-19  Score=114.03  Aligned_cols=81  Identities=25%  Similarity=0.242  Sum_probs=73.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCee--------EEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV  157 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~  157 (170)
                      ...+|||+|||+.+++++|+++|+.||.|.        .+.+..++.++.++|||||+|.+.++|.+|++.|||   ..+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g---~~~   83 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDG---KDF   83 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTT---CEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCC---CEE
Confidence            356999999999999999999999999873        466677777889999999999999999999999999   999


Q ss_pred             CCeeEEEEeecc
Q psy7847         158 GDLKTRSSITLK  169 (170)
Q Consensus       158 ~~~~i~v~~~~~  169 (170)
                      +|++|+|+++.+
T Consensus        84 ~gr~i~V~~a~~   95 (101)
T d2cpea1          84 QGSKLKVSLARK   95 (101)
T ss_dssp             TTEECEEECSSC
T ss_pred             CCEEEEEEEcCC
Confidence            999999999864

>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=99.79  E-value=4.9e-19  Score=112.01  Aligned_cols=78  Identities=22%  Similarity=0.342  Sum_probs=71.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|+++|++||.|..+.+..+   ..++|||||+|.+.++|..|++.|||   ..++|++|+|+
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g---~~~~g~~l~V~   86 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDG---YDYDGYRLRVE   86 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTT---CEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            4568999999999999999999999999999887554   45689999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ||..
T Consensus        87 ~a~~   90 (95)
T d1x4aa1          87 FPRS   90 (95)
T ss_dssp             CCCC
T ss_pred             eccC
Confidence            9875

>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=99.79  E-value=1.6e-19  Score=112.30  Aligned_cols=79  Identities=13%  Similarity=0.176  Sum_probs=70.2

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|+|+|||+++++++|+++|+.||.+....++.+..++.++|+|||+|.+.++|.+|++.||+   ..++|++|+|+
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~---~~l~gr~i~v~   84 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND---RPIGSRKVKLV   84 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTT---CEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCC---CEECCEEEEEE
Confidence            456799999999999999999999999987643333445889999999999999999999999999   99999999998


Q ss_pred             ee
Q psy7847         166 IT  167 (170)
Q Consensus       166 ~~  167 (170)
                      ++
T Consensus        85 l~   86 (86)
T d2cqpa1          85 LG   86 (86)
T ss_dssp             ES
T ss_pred             EC
Confidence            75

>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=99.78  E-value=2e-19  Score=115.14  Aligned_cols=79  Identities=15%  Similarity=0.288  Sum_probs=73.0

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|.+|++.|||   ..++|+++.|.+
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng---~~i~gr~~~v~~   93 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNG---KFIKTPPGVSAP   93 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBT---CCCCCCTTSCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCC---CEECCcCCccCC
Confidence            4689999999999999999999999999999988875 788999999999999999999999999   999999998877


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            653

>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=99.78  E-value=5.9e-19  Score=111.20  Aligned_cols=72  Identities=26%  Similarity=0.421  Sum_probs=66.4

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+..+.++|||+|||.++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.+++.
T Consensus         3 ~~~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~   74 (93)
T d1x5ua1           3 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMI   74 (93)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSC
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCC
Confidence            344556689999999999999999999999999999999999989999999999999999999999999863

>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=99.77  E-value=1e-18  Score=108.33  Aligned_cols=77  Identities=12%  Similarity=0.027  Sum_probs=71.6

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|+.||.|..+.+.+++ ++.++|+|||+|.+.++|.+|++ +++   ..++|+.|+|.|
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~---~~~~g~~l~v~~   80 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPG---QKYKETDLLILF   80 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCC---CEETTEECEEEE
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCC---CEECCEEEEEEE
Confidence            4689999999999999999999999999999998876 78899999999999999999996 688   999999999998


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        81 ~~   82 (85)
T d1zh5a2          81 KD   82 (85)
T ss_dssp             GG
T ss_pred             cC
Confidence            64

>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=99.77  E-value=5.6e-20  Score=117.89  Aligned_cols=80  Identities=15%  Similarity=0.154  Sum_probs=75.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||.++++++|+++|++||.+..+.+..+..++.++|||||+|.+.++|.+|++.|||   ..++|++|+|+|
T Consensus        18 s~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g---~~~~g~~l~V~~   94 (102)
T d2cpxa1          18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG---YKLYGKILVIEF   94 (102)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTT---CBCSSCBCEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCC---CEECCEEEEEEe
Confidence            57999999999999999999999999999888887777889999999999999999999999999   899999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      |.+
T Consensus        95 ak~   97 (102)
T d2cpxa1          95 GKN   97 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            975

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.2e-19  Score=112.55  Aligned_cols=81  Identities=17%  Similarity=0.237  Sum_probs=71.8

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCC-eeEEEEeecCC-CCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~-i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ++|||+|||..+++++|+++|+.||. +..+.++++.. .+.++|||||+|.+.++|..|++.|++. ...++|++|+|+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~-~~~~~g~~i~V~   80 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG-RIQLWGHQIAVD   80 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTC-CSCBTTBCCEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCC-CeEECCEEEEEE
Confidence            57999999999999999999999995 88999888753 6789999999999999999999999752 256689999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ||.+
T Consensus        81 ~A~p   84 (96)
T d2disa1          81 WAEP   84 (96)
T ss_dssp             ESCS
T ss_pred             EcCC
Confidence            9975

>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=99.77  E-value=6.3e-19  Score=114.19  Aligned_cols=75  Identities=20%  Similarity=0.221  Sum_probs=69.4

Q ss_pred             CCceEEecCCCC-CCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEE
Q psy7847          86 DDFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRS  164 (170)
Q Consensus        86 ~~~~l~v~nlp~-~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v  164 (170)
                      |+.+|||+|||+ .+++++|+++|+.||.|..+.+++++     +|+|||+|.+.++|.+|++.|||   ..++|+.|+|
T Consensus         1 g~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng---~~l~g~~l~v   72 (109)
T d2adca1           1 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNG---HKLHGKPIRI   72 (109)
T ss_dssp             CCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTT---CBCSSSBCEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCC---CEECCEEEEE
Confidence            457899999966 59999999999999999999998874     78999999999999999999999   9999999999


Q ss_pred             Eeec
Q psy7847         165 SITL  168 (170)
Q Consensus       165 ~~~~  168 (170)
                      +|+.
T Consensus        73 ~~s~   76 (109)
T d2adca1          73 TLSK   76 (109)
T ss_dssp             ECCS
T ss_pred             EECC
Confidence            9974

>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=99.77  E-value=1.5e-18  Score=107.57  Aligned_cols=68  Identities=28%  Similarity=0.496  Sum_probs=63.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...++|||+|||+++++++|+++|+.||+|.++++++++.+|.++|||||+|.+.++|.+|++.+|+.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   71 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV   71 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCC
Confidence            35667999999999999999999999999999999999989999999999999999999999998863

>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=99.76  E-value=9.8e-19  Score=108.14  Aligned_cols=66  Identities=32%  Similarity=0.537  Sum_probs=62.1

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      +|.+.++|||+|||+++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|.+|++.
T Consensus         2 epe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~   67 (84)
T d1l3ka1           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA   67 (84)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh
Confidence            455678999999999999999999999999999999999999999999999999999999999974

>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=99.76  E-value=1e-18  Score=109.34  Aligned_cols=66  Identities=26%  Similarity=0.380  Sum_probs=61.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      ....++|||+|||+++|+++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|++..
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~   70 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR   70 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC
Confidence            345678999999999999999999999999999999999989999999999999999999999753

>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=99.76  E-value=2.9e-18  Score=106.45  Aligned_cols=75  Identities=16%  Similarity=0.276  Sum_probs=68.6

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..++|||+|||+++++++|.++|++||.+..+.+.+      ++|||||+|.+.++|.+|+..|||   ..++|++|+|+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~---~~i~g~~i~V~   77 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNG---KVLDGSPIEVT   77 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSS---EEETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            346899999999999999999999999988877643      478999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        78 ~akP   81 (86)
T d2cpda1          78 LAKP   81 (86)
T ss_dssp             CCCC
T ss_pred             eccC
Confidence            9865

>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=99.76  E-value=8.6e-19  Score=108.62  Aligned_cols=65  Identities=23%  Similarity=0.389  Sum_probs=62.5

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +++|||+|||+++|+++|+++|+.||+|.++++++++.+|.++|||||+|.++++|..|+..+++
T Consensus         1 a~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~   65 (85)
T d2u2fa_           1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG   65 (85)
T ss_dssp             CCCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCC
Confidence            36899999999999999999999999999999999998999999999999999999999999886

>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=99.76  E-value=2.9e-18  Score=106.91  Aligned_cols=78  Identities=14%  Similarity=0.159  Sum_probs=68.8

Q ss_pred             CCCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc-CCeeEE
Q psy7847          85 NDDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV-GDLKTR  163 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~-~~~~i~  163 (170)
                      +...+|||+|||+++++++|+++|+.||.+..+.+..+    ..+|+|||+|.+.++|.+|+..|||   ..+ .|++|+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~---~~i~~g~~l~   80 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHN---HDLGENHHLR   80 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTT---CBSSSSCBCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccC---CEecCCCEEE
Confidence            45679999999999999999999999999988766543    3478999999999999999999999   666 589999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |+|+..
T Consensus        81 v~~sk~   86 (88)
T d2adca2          81 VSFSKS   86 (88)
T ss_dssp             EEECSS
T ss_pred             EEeCCC
Confidence            999865

>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=99.76  E-value=4.6e-19  Score=108.66  Aligned_cols=72  Identities=22%  Similarity=0.314  Sum_probs=65.8

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcc-ccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHL-FVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~-~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|++||.+..+.+...      +|||||+|.+.++|.+|++.|||   . .++|++|+|.|+
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng---~~~~~G~~i~V~~a   73 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSG---KVELHGKIMEVDYS   73 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTT---TCEETTEECEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCC---CeEECCEEEEEEEc
Confidence            6999999999999999999999999877666553      78999999999999999999998   6 499999999998


Q ss_pred             cc
Q psy7847         168 LK  169 (170)
Q Consensus       168 ~~  169 (170)
                      .+
T Consensus        74 ~~   75 (80)
T d2cqha1          74 VS   75 (80)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=5.7e-19  Score=112.86  Aligned_cols=66  Identities=20%  Similarity=0.353  Sum_probs=61.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.++|||+|||+++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|+. +++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g   81 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTG   81 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTT
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCC
Confidence            345789999999999999999999999999999999998899999999999999999999995 776

>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=99.76  E-value=1.7e-18  Score=107.24  Aligned_cols=67  Identities=25%  Similarity=0.467  Sum_probs=63.2

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.+|||+|||+++|+++|+++|++||+|.++++++++.+|.++|||||+|.+.++|.+|++.+|+.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~   71 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ   71 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCC
Confidence            3567999999999999999999999999999999999888999999999999999999999999863

>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=99.76  E-value=1.4e-18  Score=112.83  Aligned_cols=74  Identities=12%  Similarity=0.082  Sum_probs=68.3

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +++|||+|||+.+++++|+++|++||.|..+.+..      .+|||||+|.+.++|.+|++.|||   ..+.|++|+|.|
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng---~~~~gr~l~v~~   80 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAY---SKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTT---CBSSSSBCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcC---CccCCCeEEEEE
Confidence            46899999999999999999999999999998743      478999999999999999999999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus        81 a~~   83 (111)
T d1whxa_          81 API   83 (111)
T ss_dssp             EET
T ss_pred             CCC
Confidence            854

>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=99.76  E-value=9.5e-20  Score=114.43  Aligned_cols=78  Identities=23%  Similarity=0.286  Sum_probs=71.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+|++ |||   ..++|++|+|.+
T Consensus        13 ~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~-~~g---~~~~g~~i~V~~   87 (91)
T d1fjeb1          13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE-LTG---LKVFGNEIKLEK   87 (91)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHH-GGG---EEETTEEEEEEC
T ss_pred             CcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHh-cCC---cEECCEEEEEEe
Confidence            4689999999999999999999999999888776553 78899999999999999999996 999   999999999999


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      |.+
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.76  E-value=1.5e-18  Score=106.75  Aligned_cols=66  Identities=29%  Similarity=0.390  Sum_probs=62.9

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++|||+|||+++++++|+++|++||.|.++++.+++.+|.++|||||+|.+.++|.+|++.+++.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~   67 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI   67 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCC
Confidence            467999999999999999999999999999999999889999999999999999999999999973

>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=99.75  E-value=2.3e-18  Score=104.18  Aligned_cols=73  Identities=14%  Similarity=0.170  Sum_probs=67.1

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      +|||+|||+++++++|+++|+.+|.|..+.+..++.  ..+|+|||+|.++++|.+|+. +|+   ..++|++|.|+.+
T Consensus         2 tv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~---~~i~g~~i~V~~~   74 (75)
T d2ghpa2           2 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTH---KVVGQNEIIVSHL   74 (75)
T ss_dssp             EEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTT---CEETTEECEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcC---cEECCEEEEEEEC
Confidence            799999999999999999999999999999998863  346799999999999999985 899   9999999999865

>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=99.75  E-value=3.1e-18  Score=106.74  Aligned_cols=68  Identities=18%  Similarity=0.409  Sum_probs=63.7

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.++|||+|||.++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|+..+|+.
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~   72 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA   72 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCC
Confidence            35689999999999999999999999999999999999889999999999999999999999999863

>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=99.75  E-value=3.2e-18  Score=104.57  Aligned_cols=73  Identities=19%  Similarity=0.255  Sum_probs=67.2

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|++  +++++|+++|++||.|..+.+.++      +|+|||+|.+.++|.+|++.|||   ..++|++|+|+|
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng---~~~~g~~l~V~~   73 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNG---TQVESVQLKVNI   73 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTT---CBCSSCBCEEEE
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCC---CEECCEEEEEEE
Confidence            4689999986  899999999999999999988654      68999999999999999999999   999999999999


Q ss_pred             eccC
Q psy7847         167 TLKG  170 (170)
Q Consensus       167 ~~~~  170 (170)
                      +.+.
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9763

>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=99.75  E-value=2.9e-18  Score=107.33  Aligned_cols=68  Identities=25%  Similarity=0.434  Sum_probs=64.0

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+..+|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|++.+++
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g   72 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG   72 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCC
Confidence            34567899999999999999999999999999999999988899999999999999999999999986

>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=99.75  E-value=2.5e-18  Score=105.28  Aligned_cols=64  Identities=39%  Similarity=0.619  Sum_probs=61.5

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .|||+|||+++|+++|+++|+.||+|.++++++++.+|.++|||||+|.++++|..|++.+++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~   65 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD   65 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCC
Confidence            5999999999999999999999999999999999989999999999999999999999998863

>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=99.75  E-value=3.9e-18  Score=107.37  Aligned_cols=68  Identities=26%  Similarity=0.331  Sum_probs=64.3

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+++|||+|||+++|+++|+++|+.||+|.++.+++++.+|.++|||||+|.+.++|..|++.+++.
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~   72 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGT   72 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCC
Confidence            35789999999999999999999999999999999999989999999999999999999999999863

>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=99.74  E-value=5.2e-18  Score=114.40  Aligned_cols=69  Identities=25%  Similarity=0.406  Sum_probs=64.5

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++...++|||+|||+++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|..|++.+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng  106 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG  106 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCC
Confidence            344567899999999999999999999999999999999998999999999999999999999999986

>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=99.74  E-value=1.7e-18  Score=108.19  Aligned_cols=66  Identities=29%  Similarity=0.490  Sum_probs=63.1

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++|||+|||+++++++|+++|+.||+|.++.+++++.+|.++|||||+|.+.++|..|+..+++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~   69 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE   69 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCC
Confidence            457899999999999999999999999999999999998899999999999999999999999886

>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=99.74  E-value=5e-18  Score=108.84  Aligned_cols=66  Identities=32%  Similarity=0.502  Sum_probs=62.1

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++|||+|||+++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|.+|++.+++
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~   74 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP   74 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC
Confidence            346799999999999999999999999999999999998999999999999999999999988764

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=9.9e-18  Score=101.31  Aligned_cols=70  Identities=19%  Similarity=0.226  Sum_probs=62.6

Q ss_pred             EEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847          90 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus        90 l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|+|||+|.+.++|.+|++.|||   ..+.|++|+|+|+..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~---~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQ---SRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTT---EESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCC---ccCCCCEEEEEEeCC
Confidence            79999999999999999999998 444443      33589999999999999999999999   999999999999854

>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=99.74  E-value=5.9e-18  Score=108.67  Aligned_cols=79  Identities=15%  Similarity=0.079  Sum_probs=71.8

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+++++++|+++|..+|.+....++.++.++.++|+|||+|.++++|++|++ +|+   ..++++.|+|..
T Consensus        15 ~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~---~~i~gR~i~V~~   90 (104)
T d1wg5a_          15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHK---ERIGHRYIEIFK   90 (104)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTT---CCSSSSCCEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCC---CEEcceEEEEEE
Confidence            4589999999999999999999999998887666666688999999999999999999996 899   999999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        91 ~~~   93 (104)
T d1wg5a_          91 SSR   93 (104)
T ss_dssp             ECT
T ss_pred             CCH
Confidence            865

>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=99.74  E-value=2.3e-18  Score=109.05  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=69.0

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+++++++|+++|++||.+..+..     ++.++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~---~~~~gr~i~V~   86 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQG---AEIDGRSVSLY   86 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTE---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            3579999999999999999999999998766532     567899999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        87 ~a~~   90 (96)
T d1fjca_          87 YTGE   90 (96)
T ss_dssp             ECSS
T ss_pred             EeCC
Confidence            9876

>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=99.74  E-value=7.1e-18  Score=107.36  Aligned_cols=67  Identities=31%  Similarity=0.462  Sum_probs=63.6

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+.+|||+|||+++++++|+++|+.||.|.++++++++.++.++|||||+|.+.++|.+|++.+|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g   72 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG   72 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCC
Confidence            4467899999999999999999999999999999999988999999999999999999999999986

>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=99.74  E-value=7e-18  Score=103.71  Aligned_cols=65  Identities=31%  Similarity=0.454  Sum_probs=61.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+|||+|||+++++++|+++|+.||.|.+++++++..+|.++|||||+|.+.++|..|+..+++.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~   67 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL   67 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCC
Confidence            56999999999999999999999999999999999888999999999999999999999999863

>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=99.74  E-value=6.7e-18  Score=108.39  Aligned_cols=86  Identities=24%  Similarity=0.403  Sum_probs=71.0

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----ceEEecCCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----FRLFCGDLGN   97 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~~l~v~nlp~   97 (170)
                      .++|||+|||+++++++|+++|+.||.|.++++++++.+|.++|||||+|.+.++|..|++.+++.    +.|.|.--..
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            468999999999999999999999999999999999989999999999999999999999998863    3555543333


Q ss_pred             CCCHHHHHHH
Q psy7847          98 DVTDELLIRT  107 (170)
Q Consensus        98 ~~~~~~l~~~  107 (170)
                      .-..++.+..
T Consensus        88 ~~~~~~~~~~   97 (104)
T d1p1ta_          88 EKNKEELKSL   97 (104)
T ss_dssp             TTHHHHHHHH
T ss_pred             CCCccccccC
Confidence            3334444443

>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=99.74  E-value=1.3e-18  Score=105.27  Aligned_cols=61  Identities=25%  Similarity=0.505  Sum_probs=58.2

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHc
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM   84 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~   84 (170)
                      +|||+|||+++|+++|+++|+.||+|.++++++++.++.++|||||+|.+.++|.+|++..
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~   61 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK   61 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCS
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhC
Confidence            5899999999999999999999999999999999989999999999999999999999653

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=6.2e-18  Score=109.30  Aligned_cols=76  Identities=18%  Similarity=0.217  Sum_probs=68.4

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCcccc--CCeeEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFV--GDLKTRS  164 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~--~~~~i~v  164 (170)
                      ..+|||+|||+.+|+++|+++|++||.|..+.+.+++    ++|+|||+|.+.++|++|+..|||   ..+  ++++|+|
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~---~~l~~~~~~l~v   79 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDG---QNIYNACCTLRI   79 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHS---CCSSTTCCCCEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCC---CEeccCCcEEEE
Confidence            3579999999999999999999999999999988764    479999999999999999999999   655  6789999


Q ss_pred             Eeecc
Q psy7847         165 SITLK  169 (170)
Q Consensus       165 ~~~~~  169 (170)
                      .|+..
T Consensus        80 ~~s~~   84 (108)
T d2adba1          80 DFSKL   84 (108)
T ss_dssp             EECSS
T ss_pred             EecCC
Confidence            98854

>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=99.73  E-value=1e-17  Score=107.19  Aligned_cols=66  Identities=35%  Similarity=0.505  Sum_probs=63.1

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++.+|||+|||+++++++|+++|+.||.+.++.++.++.+|.++|||||+|.+.++|..|++.+|+
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng   82 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNG   82 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCC
Confidence            457899999999999999999999999999999999998999999999999999999999999986

>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=99.73  E-value=6.2e-18  Score=102.24  Aligned_cols=60  Identities=30%  Similarity=0.529  Sum_probs=57.8

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      +|||+|||+++++++|+++|++||+|.++.+++++.+|.++|||||+|.++++|++|++.
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~   60 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ   60 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHT
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhc
Confidence            589999999999999999999999999999999998999999999999999999999974

>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=99.73  E-value=9.1e-18  Score=104.58  Aligned_cols=74  Identities=11%  Similarity=0.094  Sum_probs=64.5

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +..+|||+|||+++++++|+++|++||. ..+.+      +..+|||||+|.+.++|++|++.||+   ..++|++|+|+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~---~~~~G~~l~V~   73 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQ---YSFRGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTT---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCC---CEECCEEEEEE
Confidence            4568999999999999999999999993 33333      23488999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++..
T Consensus        74 ~a~~   77 (88)
T d1wg1a_          74 LQPT   77 (88)
T ss_dssp             ECCC
T ss_pred             EcCC
Confidence            9853

>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=99.73  E-value=4.1e-18  Score=106.87  Aligned_cols=77  Identities=22%  Similarity=0.345  Sum_probs=69.0

Q ss_pred             CceEEecCCCCCCCHHHHHH----HhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          87 DFRLFCGDLGNDVTDELLIR----TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~----~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      +++|||+|||+++++++|++    +|++||.|..|.+.+   ++.++|||||+|.+.++|.+|++.+||   ..++|++|
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~---~~~~g~~l   76 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG---FPFYDKPM   76 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTT---CEETTEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCC---CEECCEEE
Confidence            57999999999999998864    689999999988754   355789999999999999999999999   99999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|.||.+
T Consensus        77 ~v~~ak~   83 (91)
T d1nu4a_          77 RIQYAKT   83 (91)
T ss_dssp             EEEECSS
T ss_pred             EEEEeCC
Confidence            9999865

>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=99.73  E-value=4.6e-18  Score=108.99  Aligned_cols=78  Identities=12%  Similarity=0.112  Sum_probs=70.0

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      +.+|||+|||+++++++|.++|..||.+..+.++.....+.++|+|||+|.+.++|.+|++ +|+   ..++|+.|.|.+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~---~~i~gr~i~V~~   83 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHR---KKLNGREAFVHV   83 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCS---EEETTEEEEEEE
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCC---CeECCcEEEEEE
Confidence            5689999999999999999999999998875444455588999999999999999999996 899   999999999988


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        84 ~~   85 (103)
T d2cpya1          84 VT   85 (103)
T ss_dssp             EC
T ss_pred             CC
Confidence            75

>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=99.72  E-value=1.5e-17  Score=105.38  Aligned_cols=75  Identities=20%  Similarity=0.369  Sum_probs=67.8

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC--eeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD--LKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~--~~i~  163 (170)
                      ..++|||+|||+++++++|+++|++||.|..+.+.++      +++|||+|.+.++|.+|++.||+   ..+++  ++|+
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~---~~i~g~~~~l~   86 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRG---FPLGGPDRRLR   86 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTT---CBCSSSSCBCE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCC---CEeCCCceEEE
Confidence            3579999999999999999999999999999988654      67999999999999999999999   76765  6899


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |+|+..
T Consensus        87 v~~ak~   92 (97)
T d1whya_          87 VDFAKS   92 (97)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            999875

>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=99.72  E-value=3.2e-18  Score=104.00  Aligned_cols=61  Identities=30%  Similarity=0.510  Sum_probs=58.4

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      .+|||+|||+++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~   61 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ   61 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHT
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHc
Confidence            4799999999999999999999999999999999999999999999999999999999974

>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=99.72  E-value=1.2e-17  Score=107.23  Aligned_cols=78  Identities=26%  Similarity=0.485  Sum_probs=68.7

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecC-CCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK-RTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      .++|||+|||+++++++|+++|+.|| +..+.++.++ ..+.++|||||+|.+.++|++|+ .||+   ..++|+.|+|.
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~---~~~~gr~l~V~   89 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNE---ESLGNKRIRVD   89 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGT---CEETTEECEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCC---CEECCEEEEEE
Confidence            47999999999999999999999998 6777766654 36788999999999999998766 5999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        90 ~a~~   93 (104)
T d1wi8a_          90 VADQ   93 (104)
T ss_dssp             ECCC
T ss_pred             ECCC
Confidence            9864

>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=99.72  E-value=7.1e-18  Score=107.10  Aligned_cols=72  Identities=22%  Similarity=0.334  Sum_probs=66.1

Q ss_pred             CceEEecCCC-CCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          87 DFRLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp-~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ..+|||+||| ..+++++|+++|++||.|..+.+        ++|||||+|.+.++|.+|++.|||   ..++|++|+|.
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng---~~~~g~~l~V~   83 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDG---RMIAGQVLDIN   83 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTT---CEETTEECEEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCC---CEECCEEEEEE
Confidence            4589999997 46888999999999999999988        368999999999999999999999   99999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+.+
T Consensus        84 ~a~~   87 (98)
T d1wf2a_          84 LAAE   87 (98)
T ss_dssp             ETTS
T ss_pred             ECCC
Confidence            9864

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.4e-18  Score=107.05  Aligned_cols=70  Identities=17%  Similarity=0.167  Sum_probs=64.9

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeec
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITL  168 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~  168 (170)
                      +|||+|||+.+++++|+++|++||.|..+.+.+       .|||||+|.+.++|.+|+..|||   ..++|+.|+|.++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~l~g---~~~~g~~i~v~~~~   71 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAVRKLDN---TKFRSHEGETAYIR   71 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-------TSEEEEEESSHHHHHHHHHHHTT---CBCCCTTSCCCBCE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhcccccccccc-------cceeeEEeCCHHHHHHHHHHhCC---CEECCcEeEEeEEe
Confidence            699999999999999999999999999998754       37999999999999999999999   99999999988764

>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=99.72  E-value=1.1e-17  Score=104.63  Aligned_cols=67  Identities=36%  Similarity=0.619  Sum_probs=63.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++++|||+|||+++++++|+++|+.||.|..+.++.+..+|.++|||||+|.++++|..|+..+++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~   69 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNG   69 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCC
Confidence            3567899999999999999999999999999999999888899999999999999999999999886

>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=99.72  E-value=8.7e-18  Score=107.50  Aligned_cols=77  Identities=12%  Similarity=0.097  Sum_probs=69.1

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+++|+++|+++|..+|. ..+.+..+. .+.++|||||+|.+.++|++|++ +|+   ..++||.|+|.+
T Consensus        15 ~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~---~~i~gR~I~V~~   88 (102)
T d1weza_          15 GHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDK---ANMQHRYVELFL   88 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSS---CCSSSSCCEEEE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCC---CEECCEEEEEEE
Confidence            469999999999999999999999974 567777765 68899999999999999999986 899   999999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +..
T Consensus        89 s~~   91 (102)
T d1weza_          89 NST   91 (102)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            864

>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=99.71  E-value=1.4e-17  Score=101.38  Aligned_cols=63  Identities=25%  Similarity=0.387  Sum_probs=60.1

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +|||+|||+++++++|+++|+.||.|.++++..++ +|.++|||||+|.+.++|..|++.+|+.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~   64 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV   64 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCC
Confidence            69999999999999999999999999999999986 8999999999999999999999999873

>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=99.71  E-value=2.7e-17  Score=103.62  Aligned_cols=68  Identities=18%  Similarity=0.365  Sum_probs=61.6

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCC-CCCcCCEEEEEeCCHHHHHHHHHHc-CC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEM-ND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~-~~~~~~~afv~f~~~~~a~~~~~~~-~~   86 (170)
                      ...+.+|||+|||+++++++|+++|+.||.|.++++++++. +|.++|||||.|.+.++|.+|+..+ ++
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~   74 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS   74 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCC
Confidence            34567899999999999999999999999999999988753 6899999999999999999999987 54

>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=99.71  E-value=2.9e-17  Score=104.18  Aligned_cols=69  Identities=17%  Similarity=0.240  Sum_probs=63.9

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..+.++|||+|||+++|+++|+++|+.||.+.++.++.++.++.++|||||+|.+.++|.+|++.+++
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~   72 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASL   72 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCT
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHccc
Confidence            344578999999999999999999999999999999999988899999999999999999999998874

>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=99.71  E-value=9.1e-18  Score=107.50  Aligned_cols=63  Identities=27%  Similarity=0.478  Sum_probs=59.6

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      +.++|||+|||+++++++|+++|++||.|.++.+.+++.++.++|||||+|.+.++|.+|+..
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~   81 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA   81 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHh
Confidence            357899999999999999999999999999999999998899999999999999999999953

>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=99.71  E-value=7.4e-18  Score=105.00  Aligned_cols=74  Identities=22%  Similarity=0.327  Sum_probs=66.3

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      +..+|||+|||+.+++++|+++|++||.|..+.+..     .++|||||+|.+.++|++|+.  ++   ..++|++|+|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~---~~i~g~~l~v~   73 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--ED---LIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CE---EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CC---CEECCEEeEEE
Confidence            467999999999999999999999999999987643     358999999999999999985  66   88999999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      ++.+
T Consensus        74 ~a~~   77 (88)
T d1wf0a_          74 NAEP   77 (88)
T ss_dssp             CCCC
T ss_pred             eCCC
Confidence            9864

>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=99.71  E-value=3.3e-17  Score=102.44  Aligned_cols=67  Identities=27%  Similarity=0.474  Sum_probs=60.6

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +..+.++|||+|||+++++++|+++|+.||+|.++++++++.+  .++||||+|.+.++|..|+..+++
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~   70 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNG   70 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCC
Confidence            4455789999999999999999999999999999999988644  378999999999999999999886

>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=99.70  E-value=1.4e-17  Score=99.89  Aligned_cols=62  Identities=32%  Similarity=0.550  Sum_probs=59.7

Q ss_pred             EEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        25 v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      |||+|||+++|+++|+++|+.||.+..+++.+++.++.++|+|||+|.+.++|.+|+..+|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng   62 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA   62 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCC
Confidence            79999999999999999999999999999999988999999999999999999999998875

>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=99.70  E-value=6.7e-17  Score=100.57  Aligned_cols=75  Identities=11%  Similarity=0.049  Sum_probs=67.7

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHh--cCCCccccCCeeEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM--NEFPHLFVGDLKTR  163 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~~~~i~  163 (170)
                      ..++|||+|||+++++++|.++|++||.|..+.+.++      +|+|||+|.+.++|..|++.+  ++   ..++|++|+
T Consensus         7 Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~---~~~~g~~l~   77 (88)
T d2cq1a1           7 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVT---PHLRNQPIY   77 (88)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSC---CEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCC---CccCCCEEE
Confidence            4679999999999999999999999999999988754      579999999999999999976  45   788999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |+|+..
T Consensus        78 v~~sk~   83 (88)
T d2cq1a1          78 IQYSNH   83 (88)
T ss_dssp             EEECSC
T ss_pred             EEECCC
Confidence            999853

>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=99.70  E-value=2e-17  Score=101.43  Aligned_cols=66  Identities=11%  Similarity=0.155  Sum_probs=55.4

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.+|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|.+|++.+|+.
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~   66 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL   66 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCC
Confidence            368999999999999999999999999988888877778999999999999999999999999874

>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=99.69  E-value=6e-17  Score=98.76  Aligned_cols=64  Identities=22%  Similarity=0.422  Sum_probs=59.8

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      -++|||+|||+++|+++|+++|+.||.+..+.+..++.++.++|||||+|.+++++.++++ +++
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~   65 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKY   65 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCC
Confidence            4689999999999999999999999999999999999899999999999999999999985 554

>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=99.69  E-value=1.1e-16  Score=102.05  Aligned_cols=66  Identities=14%  Similarity=0.358  Sum_probs=61.8

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.++|||+|||+++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+|++.+|+.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~   82 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGK   82 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCC
Confidence            45789999999999999999999999999999998884 7899999999999999999999999974

>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=99.68  E-value=1.6e-16  Score=101.87  Aligned_cols=77  Identities=9%  Similarity=0.098  Sum_probs=67.9

Q ss_pred             CCceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEE
Q psy7847          86 DDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSS  165 (170)
Q Consensus        86 ~~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~  165 (170)
                      ...+|||+|||+.+++++|.++|++||.|..+.+.++      +|+|||+|.+.++|+.|+..+++. ...++|++|+|.
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~-~~~~~g~~l~v~   86 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADV-PVYIAGQQAFFN   86 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHS-CCBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCC-CcEEeeEEEEEE
Confidence            4569999999999999999999999999999988654      689999999999999999988531 167899999999


Q ss_pred             eecc
Q psy7847         166 ITLK  169 (170)
Q Consensus       166 ~~~~  169 (170)
                      |+..
T Consensus        87 ~s~~   90 (104)
T d1wexa_          87 YSTS   90 (104)
T ss_dssp             ECSS
T ss_pred             EcCC
Confidence            9854

>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=99.68  E-value=1.9e-16  Score=99.44  Aligned_cols=70  Identities=23%  Similarity=0.441  Sum_probs=62.4

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+.....++|||+|||+++++++|+++|+.||+|.+++++.++  +.++|||||+|.+.++|.+|+..+|+.
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~   74 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGT   74 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCC
Confidence            3445567789999999999999999999999999999999885  347899999999999999999999873

>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=99.68  E-value=3.5e-17  Score=100.77  Aligned_cols=63  Identities=32%  Similarity=0.596  Sum_probs=58.4

Q ss_pred             EEEcCCCCCccHHHHHHHhhcCCCeeE-EEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          25 LFCGDLGNDVTDELLIRTFSKYPSFLK-AKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        25 v~v~nLp~~~t~~~l~~~f~~~g~v~~-i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      |||+|||+++++++|+++|+.||.+.+ +++++++.+|+++|||||+|.+.++|.+|++.+++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~   64 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQ   64 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCc
Confidence            799999999999999999999999865 578888888999999999999999999999998863

>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=99.68  E-value=5.2e-17  Score=103.04  Aligned_cols=72  Identities=18%  Similarity=0.228  Sum_probs=67.2

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+|||+|||+.+++++|+++|++||.|..+.+.+       +|+|||+|.+.++|.+|++.|||   ..+.|+.|+|.+
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng---~~~~g~~i~v~~   84 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDD---TKFRSHEGETSY   84 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSS---EEEECTTSCEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCC---CEeCCeEEEEEE
Confidence            46899999999999999999999999999998853       58999999999999999999999   999999999998


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        85 ~~   86 (98)
T d1wg4a_          85 IR   86 (98)
T ss_dssp             EE
T ss_pred             Ee
Confidence            75

>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=99.68  E-value=1.2e-16  Score=104.07  Aligned_cols=66  Identities=24%  Similarity=0.318  Sum_probs=60.0

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +..+++|||+|||.++++++|+++|+.||.|.+|++..   ++.++|||||+|.+.++|..|++.+++.
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~   69 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGF   69 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCC
Confidence            44578999999999999999999999999999999875   4677899999999999999999999974

>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=99.68  E-value=6.7e-17  Score=99.90  Aligned_cols=63  Identities=30%  Similarity=0.502  Sum_probs=58.2

Q ss_pred             EEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCC---CcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN---KTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        25 v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~---~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      |||+|||+++|+++|+++|+.||+|.++.+++++.++   .++|||||+|.+.++|.+|++.+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~   66 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH   66 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCC
Confidence            7999999999999999999999999999999887655   46899999999999999999999863

>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=99.68  E-value=9.6e-17  Score=100.02  Aligned_cols=75  Identities=11%  Similarity=0.060  Sum_probs=67.3

Q ss_pred             CCceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHh--cCCCccccCCeeE
Q psy7847          86 DDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEM--NEFPHLFVGDLKT  162 (170)
Q Consensus        86 ~~~~l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l--~~~~~~~~~~~~i  162 (170)
                      ..++|||+|||.. +|+++|.++|++||.|..+.+.++      +++|||+|.+.++|..|++.+  ++   ..++|++|
T Consensus         7 ~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~---~~~~gr~l   77 (89)
T d1x4da1           7 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTP---ALVFGKPV   77 (89)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSC---CEETTEEC
T ss_pred             CCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCC---CccCCceE
Confidence            4578999999986 889999999999999999999765      468999999999999999966  56   88999999


Q ss_pred             EEEeecc
Q psy7847         163 RSSITLK  169 (170)
Q Consensus       163 ~v~~~~~  169 (170)
                      +|+||.+
T Consensus        78 ~V~~s~~   84 (89)
T d1x4da1          78 RVHLSQK   84 (89)
T ss_dssp             EEEEECC
T ss_pred             EEEECCC
Confidence            9999864

>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=99.68  E-value=1.5e-17  Score=108.08  Aligned_cols=79  Identities=19%  Similarity=0.273  Sum_probs=70.8

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      .++|||+|||+.+++++|.++|+.+|.+..+.++.+..+|.++|+|||+|.+.++|.+|++ +||   ..++|+.|.|..
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~---~~i~gR~i~V~~   93 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHK---QYMGNRFIQVHP   93 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCS---BCSTTSCBEEEE
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCC---CcCCCEEEEEEE
Confidence            4699999999999999999999999998765555555689999999999999999999996 899   999999999998


Q ss_pred             ecc
Q psy7847         167 TLK  169 (170)
Q Consensus       167 ~~~  169 (170)
                      +.+
T Consensus        94 ~~~   96 (112)
T d1wela1          94 ITK   96 (112)
T ss_dssp             ECH
T ss_pred             cCh
Confidence            754

>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=99.67  E-value=7.3e-17  Score=102.54  Aligned_cols=74  Identities=12%  Similarity=0.180  Sum_probs=67.0

Q ss_pred             CceEEecCCCCC-CCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHH--HhcCCCccccCCeeEE
Q psy7847          87 DFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK--EMNEFPHLFVGDLKTR  163 (170)
Q Consensus        87 ~~~l~v~nlp~~-~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~--~l~~~~~~~~~~~~i~  163 (170)
                      .++|||+|||.+ +++++|.++|+.||.|..+.+.++      +|+|||+|.+.++|.+|++  .+|+   ..++|++|+
T Consensus        18 ~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~---~~~~gr~l~   88 (99)
T d1x4fa1          18 GRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKA---LWFQGRCVK   88 (99)
T ss_dssp             CCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSC---CCSSSSCCE
T ss_pred             CCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCC---ceECCEEEE
Confidence            468999999985 899999999999999999998765      6899999999999999998  4677   889999999


Q ss_pred             EEeecc
Q psy7847         164 SSITLK  169 (170)
Q Consensus       164 v~~~~~  169 (170)
                      |++|.+
T Consensus        89 V~~s~~   94 (99)
T d1x4fa1          89 VDLSEK   94 (99)
T ss_dssp             EEEECS
T ss_pred             EEEcCC
Confidence            999965

>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=99.67  E-value=6.7e-17  Score=97.52  Aligned_cols=62  Identities=27%  Similarity=0.466  Sum_probs=58.6

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +|||+|||+++|+++|+++|+.||.+..+.++.++.++.++++|||+|.+.++|.+|++ +++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~   62 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHF   62 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSS
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCC
Confidence            58999999999999999999999999999999998889999999999999999999996 665

>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=99.67  E-value=1.4e-16  Score=98.49  Aligned_cols=62  Identities=15%  Similarity=0.132  Sum_probs=57.9

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      ..++|||+|||.++|+++|+++|+.||++.++++++++ +|.++|||||+|.++++|.+|++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~   66 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET   66 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTC
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHH
Confidence            35789999999999999999999999999999998885 899999999999999999999963

>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=99.64  E-value=5.4e-16  Score=95.34  Aligned_cols=63  Identities=19%  Similarity=0.396  Sum_probs=57.1

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++++|||+|||.++++++|+++|+.||.|.++++.++     .+++|||+|.+.++|..|++.+++
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g   67 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQG   67 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCC
Confidence            335789999999999999999999999999999999754     368999999999999999999986

>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=99.64  E-value=6.6e-16  Score=98.89  Aligned_cols=72  Identities=17%  Similarity=0.128  Sum_probs=61.2

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...++..++..|||+|||+++|+++|+++|..+|.+....++....++.++|+|||+|.++++|.+|++ +++
T Consensus         7 ~~~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~   78 (104)
T d1wg5a_           7 GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHK   78 (104)
T ss_dssp             CCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTT
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCC
Confidence            334445566789999999999999999999999988876666666789999999999999999999996 554

>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=99.64  E-value=4e-16  Score=99.35  Aligned_cols=70  Identities=26%  Similarity=0.312  Sum_probs=62.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCee--------EEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFL--------KAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~--------~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +..+..+|||+|||.++|+++|+++|+.||.|.        .+.+..++.+|.+++||||+|.+.++|.+|++.+++.
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~   81 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   81 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCC
Confidence            344678999999999999999999999999873        5667777778999999999999999999999999873

>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=99.64  E-value=2.2e-17  Score=103.43  Aligned_cols=69  Identities=26%  Similarity=0.392  Sum_probs=61.4

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++...++|||+|||+++++++|+++|+.||.+.+++++.+ .+|.++|||||.|.+.++|.+|++ +++
T Consensus         7 ~~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g   75 (91)
T d1fjeb1           7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTG   75 (91)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGG
T ss_pred             CCCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCC
Confidence            344556789999999999999999999999999998888765 489999999999999999999995 665

>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=99.64  E-value=1e-16  Score=99.94  Aligned_cols=63  Identities=35%  Similarity=0.561  Sum_probs=58.3

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+|||+|||+++++++|+++|+.||.|.+++++.++  +.++|||||+|.+.++|.+|++.+|+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g   70 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNG   70 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCC
Confidence            4579999999999999999999999999999999885  45789999999999999999998885

>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=99.64  E-value=9.1e-17  Score=102.61  Aligned_cols=67  Identities=19%  Similarity=0.280  Sum_probs=63.0

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++++|||+|||.++++++|+++|+.||.+..+.+..+..+|.+++||||+|.+.++|..|++.+|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g   82 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNG   82 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCC
Confidence            4578999999999999999999999999999999988877899999999999999999999999986

>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=99.63  E-value=1.6e-16  Score=98.96  Aligned_cols=66  Identities=17%  Similarity=0.260  Sum_probs=59.3

Q ss_pred             CCcEEEEcCCCCCccHHHH---HHHhhcCCCeeEEEEEecCCCCCc---CCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELL---IRTFSKYPSFLKAKVVRDKRTNKT---KGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l---~~~f~~~g~v~~i~~~~~~~~~~~---~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +.++|||+|||+++++++|   +++|++||+|.++.+++++.++.+   ++||||+|.+.++|.+|++.+|+
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng   78 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN   78 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTT
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCC
Confidence            3567999999999999999   678999999999999999866544   48999999999999999999997

>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=99.63  E-value=1.4e-16  Score=102.10  Aligned_cols=76  Identities=11%  Similarity=0.050  Sum_probs=67.5

Q ss_pred             CCCceEEecCCCCCC-C----HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCC
Q psy7847          85 NDDFRLFCGDLGNDV-T----DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGD  159 (170)
Q Consensus        85 ~~~~~l~v~nlp~~~-~----~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~  159 (170)
                      .+..+|||+||+.++ +    +++|+++|++||.|..+.+.+.      +|||||+|.+.++|.+|++.|||   ..++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng---~~~~g   73 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHK---TEFLG   73 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTT---SEETT
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcc---cccCC
Confidence            356789999999876 3    3679999999999999988753      77999999999999999999999   99999


Q ss_pred             eeEEEEeecc
Q psy7847         160 LKTRSSITLK  169 (170)
Q Consensus       160 ~~i~v~~~~~  169 (170)
                      ++|+|.|+..
T Consensus        74 ~~l~v~~a~~   83 (104)
T d1weya_          74 KEMKLYFAQT   83 (104)
T ss_dssp             EECEEECCCC
T ss_pred             CEeEEeeccc
Confidence            9999999864

>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=99.63  E-value=3.8e-16  Score=96.66  Aligned_cols=67  Identities=13%  Similarity=0.185  Sum_probs=58.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..++|||+|||+++++++|+++|+.||.+....++....+|.++|+|||+|.+.++|.+|+..+|+.
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~   74 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDR   74 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCC
Confidence            3567999999999999999999999998876433344468999999999999999999999999874

>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=99.62  E-value=2.2e-16  Score=97.75  Aligned_cols=65  Identities=20%  Similarity=0.325  Sum_probs=55.2

Q ss_pred             CCcEEEEcCCCCCcc-HHHHHHHhhcCCCeeEEEEEec-CCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVT-DELLIRTFSKYPSFLKAKVVRD-KRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t-~~~l~~~f~~~g~v~~i~~~~~-~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      +.++|||+|||++++ +++|+++|+.||.|.++++..+ +.++.++|||||+|.+.++|.+|++ +|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~   69 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNR   69 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTT
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCC
Confidence            468999999999976 5669999999999999998764 4578999999999999999999995 775

>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=99.61  E-value=4.3e-16  Score=101.09  Aligned_cols=72  Identities=19%  Similarity=0.292  Sum_probs=61.4

Q ss_pred             ccCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          14 KKTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        14 ~~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .........++|||+|||+++|+++|+++|+.+|.+..+.++....+|.++|+|||+|.+.++|.+|++ +|+
T Consensus        10 ~~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~   81 (112)
T d1wela1          10 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHK   81 (112)
T ss_dssp             CCSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCS
T ss_pred             CCCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCC
Confidence            344445567899999999999999999999999988776666655689999999999999999999995 665

>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=99.61  E-value=2.4e-15  Score=94.71  Aligned_cols=67  Identities=25%  Similarity=0.406  Sum_probs=59.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...++++|||+|||+++++++|+++|+.||.|..+.+..+   +.+++||||+|.+.++|..|++.+|+.
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~   76 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGY   76 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCC
Confidence            3455678999999999999999999999999999887543   467899999999999999999999863

>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=99.60  E-value=9.2e-16  Score=96.80  Aligned_cols=64  Identities=22%  Similarity=0.367  Sum_probs=58.5

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCC-eeEEEEEecCC-CCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPS-FLKAKVVRDKR-TNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~-v~~i~~~~~~~-~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+|||+|||.++++++|+++|+.||+ +.++.++++.. +|.++|||||+|.+.++|..|++.+++
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~   67 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMP   67 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTT
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcC
Confidence            58999999999999999999999995 89999988753 578999999999999999999988864

>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=99.60  E-value=1.8e-15  Score=91.16  Aligned_cols=61  Identities=11%  Similarity=0.181  Sum_probs=54.5

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+|||+|||+++++++|+++|+.||+|.++++..++.  ..+++|||+|.++++|.+|+. +++
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~   61 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTH   61 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcC
Confidence            3799999999999999999999999999999998863  345799999999999999985 554

>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=99.60  E-value=2.9e-15  Score=95.83  Aligned_cols=65  Identities=26%  Similarity=0.520  Sum_probs=55.9

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecC-CCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDK-RTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~-~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+.++|||+|||+++++++|+++|+.|| +.++.++.+. .++.++|||||+|.+.++|++++ .+|+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~   78 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNE   78 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGT
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCC
Confidence            3468999999999999999999999999 7777777665 35789999999999999998777 4664

>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=99.60  E-value=8e-17  Score=103.17  Aligned_cols=75  Identities=13%  Similarity=0.209  Sum_probs=68.7

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      .+++.+++..+++++|+++|++||.|..+.++++. ++.++|+|||+|.+.++|.+|++.|||   ..++|++|+|.++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng---~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNN---RWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTT---CEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCC---CEECCEEEEEEEC
Confidence            35566777889999999999999999999998775 789999999999999999999999999   9999999999885

>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=99.58  E-value=3.6e-15  Score=92.54  Aligned_cols=64  Identities=14%  Similarity=0.199  Sum_probs=56.5

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .++++|||+|||+++++++|+++|+.||.+.++.+..    +..+++|||+|.+.++|.+|+..+++.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~   71 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNH   71 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCC
Confidence            3578999999999999999999999999998877654    345789999999999999999998863

>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=99.58  E-value=1.8e-15  Score=97.50  Aligned_cols=65  Identities=20%  Similarity=0.291  Sum_probs=58.5

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.+..+|||+|||+++|+++|+++|+.||.|.++.+++++    ++|+|||+|.+.++|..|+..+++.
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~   68 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQ   68 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSC
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCC
Confidence            4456679999999999999999999999999999998764    4789999999999999999998863

>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=99.58  E-value=3.3e-15  Score=94.22  Aligned_cols=61  Identities=26%  Similarity=0.600  Sum_probs=56.6

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.++|||+|||.++++++|+++|+.||.|.++++.++      +|||||+|.+.++|..|+..+++.
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~   77 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGT   77 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCC
Confidence            4578999999999999999999999999999999876      589999999999999999999863

>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=99.58  E-value=1.9e-15  Score=97.75  Aligned_cols=61  Identities=15%  Similarity=0.191  Sum_probs=55.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..++|||+|||+++++++|+++|+.||.|..|.+..      .++||||+|.+.++|.+|++.||+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~   69 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYS   69 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCC
Confidence            457899999999999999999999999999998743      4689999999999999999999873

>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=99.58  E-value=2.7e-15  Score=95.67  Aligned_cols=68  Identities=13%  Similarity=0.155  Sum_probs=58.6

Q ss_pred             CCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          16 TCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        16 ~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+...++|||+|||+++|+++|+++|..+| +..+.++.+. ++.++|||||+|.+.++|++|++ +++
T Consensus         9 ~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~   76 (102)
T d1weza_           9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDK   76 (102)
T ss_dssp             SCCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSS
T ss_pred             CCcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCC
Confidence            33455678999999999999999999999998 4578888774 78999999999999999999986 564

>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=99.58  E-value=3.8e-15  Score=92.02  Aligned_cols=59  Identities=32%  Similarity=0.518  Sum_probs=55.0

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..+|||+|||.++++++|+++|+.||+|.++++.++      ++||||+|.+.++|.+|++.+|+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g   66 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDN   66 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCC
Confidence            457999999999999999999999999999999865      47999999999999999999986

>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=99.57  E-value=1.6e-15  Score=93.94  Aligned_cols=58  Identities=22%  Similarity=0.257  Sum_probs=53.4

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ++|||+|||+++++++|+++|+.||.|.++++.++       |||||+|.+.++|.+|+..+++.
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~   58 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNT   58 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCC
Confidence            36999999999999999999999999999988643       79999999999999999999874

>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=99.57  E-value=2.6e-15  Score=95.86  Aligned_cols=73  Identities=14%  Similarity=0.154  Sum_probs=60.8

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC----ceEEec
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD----FRLFCG   93 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~----~~l~v~   93 (170)
                      .....|||+|||+++|+++|+++|..||.+..+.++....+|.++|+|||+|.+.++|.+|+. +++.    +.|.|.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~   82 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVH   82 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEE
Confidence            345679999999999999999999999988775555555689999999999999999999996 6652    455553

>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=99.57  E-value=1.8e-17  Score=103.61  Aligned_cols=76  Identities=16%  Similarity=0.276  Sum_probs=65.0

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEe-----ecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeE
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVV-----RDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKT  162 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~-----~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i  162 (170)
                      ++|||+|||+++++++|.++|+++|.+..+.+.     .+...+.++|||||+|.+.++|..|++ |||   ..+.|++|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g---~~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDG---IIFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSS---CCSSSSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCC---cEECCEEE
Confidence            479999999999999999999999877655432     234466789999999999999999985 999   99999999


Q ss_pred             EEEee
Q psy7847         163 RSSIT  167 (170)
Q Consensus       163 ~v~~~  167 (170)
                      +|+.+
T Consensus        78 ~V~r~   82 (90)
T d1u2fa_          78 KIRRP   82 (90)
T ss_dssp             CCBCT
T ss_pred             EECCC
Confidence            99754

>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=99.56  E-value=1.2e-14  Score=91.83  Aligned_cols=60  Identities=22%  Similarity=0.326  Sum_probs=55.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...++|||+|||+++++++|+++|+.||.|.++.+.+       +|+|||+|.+.++|.+|++.+|+
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng   72 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDD   72 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCC
Confidence            4567899999999999999999999999999998853       47999999999999999999986

>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=99.56  E-value=4.6e-15  Score=95.59  Aligned_cols=61  Identities=23%  Similarity=0.286  Sum_probs=55.5

Q ss_pred             CcEEEEcCCCC-CccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          22 DFRLFCGDLGN-DVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        22 ~~~v~v~nLp~-~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +.+|||+|||+ .+++++|+++|+.||.|.++.+++++     +|+|||+|.+.++|.+|++.+++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~   63 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGH   63 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCC
Confidence            56899999965 59999999999999999999998864     689999999999999999999864

>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=99.56  E-value=8e-15  Score=92.57  Aligned_cols=61  Identities=21%  Similarity=0.409  Sum_probs=56.2

Q ss_pred             CCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          20 ENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        20 ~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++++|||+|||+++++++|+++|++||.|..+++.++      +++|||+|.+.++|..|++.+++
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~   75 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRG   75 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCC
Confidence            35789999999999999999999999999999998764      47999999999999999999986

>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=99.55  E-value=8.6e-15  Score=90.79  Aligned_cols=62  Identities=13%  Similarity=0.129  Sum_probs=56.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      +..++++|||+|||+++++++|+++|++||.|.++++.++      +++|||+|.+.++|..|+..++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~   65 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYS   65 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHc
Confidence            4567899999999999999999999999999999998765      3799999999999999998654

>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=99.55  E-value=3.7e-15  Score=90.86  Aligned_cols=59  Identities=27%  Similarity=0.416  Sum_probs=53.3

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .+|||+|||.++++++|+++|+.||.+.++++...      +|||||+|.+.++|.+|++.+++.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~   60 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGK   60 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCC
Confidence            36999999999999999999999999887777654      589999999999999999999874

>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=99.54  E-value=6.5e-15  Score=95.52  Aligned_cols=72  Identities=21%  Similarity=0.220  Sum_probs=62.6

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCH-HHHHHHHHHhcCCCccccCCeeEEEEe
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP-QDFIRANKEMNEFPHLFVGDLKTRSSI  166 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~-~~a~~a~~~l~~~~~~~~~~~~i~v~~  166 (170)
                      ..+||+|||+.+|+++|+.+|++||.|.++.++++      +|+|||.|.++ ++|..|+..+|+   ..+.++.+.|.|
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~---~~l~~~~~~v~~   82 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANN---GNLQLRNKEVTW   82 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTT---SCBCTTSSSEEE
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcC---CceecCceEEEE
Confidence            46799999999999999999999999999999764      78999999985 789999999999   777766666666


Q ss_pred             ec
Q psy7847         167 TL  168 (170)
Q Consensus       167 ~~  168 (170)
                      +.
T Consensus        83 ~~   84 (113)
T d1owxa_          83 EV   84 (113)
T ss_dssp             EE
T ss_pred             ee
Confidence            54

>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=99.53  E-value=4.2e-15  Score=92.81  Aligned_cols=63  Identities=24%  Similarity=0.438  Sum_probs=56.0

Q ss_pred             CCcEEEEcCCCCCccHHHHHH----HhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIR----TFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~----~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ++++|||+|||+++++++|++    +|++||+|.+|++.+   ++.++|||||+|.+.++|..|+..+|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~   68 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQG   68 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCC
Confidence            468999999999999999864    589999999988754   467899999999999999999999986

>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=99.53  E-value=2.6e-14  Score=91.28  Aligned_cols=63  Identities=11%  Similarity=0.070  Sum_probs=56.1

Q ss_pred             CCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          17 CEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        17 ~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ....++++|||+|||.++++++|+++|+.||.|.++.+.++      +++|||+|.+.++|..|+..++
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~   72 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAA   72 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHH
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHc
Confidence            34456889999999999999999999999999999998754      5799999999999999998664

>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=99.53  E-value=5e-15  Score=93.36  Aligned_cols=64  Identities=19%  Similarity=0.294  Sum_probs=56.0

Q ss_pred             CCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ...+.++|||+|||+++++++|+++|+.||.+..+.     .++.+++||||+|.+.++|.+|+..+|+
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~   75 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQG   75 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCC
Confidence            344568999999999999999999999999776553     2678899999999999999999999985

>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=99.53  E-value=8.2e-15  Score=93.14  Aligned_cols=61  Identities=20%  Similarity=0.266  Sum_probs=54.5

Q ss_pred             CCceEEec--CCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCC
Q psy7847          86 DDFRLFCG--DLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEF  152 (170)
Q Consensus        86 ~~~~l~v~--nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~  152 (170)
                      ...+++|.  |||+.+++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|||.
T Consensus        17 pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCC
Confidence            34678885  59999999999999999999999988654      679999999999999999999994

>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=99.52  E-value=1.9e-14  Score=90.92  Aligned_cols=60  Identities=27%  Similarity=0.379  Sum_probs=53.1

Q ss_pred             CCCcEEEEcCCC-CCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          20 ENDFRLFCGDLG-NDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        20 ~~~~~v~v~nLp-~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ....+|||+||| ..+++++|+++|++||.|.++.+.        ++||||+|.+.++|.+|+..+|+.
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~   73 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGR   73 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTC
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCC
Confidence            345679999997 578899999999999999999883        579999999999999999999873

>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=99.51  E-value=5.7e-14  Score=86.61  Aligned_cols=60  Identities=20%  Similarity=0.361  Sum_probs=54.1

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ..++|||+|||+++++++|+++|+.||.+..+.+..      ++|||||+|.+.++|..|+..+|+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~   66 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNG   66 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSS
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCC
Confidence            357899999999999999999999999988877644      468999999999999999999986

>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=99.50  E-value=3.9e-14  Score=85.98  Aligned_cols=61  Identities=18%  Similarity=0.266  Sum_probs=54.6

Q ss_pred             CCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      |...++|||+|+|  +|+++|+++|++||.|.++++.++      +++|||+|.+.++|..|+..+++.
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~   62 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGT   62 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTC
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCC
Confidence            5567899999985  899999999999999999998754      479999999999999999999863

>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=99.49  E-value=1.8e-14  Score=89.29  Aligned_cols=57  Identities=25%  Similarity=0.362  Sum_probs=51.3

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHH
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK   82 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~   82 (170)
                      .+++|||+|||+++|+++|+++|+.||.|.++++.     ..+++||||+|.+.++|+.|+.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~   60 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh
Confidence            47799999999999999999999999999998764     3467899999999999999975

>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=99.49  E-value=5.3e-14  Score=89.05  Aligned_cols=60  Identities=13%  Similarity=0.210  Sum_probs=53.6

Q ss_pred             CCCCCcEEEEcCCCCC-ccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          18 EDENDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~-~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      .+..+++|||+|||.+ +|+++|.++|+.||.|.++.++++      +++|||+|.+.++|..|+..
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~   74 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH   74 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHH
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHH
Confidence            3456789999999986 899999999999999999999865      47999999999999999974

>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=99.47  E-value=1.7e-13  Score=95.61  Aligned_cols=76  Identities=26%  Similarity=0.413  Sum_probs=67.5

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEee
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSIT  167 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~  167 (170)
                      ++|||+|||+.+++++|+++|++||.|..+.+.++..++.++|+|||+|.+.++|..|+..++    ..++++.+.+...
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~----~~~~~~~~~~~~~   82 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP----HKVDGRVVEPKRA   82 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS----CEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcC----Ccccccchhhhhh
Confidence            589999999999999999999999999999999998899999999999999999999998544    5566666666543

>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=99.46  E-value=1.1e-13  Score=87.59  Aligned_cols=77  Identities=17%  Similarity=0.186  Sum_probs=65.8

Q ss_pred             CCceEEecCC--CCCC---------CHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCc
Q psy7847          86 DDFRLFCGDL--GNDV---------TDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPH  154 (170)
Q Consensus        86 ~~~~l~v~nl--p~~~---------~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~  154 (170)
                      ..++|+|.|+  |.++         .+++|++.|++||.|..+.+..+    .++|+|||+|.+.++|.+|+..|||   
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng---   79 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG---   79 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT---
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC---
Confidence            4568999998  5432         13789999999999999987654    3579999999999999999999999   


Q ss_pred             cccCCeeEEEEeecc
Q psy7847         155 LFVGDLKTRSSITLK  169 (170)
Q Consensus       155 ~~~~~~~i~v~~~~~  169 (170)
                      ..++|++|+|.+.++
T Consensus        80 ~~~~gr~i~v~~~~g   94 (99)
T d2dita1          80 RWFGGRQITAQAWDG   94 (99)
T ss_dssp             CEETTEECEEEECCS
T ss_pred             cEECCEEEEEEEeCC
Confidence            999999999998754

>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=99.45  E-value=8.7e-14  Score=86.14  Aligned_cols=59  Identities=14%  Similarity=0.189  Sum_probs=50.7

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+++|||+|||+++++++|+++|++|| +..+.+      +..++||||+|.+.++|.+|++.+|+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~   62 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQ   62 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTT
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCC
Confidence            357899999999999999999999999 323333      34578999999999999999999997

>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=99.45  E-value=2e-13  Score=81.94  Aligned_cols=55  Identities=24%  Similarity=0.309  Sum_probs=48.7

Q ss_pred             EEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          25 LFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        25 v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|+|||+|.+.++|.+|+..+|+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~   55 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQ   55 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCC
Confidence            79999999999999999999999 444433      45679999999999999999999986

>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=99.43  E-value=2.6e-15  Score=93.57  Aligned_cols=64  Identities=19%  Similarity=0.337  Sum_probs=54.5

Q ss_pred             CcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEE-----ecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          22 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVV-----RDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        22 ~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~-----~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .++|||+|||+++|+++|+++|+.+|.+..+.+.     .+..++.++|||||+|.+.++|.+|++ +++
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g   69 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDG   69 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSS
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCC
Confidence            4789999999999999999999999987665543     344567889999999999999999985 776

>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=99.43  E-value=1.3e-13  Score=87.47  Aligned_cols=63  Identities=21%  Similarity=0.303  Sum_probs=55.2

Q ss_pred             CCCCcEEEE--cCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          19 DENDFRLFC--GDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        19 ~~~~~~v~v--~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ..+..+++|  +|||.++|+++|+++|++||.+.++.+..+      ++||||+|.+.++|..|+..+|+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~   79 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGK   79 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTC
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCC
Confidence            344567888  559999999999999999999999988765      479999999999999999999974

>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=99.42  E-value=2.7e-13  Score=84.01  Aligned_cols=62  Identities=10%  Similarity=0.052  Sum_probs=54.9

Q ss_pred             CCCCCcEEEEcCCCCC-ccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcC
Q psy7847          18 EDENDFRLFCGDLGND-VTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMN   85 (170)
Q Consensus        18 ~~~~~~~v~v~nLp~~-~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~   85 (170)
                      ..+.+++|||+|||.. +|++||.++|+.||.|.++.+.+++      ++|||+|.+.++|..|+..++
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~   66 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYT   66 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHh
Confidence            3456889999999986 8999999999999999999998654      689999999999999998653

>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=99.41  E-value=2.1e-13  Score=86.95  Aligned_cols=81  Identities=15%  Similarity=0.028  Sum_probs=67.6

Q ss_pred             CCceEEecCC--CCCC--------CHHHHHHHhccCCCeeEEEEeecCCC--CCcccEEEEEecCHHHHHHHHHHhcCCC
Q psy7847          86 DDFRLFCGDL--GNDV--------TDELLIRTFSKYPSFLKAKVVRDKRT--NKTKGFGFVSFKDPQDFIRANKEMNEFP  153 (170)
Q Consensus        86 ~~~~l~v~nl--p~~~--------~~~~l~~~f~~~g~i~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~a~~~l~~~~  153 (170)
                      .+.+|.+.|+  |..+        ..++|++.|++||.|..+.+.++...  ....|++||+|.+.++|.+|+..|||  
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~G--   80 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG--   80 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS--
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC--
Confidence            3567888888  4333        24679999999999999999876543  33568999999999999999999999  


Q ss_pred             ccccCCeeEEEEeecc
Q psy7847         154 HLFVGDLKTRSSITLK  169 (170)
Q Consensus       154 ~~~~~~~~i~v~~~~~  169 (170)
                       ..++||+|++.+..+
T Consensus        81 -r~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          81 -RKFANRVVVTKYCDP   95 (104)
T ss_dssp             -CCSSSSCCEEEEECH
T ss_pred             -CEECCeEEEEEEcCH
Confidence             999999999999763

>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=99.40  E-value=4.9e-13  Score=86.48  Aligned_cols=67  Identities=24%  Similarity=0.271  Sum_probs=56.8

Q ss_pred             cCCCCCCCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCH-HHHHHHHHHcCCC
Q psy7847          15 KTCEDENDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDP-QDFIRANKEMNDD   87 (170)
Q Consensus        15 ~~~~~~~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~-~~a~~~~~~~~~~   87 (170)
                      ..+.+.-....||+|||.++|+++|+++|+.||+|.+|+++++      +++|||.|.++ ++|..++..+++.
T Consensus         4 ~~~~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~   71 (113)
T d1owxa_           4 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNG   71 (113)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTS
T ss_pred             CcCCCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCC
Confidence            3444555667899999999999999999999999999999864      58999999996 6788898888763

>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=99.35  E-value=1.1e-12  Score=79.71  Aligned_cols=70  Identities=13%  Similarity=0.135  Sum_probs=58.0

Q ss_pred             CceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCee-EEEE
Q psy7847          87 DFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLK-TRSS  165 (170)
Q Consensus        87 ~~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~-i~v~  165 (170)
                      ...++|.++|++.+++.| +.|++||.|..+.+.+      ++|||||+|.++++|++|++ +||   ..++|+. |.|.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG---~~~~g~~~vgV~   72 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDG---RIFGESIMIGVK   72 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTT---CEETTTEECEEE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCC---CeECCcEEEEEE
Confidence            346899999999987666 5799999999998743      37899999999999999996 899   9999874 5565


Q ss_pred             ee
Q psy7847         166 IT  167 (170)
Q Consensus       166 ~~  167 (170)
                      -.
T Consensus        73 ~~   74 (81)
T d1wwha1          73 PC   74 (81)
T ss_dssp             EC
T ss_pred             eC
Confidence            43

>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=99.27  E-value=3.5e-13  Score=85.85  Aligned_cols=63  Identities=16%  Similarity=0.224  Sum_probs=58.6

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      .++|++++.++++++|+++|++||.|.++.|+++ .+|.++|+|||+|.+.++|.+|+..+++.
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~   91 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNR   91 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCC
Confidence            4788899999999999999999999999999887 48999999999999999999999999974

>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=99.21  E-value=8.2e-12  Score=79.37  Aligned_cols=61  Identities=13%  Similarity=0.137  Sum_probs=53.1

Q ss_pred             CCcEEEEcCCCCCc-cH----HHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDV-TD----ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~-t~----~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ...+|||+||+.++ ++    ++|+++|+.||.|.++++++.      +++|||+|.+.++|.+|+..+|+.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~   69 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKT   69 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTS
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhccc
Confidence            45689999999986 33    569999999999999999754      579999999999999999999974

>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=99.20  E-value=2.3e-11  Score=73.73  Aligned_cols=59  Identities=14%  Similarity=0.187  Sum_probs=49.8

Q ss_pred             CCcEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      ++..|+|.|+|++.+++.| +.|+.||+|.++++.      ..++||||.|.++++|++|+. +|+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~   61 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGR   61 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCC
Confidence            4568999999999997655 579999999999764      346899999999999999995 6763

>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=99.07  E-value=3.2e-10  Score=71.19  Aligned_cols=66  Identities=18%  Similarity=0.222  Sum_probs=55.2

Q ss_pred             CCCCCcEEEEcCC--CCCcc---------HHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          18 EDENDFRLFCGDL--GNDVT---------DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        18 ~~~~~~~v~v~nL--p~~~t---------~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      ....+++|+|+||  |.++.         +++|++.|++||.|..+.+..+    ..+|+|||+|.+.++|.+|+..+|+
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            4456889999999  66542         3688999999999999988654    4578999999999999999999997


Q ss_pred             C
Q psy7847          87 D   87 (170)
Q Consensus        87 ~   87 (170)
                      .
T Consensus        80 ~   80 (99)
T d2dita1          80 R   80 (99)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.96  E-value=7.7e-10  Score=69.99  Aligned_cols=67  Identities=18%  Similarity=0.098  Sum_probs=55.2

Q ss_pred             CCcEEEEcCC--CCCc--------cHHHHHHHhhcCCCeeEEEEEecCCCC--CcCCEEEEEeCCHHHHHHHHHHcCCC
Q psy7847          21 NDFRLFCGDL--GNDV--------TDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANKEMNDD   87 (170)
Q Consensus        21 ~~~~v~v~nL--p~~~--------t~~~l~~~f~~~g~v~~i~~~~~~~~~--~~~~~afv~f~~~~~a~~~~~~~~~~   87 (170)
                      +++.|.|+|+  |.++        ..++|++.|++||.|.++.+.++..+.  ...|++||+|.+.++|.+|+..||+.
T Consensus         3 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_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            5778999999  4433        346789999999999999998865442  44689999999999999999999973

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=9.8e-06  Score=49.01  Aligned_cols=64  Identities=14%  Similarity=0.219  Sum_probs=54.9

Q ss_pred             cEEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCC--CcCCEEEEEeCCHHHHHHHHHHcCC
Q psy7847          23 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTN--KTKGFGFVSFKDPQDFIRANKEMND   86 (170)
Q Consensus        23 ~~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~--~~~~~afv~f~~~~~a~~~~~~~~~   86 (170)
                      .+|.|+.||+.+|+++..+.++..|.+........+.+-  ..-+-|||.|.+.+++.......++
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g   67 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDG   67 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCC
Confidence            478999999999999999999999999888887766543  2346899999999999999988876

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.98  E-value=1.8e-05  Score=47.83  Aligned_cols=63  Identities=14%  Similarity=0.222  Sum_probs=54.3

Q ss_pred             eEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCc--ccEEEEEecCHHHHHHHHHHhcC
Q psy7847          89 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKT--KGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        89 ~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~--~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      .|.|+.||+.+|++++.+.++..|.+.+......+.+..+  -..|+|.|.+.++.....+.++|
T Consensus         3 KvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g   67 (91)
T d1uw4a_           3 KVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDG   67 (91)
T ss_dssp             EEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTT
T ss_pred             eEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCC
Confidence            6889999999999999999999999998887766544332  34599999999999999999999

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=6.4e-05  Score=42.66  Aligned_cols=63  Identities=17%  Similarity=0.214  Sum_probs=52.1

Q ss_pred             HHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeecc
Q psy7847         101 DELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLK  169 (170)
Q Consensus       101 ~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~  169 (170)
                      ++.|...|.+++.|..+.+.... .+..  .|-|...+.++|.-|+..||-   .-+|+++|-|++++.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~LhR---~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNSLHR---YKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHHHTT---EEETTEEEEEEECCC
T ss_pred             HHHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHHHHH---HhcCCeEEEEEEecC
Confidence            34566788999999988775432 3333  588999999999999999999   999999999999874

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.26  E-value=0.00021  Score=42.54  Aligned_cols=57  Identities=16%  Similarity=0.268  Sum_probs=49.3

Q ss_pred             HHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcCCCccccCCeeEEEEeeccC
Q psy7847         102 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNEFPHLFVGDLKTRSSITLKG  170 (170)
Q Consensus       102 ~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~~~~~~~~~~~i~v~~~~~~  170 (170)
                      .+|.+.|..||++.-+++..+.        ..|+|.+-++|-+|++ ++|   ..++|+.|+|+-..++
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~-l~g---~~v~G~~l~It~~~~~   95 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDG---MKVKGRAVKISGPSSG   95 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGG---SEETTEEEEEECCCCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhc-cCC---eEEcceEEEEecCCCC
Confidence            5677888999999999987663        6799999999999999 899   9999999999876553

>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=96.66  E-value=0.0093  Score=35.79  Aligned_cols=52  Identities=17%  Similarity=0.245  Sum_probs=42.3

Q ss_pred             EEEEcCCCCCccHHHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHH
Q psy7847          24 RLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKE   83 (170)
Q Consensus        24 ~v~v~nLp~~~t~~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~   83 (170)
                      .||.-..|......||.++|+.||.|. |..+.+.       .|||...+.++|..++..
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHH
Confidence            366669999999999999999999663 5555543       699999999998887753

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.43  E-value=0.028  Score=33.64  Aligned_cols=56  Identities=16%  Similarity=0.172  Sum_probs=44.1

Q ss_pred             ceEEecCCCCCCCHHHHHHHhccCCCeeEEEEeecCCCCCcccEEEEEecCHHHHHHHHHHhcC
Q psy7847          88 FRLFCGDLGNDVTDELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMNE  151 (170)
Q Consensus        88 ~~l~v~nlp~~~~~~~l~~~f~~~g~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~~  151 (170)
                      ..+|.-..|..+...+|.++|++||.|.---+  |.      -.|||...+.+++..+++.++.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI--dd------TSa~V~L~~~e~~~~v~~~~~~   71 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI--DD------TSAFVSLSQPEQVQIAVNTSKY   71 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE--ET------TEEEEECSCHHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceEEEEe--cC------ceEEEEecCHHHHHHHHHHhcc
Confidence            35777789999999999999999998643323  32      2699999999999998876553

>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=93.32  E-value=0.23  Score=27.58  Aligned_cols=53  Identities=15%  Similarity=0.207  Sum_probs=40.6

Q ss_pred             HHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHHHcCC----CceEEe
Q psy7847          37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANKEMND----DFRLFC   92 (170)
Q Consensus        37 ~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~~~~~----~~~l~v   92 (170)
                      +.|.+.|.++|.|.++.+.... +|  .-.|-|...+..+|..++..+|.    ..++.|
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~V   67 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   67 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEE
Confidence            4556778999999999886542 23  34689999999999999999984    345554

>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=91.55  E-value=0.17  Score=29.67  Aligned_cols=38  Identities=16%  Similarity=0.352  Sum_probs=33.1

Q ss_pred             HHHHHHhhcCCCeeEEEEEecCCCCCcCCEEEEEeCCHHHHHHHHH
Q psy7847          37 ELLIRTFSKYPSFLKAKVVRDKRTNKTKGFGFVSFKDPQDFIRANK   82 (170)
Q Consensus        37 ~~l~~~f~~~g~v~~i~~~~~~~~~~~~~~afv~f~~~~~a~~~~~   82 (170)
                      .+|.+.|..||+|.-+++..+.        ..|+|.+-++|..++.
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~   76 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD   76 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH
T ss_pred             HHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhc
Confidence            5677888999999999998774        7999999999999985